EzCatDB: D00471

DB codeD00471
RLCP classification1.13.200.966
CATH domainDomain 12.40.70.10Catalytic domain
Domain 22.40.70.10Catalytic domain
E.C.3.4.23.16,2.7.7.49,2.7.7.7,3.1.26.4
CSA1a30,1hiv
MACiEM0175

CATH domainRelated DB codes (homologues)
2.40.70.10D00436,D00438,D00439,D00440,D00441,D00442,D00443,D00437,D00444,D00423,D00445,D00484,M00206,M00166,D00231,D00529

Enzyme Name
Swiss-protKEGG

P03366P04585P04587P35963
Protein nameGag-Pol polyproteinGag-Pol polyproteinGag-Pol polyproteinGag-Pol polyproteinHIV-1 retropepsin
human immunodeficiency virus type 1 protease
gag protease
HIV aspartyl protease
HIV proteinase
retroproteinase
HIV-1 protease
HIV-2 protease
SynonymsPr160Gag-Pol
Pr160Gag-Pol
Pr160Gag-Pol
Pr160Gag-Pol
ContainsMatrix protein p17
(MA)
Capsid protein p24
(CA)
Spacer peptide p2
Nucleocapsid protein p7
(NC)
Transframe peptide
(TF)
p6-pol
(p6*)
Protease
   EC 3.4.23.16
Retropepsin PR
Reverse transcriptase/ribonuclease H
   EC 2.7.7.49
   EC 2.7.7.7
   EC 3.1.26.4
p66 RT
p51 RT
p15
Integrase
(IN)
Matrix protein p17
(MA)
Capsid protein p24
(CA)
Spacer peptide p2
Nucleocapsid protein p7
(NC)
Transframe peptide
(TF)
p6-pol
(p6*)
Protease
   EC 3.4.23.16
Retropepsin PR
Reverse transcriptase/ribonuclease H
   EC 2.7.7.49
   EC 2.7.7.7
   EC 3.1.26.4
p66 RT
p51 RT
p15
Integrase
(IN)
Matrix protein p17
(MA)
Capsid protein p24
(CA)
Spacer peptide p2
Nucleocapsid protein p7
(NC)
Transframe peptide
(TF)
p6-pol
(p6*)
Protease
   EC 3.4.23.16
Retropepsin PR
Reverse transcriptase/ribonuclease H
   EC 2.7.7.49
   EC 2.7.7.7
   EC 3.1.26.4
p66 RT
p51 RT
p15
Integrase
(IN)
Matrix protein p17
(MA)
Capsid protein p24
(CA)
Spacer peptide p2
Nucleocapsid protein p7
(NC)
Transframe peptide
(TF)
p6-pol
(p6*)
Protease
   EC 3.4.23.16
Retropepsin PR
Reverse transcriptase/ribonuclease H
   EC 2.7.7.49
   EC 2.7.7.7
   EC 3.1.26.4
p66 RT
p51 RT
p15
Integrase
(IN)


Swiss-prot:Accession NumberP03366P04585P04587P35963
Entry namePOL_HV1B1POL_HV1H2POL_HV1B5POL_HV1Y2
ActivitySpecific for a P1 residue that is hydrophobic, and P1'' variable, but often Pro.,Endonucleolytic cleavage to 5''- phosphomonoester.,Deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1).Specific for a P1 residue that is hydrophobic, and P1'' variable, but often Pro.,Endonucleolytic cleavage to 5''- phosphomonoester.,Deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1).Specific for a P1 residue that is hydrophobic, and P1'' variable, but often Pro.,Endonucleolytic cleavage to 5''- phosphomonoester.,Deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1).Specific for a P1 residue that is hydrophobic, and P1'' variable, but often Pro.,Endonucleolytic cleavage to 5''- phosphomonoester.,Deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1).
SubunitPre-integration complex interacts with human HMGA1. Matrix protein p17 is a trimer. Interacts with gp120 and human BAF. Capsid is a homodimer. Interacts with human PPIA/CYPA. The protease is a homodimer, whose active site consists of two apposed aspartic acid residues. The reverse transcriptase is a heterodimer of p66 RT and p51 RT (RT p66/p51). Heterodimerization of RT is essential for DNA polymerase activity. Despite the sequence identities, p66 RT and p51 RT have distinct folding. Integrase is a homodimer and possibly can form homotetramer. Integrase interacts with human SMARCB1/INI1 and human PSIP1/LEDGF isoform 1 (By similarity).Pre-integration complex interacts with human HMGA1. Matrix protein p17 is a trimer. Interacts with gp120 and human BAF. Capsid is a homodimer. Interacts with human PPIA/CYPA. The protease is a homodimer, whose active site consists of two apposed aspartic acid residues. The reverse transcriptase is a heterodimer of p66 RT and p51 RT (RT p66/p51). Heterodimerization of RT is essential for DNA polymerase activity. Despite the sequence identities, p66 RT and p51 RT have distinct folding. Integrase is a homodimer and possibly can form homotetramer. Integrase interacts with human SMARCB1/INI1 and human PSIP1/LEDGF isoform 1.Pre-integration complex interacts with human HMGA1. Matrix protein p17 is a trimer. Interacts with gp120 and human BAF. Capsid is a homodimer. Interacts with human PPIA/CYPA. The protease is a homodimer, whose active site consists of two apposed aspartic acid residues. The reverse transcriptase is a heterodimer of p66 RT and p51 RT (RT p66/p51). Heterodimerization of RT is essential for DNA polymerase activity. Despite the sequence identities, p66 RT and p51 RT have distinct folding. Integrase is a homodimer and possibly can form homotetramer. Integrase interacts with human SMARCB1/INI1 and human PSIP1/LEDGF isoform 1 (By similarity).Pre-integration complex interacts with human HMGA1. Matrix protein p17 is a trimer. Interacts with gp120 and human BAF. Capsid is a homodimer. Interacts with human PPIA/CYPA. The protease is a homodimer, whose active site consists of two apposed aspartic acid residues. The reverse transcriptase is a heterodimer of p66 RT and p51 RT (RT p66/p51). Heterodimerization of RT is essential for DNA polymerase activity. Despite the sequence identities, p66 RT and p51 RT have distinct folding. Integrase is a homodimer and possibly can form homotetramer. Integrase interacts with human SMARCB1/INI1 and human PSIP1/LEDGF isoform 1 (By similarity).
Subcellular locationMatrix protein p17: Virion (Potential). Nucleus (By similarity). Cytoplasm (By similarity). Cell membrane, Lipid-anchor (Potential). Note=Following virus entry, the nuclear localization signal (NLS) of the matrix protein participates with Vpr to the nuclear localization of the viral genome. During virus production, the nuclear export activity of the matrix protein counteracts the NLS to maintain the Gag and Gag-Pol polyproteins in the cytoplasm, thereby directing unspliced RNA to the plasma membrane (By similarity).,Capsid protein p24: Virion (Potential).,Nucleocapsid protein p7: Virion (Potential).,Reverse transcriptase/ribonuclease H: Virion (Potential).,Integrase: Virion (Potential). Nucleus (Potential). Cytoplasm (Potential). Note=Nuclear at initial phase, cytoplasmic at assembly (Potential).Matrix protein p17: Virion (Potential). Nucleus (By similarity). Cytoplasm (By similarity). Cell membrane, Lipid-anchor (Potential). Note=Following virus entry, the nuclear localization signal (NLS) of the matrix protein participates with Vpr to the nuclear localization of the viral genome. During virus production, the nuclear export activity of the matrix protein counteracts the NLS to maintain the Gag and Gag-Pol polyproteins in the cytoplasm, thereby directing unspliced RNA to the plasma membrane (By similarity).,Capsid protein p24: Virion (Potential).,Nucleocapsid protein p7: Virion (Potential).,Reverse transcriptase/ribonuclease H: Virion (Potential).,Integrase: Virion (Potential). Nucleus (Potential). Cytoplasm (Potential). Note=Nuclear at initial phase, cytoplasmic at assembly (Potential).Matrix protein p17: Virion (Potential). Nucleus (By similarity). Cytoplasm (By similarity). Cell membrane, Lipid-anchor (Potential). Note=Following virus entry, the nuclear localization signal (NLS) of the matrix protein participates with Vpr to the nuclear localization of the viral genome. During virus production, the nuclear export activity of the matrix protein counteracts the NLS to maintain the Gag and Gag-Pol polyproteins in the cytoplasm, thereby directing unspliced RNA to the plasma membrane (By similarity).,Capsid protein p24: Virion (Potential).,Nucleocapsid protein p7: Virion (Potential).,Reverse transcriptase/ribonuclease H: Virion (Potential).,Integrase: Virion (Potential). Nucleus (Potential). Cytoplasm (Potential). Note=Nuclear at initial phase, cytoplasmic at assembly (Potential).Matrix protein p17: Virion (Potential). Nucleus (By similarity). Cytoplasm (By similarity). Cell membrane, Lipid-anchor (Potential). Note=Following virus entry, the nuclear localization signal (NLS) of the matrix protein participates with Vpr to the nuclear localization of the viral genome. During virus production, the nuclear export activity of the matrix protein counteracts the NLS to maintain the Gag and Gag-Pol polyproteins in the cytoplasm, thereby directing unspliced RNA to the plasma membrane (By similarity).,Capsid protein p24: Virion (Potential).,Nucleocapsid protein p7: Virion (Potential).,Reverse transcriptase/ribonuclease H: Virion (Potential).,Integrase: Virion (Potential). Nucleus (Potential). Cytoplasm (Potential). Note=Nuclear at initial phase, cytoplasmic at assembly (Potential).
CofactorBinds 2 magnesium ions for reverse transcriptase polymerase activity (By similarity).,Binds 2 magnesium ions for ribonuclease H (RNase H) activity. Substrate-binding is a precondition for magnesium binding (By similarity).,Magnesium ions for integrase activity. Binds at least 1, maybe 2 magnesium ions (By similarity).Binds 2 magnesium ions for reverse transcriptase polymerase activity (By similarity).,Binds 2 magnesium ions for ribonuclease H (RNase H) activity. Substrate-binding is a precondition for magnesium binding (By similarity).,Magnesium ions for integrase activity. Binds at least 1, maybe 2 magnesium ions (By similarity).Binds 2 magnesium ions for reverse transcriptase polymerase activity (By similarity).,Binds 2 magnesium ions for ribonuclease H (RNase H) activity. Substrate-binding is a precondition for magnesium binding (By similarity).,Magnesium ions for integrase activity. Binds at least 1, maybe 2 magnesium ions (By similarity).Binds 2 magnesium ions for reverse transcriptase polymerase activity (By similarity).,Binds 2 magnesium ions for ribonuclease H (RNase H) activity. Substrate-binding is a precondition for magnesium binding (By similarity).,Magnesium ions for integrase activity. Binds at least 1, maybe 2 magnesium ions (By similarity).


SubstratesProductsintermediates
KEGG-idC00017C00012C00001C00017C00012I00136
CompoundProteinPeptideH2OProteinPeptideAmino-diol-tetrahedral intermediate
Typepeptide/proteinpeptide/proteinH2Opeptide/proteinpeptide/protein
1a30AUnboundAnalogue:GLU-ASP-LEU
UnboundUnboundUnbound
1ajvAUnboundUnbound
UnboundUnboundTransition-state-analogue:NMB
1ajxAUnboundUnbound
UnboundUnboundTransition-state-analogue:AH1
1axaAUnboundAnalogue:U0E-U0E
UnboundUnboundUnbound
1bdlAUnboundUnbound
UnboundAnalogue:IM1Unbound
1bdqAUnboundAnalogue:IM1
UnboundUnboundUnbound
1bdrAUnboundAnalogue:IM1
UnboundUnboundUnbound
1bv7AUnboundUnbound
UnboundUnboundTransition-state-analogue:XV6
1bv9AUnboundUnbound
UnboundUnboundTransition-state-analogue:XV6
1bveAUnboundUnbound
UnboundUnboundTransition-state-analogue:DMP
1bvgAUnboundUnbound
UnboundUnboundTransition-state-analogue:DMP
1bwaAUnboundUnbound
UnboundUnboundTransition-state-analogue:XV6
1bwbAUnboundUnbound
UnboundUnboundTransition-state-analogue:146
1d4hAUnboundUnbound
UnboundUnboundTransition-state-analogue:BEH
1d4iAUnboundUnbound
UnboundUnboundTransition-state-analogue:BEG
1d4jAUnboundUnbound
UnboundUnboundTransition-state-analogue:MSC
1dmpAUnboundUnbound
UnboundUnboundTransition-state-analogue:DMQ
1dw6CUnboundAnalogue:ARG-VAL-DCL-PHE-GLU-ALA-NLN
UnboundUnboundUnbound
1ebkCUnboundAnalogue:ARG-VAL-DCL-PHE-GLU-ALA-NLN
UnboundUnboundUnbound
1ebkEUnboundAnalogue:ARG-VAL-DCL-PHE-GLU-ALA-NLN
UnboundUnboundUnbound
1ebwAUnboundUnbound
UnboundUnboundTransition-state-analogue:BEI
1ebyAUnboundUnbound
UnboundUnboundTransition-state-analogue:BEB
1ebzAUnboundUnbound
UnboundUnboundTransition-state-analogue:BEC
1ec0AUnboundUnbound
UnboundUnboundTransition-state-analogue:BED
1ec1AUnboundUnbound
UnboundUnboundTransition-state-analogue:BEE
1ec2AUnboundUnbound
UnboundUnboundTransition-state-analogue:BEJ
1ec3AUnboundUnbound
UnboundUnboundTransition-state-analogue:MS3
1fejCUnboundAnalogue:ACE-THR-ILE-NLE-NLE-GLN-ARG
UnboundUnboundUnbound
1ff0CUnboundAnalogue:ACE-THR-ILE-NLE-NLE-GLN-ARG
UnboundUnboundUnbound
1fffCUnboundAnalogue:ARG-VAL-DCL-PHE-GLU-ALA-NLE-NH2
UnboundUnboundUnbound
1ffiCUnboundAnalogue:ACE-THR-ILE-NLE-NLE-GLN-ARG
UnboundUnboundUnbound
1fg6CUnboundAnalogue:ACE-THR-ILE-NLE-NLE-GLN-ARG
UnboundUnboundUnbound
1fg8CUnboundAnalogue:ARG-VAL-DCL-PHE-GLU-ALA-NLE-NH2
UnboundUnboundUnbound
1fgcCUnboundAnalogue:ACE-THR-ILE-NLE-NLE-GLN-ARG
UnboundUnboundUnbound
1g2kAUnboundUnbound
UnboundUnboundTransition-state-analogue:NM1
1g6lA01UnboundUnbound
UnboundUnboundUnbound
1gnnAUnboundAnalogue:U0E-U0E
UnboundUnboundUnbound
1gnoAUnboundAnalogue:U0E-U0E
UnboundUnboundUnbound
1hbvAUnboundAnalogue:GAN
UnboundUnboundUnbound
1hefEUnboundAnalogue:ALA-ALA-PHE-OHE-PHE-VAL-VAL-OME
UnboundUnboundUnbound
1hegEUnboundAnalogue:ALA-ALA-PHE-OHE-GLY-VAL-VAL-OME
UnboundUnboundUnbound
1hihAUnboundAnalogue:C20
UnboundUnboundUnbound
1hivAUnboundAnalogue:NOA-HIS-CAV-ILE-APY
UnboundUnboundUnbound
1hosAUnboundUnbound
UnboundUnboundTransition-state-analogue:PHP
1hpsAUnboundAnalogue:RUN-RUN
UnboundUnboundUnbound
1hpvAUnboundAnalogue:478
UnboundUnboundUnbound
1hteAUnboundUnbound
Bound:LEU-GLN-GLU-SERAnalogue:G23Unbound
1htfAUnboundUnbound
Analogue:G26UnboundUnbound
1htgAUnboundAnalogue:G37
UnboundUnboundUnbound
1hvhAUnboundUnbound
UnboundUnboundTransition-state-analogue:Q82
1hviAUnboundUnbound
UnboundUnboundTransition-state-analogue:A77
1hvjAUnboundAnalogue:A78
UnboundUnboundUnbound
1hvkAUnboundUnbound
UnboundUnboundTransition-state-analogue:A79
1hvlAUnboundUnbound
UnboundUnboundTransition-state-analogue:A76
1hvrAUnboundUnbound
UnboundUnboundTransition-state-analogue:XK2
1hvsAUnboundUnbound
UnboundUnboundTransition-state-analogue:A77
1hwrAUnboundUnbound
UnboundUnboundTransition-state-analogue:216
1hxbAUnboundAnalogue:QNC-ASN-HPH-DIQ-NTB
UnboundUnboundUnbound
1k1tAUnboundAnalogue:ARG-VAL-DCL-PHE-GLU-ALA-NLE
UnboundUnboundUnbound
1k1uAUnboundAnalogue:ARG-VAL-DCL-PHE-GLU-ALA-NLE
UnboundUnboundUnbound
1k2bAUnboundAnalogue:ARG-VAL-DCL-PHE-GLU-ALA-NLE-NH2
UnboundUnboundUnbound
1k2cAUnboundAnalogue:ARG-VAL-DCL-PHE-GLU-ALA-NLE-NH2
UnboundUnboundUnbound
1k6cAUnboundAnalogue:MK1
UnboundUnboundUnbound
1k6pAUnboundAnalogue:XN3
UnboundUnboundUnbound
1k6tAUnboundAnalogue:XN1
UnboundUnboundUnbound
1k6vAUnboundAnalogue:XN2
UnboundUnboundUnbound
1lv1A01UnboundUnbound
UnboundUnboundUnbound
1merAUnboundUnbound
UnboundUnboundTransition-state-analogue:DMQ
1mesAUnboundUnbound
UnboundUnboundTransition-state-analogue:DMP
1metAUnboundUnbound
UnboundUnboundTransition-state-analogue:DMP
1meuAUnboundUnbound
UnboundUnboundTransition-state-analogue:DMP
1odwAUnboundAnalogue:BOC-HPH-DMN-HPH-BOC
UnboundUnboundUnbound
1odxAUnboundAnalogue:BOC-HPH-DMN-HPH-BOC
UnboundUnboundUnbound
1odyAUnboundAnalogue:LP1
UnboundUnboundUnbound
1qbrAUnboundUnbound
UnboundUnboundTransition-state-analogue:XV6
1qbsAUnboundUnbound
UnboundUnboundTransition-state-analogue:DMP
1qbtAUnboundUnbound
UnboundUnboundTransition-state-analogue:146
1qbuAUnboundUnbound
UnboundUnboundTransition-state-analogue:846
1sbgAUnboundAnalogue:IM1
UnboundUnboundUnbound
1tcxAUnboundAnalogue:IM1
UnboundUnboundUnbound
2bpvAUnboundAnalogue:1IN
UnboundUnboundUnbound
2bpwAUnboundAnalogue:1IN
UnboundUnboundUnbound
2bpxAUnboundAnalogue:MK1
UnboundUnboundUnbound
2bpyAUnboundAnalogue:3IN
UnboundUnboundUnbound
2bpzAUnboundAnalogue:3IN
UnboundUnboundUnbound
3phvAUnboundUnbound
UnboundUnboundUnbound
3tlhAUnboundAnalogue:INT
UnboundUnboundUnbound
9hvpAUnboundAnalogue:PHQ-VAL-COR-VAL-PHQ
UnboundUnboundUnbound
1a30BUnboundUnbound
UnboundUnboundUnbound
1ajvBUnboundUnbound
UnboundUnboundUnbound
1ajxBUnboundUnbound
UnboundUnboundUnbound
1axaBUnboundUnbound
UnboundUnboundUnbound
1bdlBUnboundUnbound
UnboundAnalogue:IM1Unbound
1bdqBUnboundUnbound
UnboundUnboundUnbound
1bdrBUnboundUnbound
UnboundUnboundUnbound
1bv7BUnboundUnbound
UnboundUnboundUnbound
1bv9BUnboundUnbound
UnboundUnboundUnbound
1bveBUnboundUnbound
UnboundUnboundUnbound
1bvgBUnboundUnbound
UnboundUnboundUnbound
1bwaBUnboundUnbound
UnboundUnboundUnbound
1bwbBUnboundUnbound
UnboundUnboundUnbound
1d4hBUnboundUnbound
UnboundUnboundUnbound
1d4iBUnboundUnbound
UnboundUnboundUnbound
1d4jBUnboundUnbound
UnboundUnboundUnbound
1dmpBUnboundUnbound
UnboundUnboundUnbound
1dw6DUnboundUnbound
UnboundUnboundUnbound
1ebkDUnboundUnbound
UnboundUnboundUnbound
1ebkFUnboundUnbound
UnboundUnboundUnbound
1ebwBUnboundUnbound
UnboundUnboundUnbound
1ebyBUnboundUnbound
UnboundUnboundUnbound
1ebzBUnboundUnbound
UnboundUnboundUnbound
1ec0BUnboundUnbound
UnboundUnboundUnbound
1ec1BUnboundUnbound
UnboundUnboundUnbound
1ec2BUnboundUnbound
UnboundUnboundUnbound
1ec3BUnboundUnbound
UnboundUnboundUnbound
1fejDUnboundUnbound
UnboundUnboundUnbound
1ff0DUnboundUnbound
UnboundUnboundUnbound
1fffDUnboundUnbound
UnboundUnboundUnbound
1ffiDUnboundUnbound
UnboundUnboundUnbound
1fg6DUnboundUnbound
UnboundUnboundUnbound
1fg8DUnboundUnbound
UnboundUnboundUnbound
1fgcDUnboundUnbound
UnboundUnboundUnbound
1g2kBUnboundUnbound
UnboundUnboundUnbound
1g6lA02UnboundUnbound
UnboundUnboundUnbound
1gnnBUnboundUnbound
UnboundUnboundUnbound
1gnoBUnboundUnbound
UnboundUnboundUnbound
1hbvBUnboundUnbound
UnboundUnboundUnbound
1hihBUnboundUnbound
UnboundUnboundUnbound
1hivBUnboundUnbound
UnboundUnboundUnbound
1hosBUnboundUnbound
UnboundUnboundUnbound
1hpsBUnboundUnbound
UnboundUnboundUnbound
1hpvBUnboundUnbound
UnboundUnboundUnbound
1hteBUnboundUnbound
UnboundUnboundUnbound
1htfBUnboundUnbound
UnboundUnboundUnbound
1htgBUnboundUnbound
UnboundUnboundUnbound
1hvhBUnboundUnbound
UnboundUnboundUnbound
1hviBUnboundUnbound
UnboundUnboundUnbound
1hvjBUnboundUnbound
UnboundUnboundUnbound
1hvkBUnboundUnbound
UnboundUnboundUnbound
1hvlBUnboundUnbound
UnboundUnboundUnbound
1hvrBUnboundUnbound
UnboundUnboundUnbound
1hvsBUnboundUnbound
UnboundUnboundUnbound
1hwrBUnboundUnbound
UnboundUnboundUnbound
1hxbBUnboundUnbound
UnboundUnboundUnbound
1k1tBUnboundUnbound
UnboundUnboundUnbound
1k1uBUnboundUnbound
UnboundUnboundUnbound
1k2bBUnboundUnbound
UnboundUnboundUnbound
1k2cBUnboundUnbound
UnboundUnboundUnbound
1k6cBUnboundUnbound
UnboundUnboundUnbound
1k6pBUnboundUnbound
UnboundUnboundUnbound
1k6tBUnboundUnbound
UnboundUnboundUnbound
1k6vBUnboundUnbound
UnboundUnboundUnbound
1lv1A02UnboundUnbound
UnboundUnboundUnbound
1merBUnboundUnbound
UnboundUnboundUnbound
1mesBUnboundUnbound
UnboundUnboundUnbound
1metBUnboundUnbound
UnboundUnboundUnbound
1meuBUnboundUnbound
UnboundUnboundUnbound
1odwBUnboundUnbound
UnboundUnboundUnbound
1odxBUnboundUnbound
UnboundUnboundUnbound
1odyBUnboundUnbound
UnboundUnboundUnbound
1qbrBUnboundUnbound
UnboundUnboundUnbound
1qbsBUnboundUnbound
UnboundUnboundUnbound
1qbtBUnboundUnbound
UnboundUnboundUnbound
1qbuBUnboundUnbound
UnboundUnboundUnbound
1sbgBUnboundUnbound
UnboundUnboundUnbound
1tcxBUnboundUnbound
UnboundUnboundUnbound
2bpvBUnboundUnbound
UnboundUnboundUnbound
2bpwBUnboundUnbound
UnboundUnboundUnbound
2bpxBUnboundUnbound
UnboundUnboundUnbound
2bpyBUnboundUnbound
UnboundUnboundUnbound
2bpzBUnboundUnbound
UnboundUnboundUnbound
9hvpBUnboundUnbound
UnboundUnboundUnbound

Active-site residues
resource
Swiss-prot;P35963
pdbCatalytic residuescomment
1a30AASP   25

1ajvAASP   25

1ajxAASP   25

1axaAASP   25
mutant A28S
1bdlAASP   25
mutant T31S, V32I, L33V, E34A, E35G, M36I, S37E
1bdqAASP   25
mutant T31S, V32I, L33V, E34A, E35G, M36I, S37E, I47V, V82I
1bdrAASP   25
mutant T31S, L33V, E34T, E35G, M36I, S37E
1bv7AASP   25

1bv9AASP   25
mutant I84V
1bveAASP   25
mutant C95A
1bvgAASP   25
mutant C95A
1bwaAASP   25
mutant V82F, I84V
1bwbAASP   25
mutant V82F, I84V
1d4hAASP   25

1d4iAASP   25

1d4jAASP   25

1dmpAASP   25

1dw6CASP   25
mutant Q7K, L33I, L63I, C67A, L90M, C95A
1ebkCASP   25
mutant Q7K, R8Q, L33I, L63I, C67A, C95A
1ebkEASP   25
mutant Q7K, R8Q, L33I, L63I, C67A, C95A
1ebwAASP   25

1ebyAASP   25

1ebzAASP   25

1ec0AASP   25

1ec1AASP   25

1ec2AASP   25

1ec3AASP   25

1fejCASP   25
mutant L90M
1ff0CASP   25
mutant K45I
1fffCASP   25
mutant D30N
1ffiCASP   25
mutant D30N
1fg6CASP   25
mutant N88D
1fg8CASP   25
mutant N88D
1fgcCASP   25

1g2kAASP   25

1g6lA01ASP   25

1gnnAASP   25
mutant V82N
1gnoAASP   25

1hbvAASP   25

1hefEASP   25

1hegEASP   25

1hihAASP   25

1hivAASP   25

1hosAASP   25

1hpsAASP   25

1hpvAASP   25

1hteAASP   25

1htfAASP   25

1htgAASP   25

1hvhAASP   25

1hviAASP   25

1hvjAASP   25

1hvkAASP   25

1hvlAASP   25

1hvrAASP   25

1hvsAASP   25
mutant V82A
1hwrAASP   25

1hxbAASP   25

1k1tAASP   25
mutant K45I, V82S
1k1uAASP   25
mutant K45I, L90M
1k2bAASP   25
mutant N88D, L90M
1k2cAASP   25
mutant D30N, V82S
1k6cAASP   25
mutant Q7K, K14R, V82T, I84V
1k6pAASP   25
mutant Q7K, K14R, V82T, I84V
1k6tAASP   25
mutant Q7K, K14R, V82T, I84V
1k6vAASP   25
mutant Q7K, K14R, V82T, I84V
1lv1A01ASP   25
mutant C95M
1merAASP   25
mutant I84V
1mesAASP   25
mutant I84V
1metAASP   25
mutant V82F
1meuAASP   25
mutant V82F, I84V
1odwAASP   25

1odxAASP   25
mutant A71T, V82A
1odyAASP   25

1qbrAASP   25

1qbsAASP   25

1qbtAASP   25

1qbuAASP   25

1sbgAASP   25

1tcxAASP   25
mutant I32V, V47I, I82V
2bpvAASP   25

2bpwAASP   25

2bpxAASP   25

2bpyAASP   25

2bpzAASP   25

3phvAASP   25

3tlhAASP   25

9hvpAASP   25

1a30BASP   25

1ajvBASP   25

1ajxBASP   25

1axaBASP   25
mutant A28S
1bdlBASP   25
mutant T31S, V32I, L33V, E34A, E35G, M36I, S37E
1bdqBASP   25
mutant T31S, V32I, L33V, E34A, E35G, M36I, S37E, I47V, V82I
1bdrBASP   25
mutant T31S, L33V, E34T, E35G, M36I, S37E
1bv7BASP   25

1bv9BASP   25
mutant I84V
1bveBASP   25
mutant C95A
1bvgBASP   25
mutant C95A
1bwaBASP   25
mutant V82F, I84V
1bwbBASP   25
mutant V82F, I84V
1d4hBASP  125

1d4iBASP  125

1d4jBASP  125

1dmpBASP   25

1dw6DASP  125
mutant Q107K, L133I, L163I, C167A, L190M, C195A
1ebkDASP  125
mutant Q107K, R108Q, L133I, L163I, C167A, C195A
1ebkFASP  125
mutant Q107K, R108Q, L133I, L163I, C167A, C195A
1ebwBASP  125

1ebyBASP  125

1ebzBASP  125

1ec0BASP  125

1ec1BASP  125

1ec2BASP  125

1ec3BASP  125

1fejDASP  125
mutant L190M
1ff0DASP  125
mutant K145I
1fffDASP  125
mutant D130N
1ffiDASP  125
mutant D130N
1fg6DASP  125
mutant N188D
1fg8DASP  125
mutant N188D
1fgcDASP  125

1g2kBASP   25

1g6lA02ASP 1025

1gnnBASP   25
mutant V82N
1gnoBASP   25

1hbvBASP   25

1hihBASP   25

1hivBASP   25

1hosBASP   25

1hpsBASP   25

1hpvBASP   25

1hteBASP   25

1htfBASP   25

1htgBASP   25

1hvhBASP   25

1hviBASP   25

1hvjBASP   25

1hvkBASP   25

1hvlBASP   25

1hvrBASP   25

1hvsBASP   25
mutant V82A
1hwrBASP   25

1hxbBASP   25

1k1tBASP  125
mutant K145I, V182S
1k1uBASP  125
mutant K145I, L190M
1k2bBASP   25
mutant N88D, L90M
1k2cBASP   25
mutant D30N, V82S
1k6cBASP   25
mutant Q7K, K14R, V82T, I84V
1k6pBASP   25
mutant Q7K, K14R, V82T, I84V
1k6tBASP   25
mutant Q7K, K14R, V82T, I84V
1k6vBASP   25
mutant Q7K,K14R,V82T,I84V
1lv1A02ASP 1025
mutant C1095A
1merBASP   25
mutant I84V
1mesBASP   25
mutant I84V
1metBASP   25
mutant V82F
1meuBASP   25
mutant V82F, I84V
1odwBASP   25

1odxBASP   25
mutant A71T, V82A
1odyBASP   25

1qbrBASP   25

1qbsBASP   25

1qbtBASP   25

1qbuBASP   25

1sbgBASP   25

1tcxBASP   25
mutant I32V, V47I, I82V
2bpvBASP   25

2bpwBASP   25

2bpxBASP   25

2bpyBASP   25

2bpzBASP   25

9hvpBASP   25


References for Catalytic Mechanism
ReferencesSectionsNo. of steps in catalysis
[1]p.302
[7]Fig.4, p.8461-8462
[8]p.1607-1608
[9]Fig.5, p.24363-24365
[14]p.7978-7979
[33]Fig.7, p.12942-12943
[39]Fig.17, p.336-339
[40]p.949
[42]p.682
[79]Fig.8, p.803
[81]Fig.1
[100]Fig.2

references
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Related PDB3phv
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[2]
Comments3D-STRUCTURE MODELING OF PROTEASE DOMAIN.
Medline ID89146134
PubMed ID2537531
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PubMed ID2201682
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Pages14209-19
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PubMed ID1812742
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Volume306
Pages455-60
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PubMed ID1993177
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Pages1600-9
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PubMed ID1761538
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Year1991
Volume266
Pages24359-66
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[10]
CommentsX-ray crystallography
PubMed ID1956054
JournalJ Med Chem
Year1991
Volume34
Pages3340-2
AuthorsKrohn A, Redshaw S, Ritchie JC, Graves BJ, Hatada MH
TitleNovel binding mode of highly potent HIV-proteinase inhibitors incorporating the (R)-hydroxyethylamine isostere.
Related PDB1hxb
[11]
CommentsX-ray crystallography
PubMed ID1429626
JournalJ Biol Chem
Year1992
Volume267
Pages22770-8
AuthorsMurthy KH, Winborne EL, Minnich MD, Culp JS, Debouck C
TitleThe crystal structures at 2.2-A resolution of hydroxyethylene-based inhibitors bound to human immunodeficiency virus type 1 protease show that the inhibitors are present in two distinct orientations.
Related PDB1heg
[12]
CommentsX-ray crystallography
PubMed ID1304383
JournalProtein Sci
Year1992
Volume1
Pages1061-72
AuthorsThanki N, Rao JK, Foundling SI, Howe WJ, Moon JB, Hui JO, Tomasselli AG, Heinrikson RL, Thaisrivongs S, Wlodawer A
TitleCrystal structure of a complex of HIV-1 protease with a dihydroxyethylene-containing inhibitor: comparisons with molecular modeling.
Related PDB1hiv
[13]
PubMed ID8352596
JournalAnnu Rev Biochem
Year1993
Volume62
Pages543-85
AuthorsWlodawer A, Erickson JW
TitleStructure-based inhibitors of HIV-1 protease.
[14]
CommentsX-ray crystallography
PubMed ID8347601
JournalBiochemistry
Year1993
Volume32
Pages7972-80
AuthorsAbdel-Meguid SS, Zhao B, Murthy KH, Winborne E, Choi JK, DesJarlais RL, Minnich MD, Culp JS, Debouck C, Tomaszek TA Jr, et al
TitleInhibition of human immunodeficiency virus-1 protease by a C2-symmetric phosphinate. Synthesis and crystallographic analysis.
Related PDB1hos
[15]
CommentsX-ray crystallography
PubMed ID7918383
JournalBiochemistry
Year1994
Volume33
Pages11671-7
AuthorsAbdel-Meguid SS, Metcalf BW, Carr TJ, Demarsh P, DesJarlais RL, Fisher S, Green DW, Ivanoff L, Lambert DM, Murthy KH, et al
TitleAn orally bioavailable HIV-1 protease inhibitor containing an imidazole-derived peptide bond replacement: crystallographic and pharmacokinetic analysis.
Related PDB1sbg
[16]
CommentsX-ray crystallography
PubMed ID8031777
JournalBiochemistry
Year1994
Volume33
Pages8417-27
AuthorsJhoti H, Singh OM, Weir MP, Cooke R, Murray-Rust P, Wonacott A
TitleX-ray crystallographic studies of a series of penicillin-derived asymmetric inhibitors of HIV-1 protease.
Related PDB1hte,1htf,1htg
[17]
CommentsX-ray crystallography
JournalJ Am Chem Soc
Year1994
Volume116
Pages847-55
AuthorsHosur MV, Bhat TN, Kempf DJ, Baldwin ET, Liu B, Gulnik S, Wideburg NE, Norbeck DW, Appelt K, Erickson JW
TitleInfluence of stereochemistry on activity and binding modes for C2 symmetry-based diol inhibitors of HIV-1 protease.
Related PDB1hvi,1hvj,1hvk,1hvl
[18]
CommentsX-ray crystallography
PubMed ID7932533
JournalJ Med Chem
Year1994
Volume37
Pages3100-7
AuthorsThompson SK, Murthy KH, Zhao B, Winborne E, Green DW, Fisher SM, DesJarlais RL, Tomaszek TA Jr, Meek TD, Gleason JG, et al
TitleRational design, synthesis, and crystallographic analysis of a hydroxyethylene-based HIV-1 protease inhibitor containing a heterocyclic P1'--P2' amide bond isostere.
Related PDB1hps
[19]
CommentsX-ray crystallography
PubMed ID8278812
JournalScience
Year1994
Volume263
Pages380-4
AuthorsLam PY, Jadhav PK, Eyermann CJ, Hodge CN, Ru Y, Bacheler LT, Meek JL, Otto MJ, Rayner MM, Wong YN, et al
TitleRational design of potent, bioavailable, nonpeptide cyclic ureas as HIV protease inhibitors.
Related PDB1hvr
[20]
PubMed ID8540354
JournalAdv Exp Med Biol
Year1995
Volume362
Pages439-44
AuthorsBhat TN, Baldwin ET, Liu B, Cheng YS, Erickson JW
TitleX-ray structure of a tethered dimer for HIV-1 protease.
[21]
PubMed ID8540357
JournalAdv Exp Med Biol
Year1995
Volume362
Pages455-60
AuthorsCollins JR, Burt SK, Erickson JW
TitleActivated dynamics of flap opening in HIV-1 protease.
[22]
PubMed ID8540356
JournalAdv Exp Med Biol
Year1995
Volume362
Pages451-4
AuthorsSilva AM, Cachau RE, Baldwin ET, Gulnik S, Sham HL, Erickson JW
TitleMolecular dynamics of HIV-1 protease in complex with a difluoroketone-containing inhibitor: implications for the catalytic mechanism.
[23]
PubMed ID9383433
JournalChem Biol
Year1995
Volume2
Pages317-24
AuthorsGehlhaar DK, Verkhivker GM, Rejto PA, Sherman CJ, Fogel DB, Fogel LJ, Freer ST
TitleMolecular recognition of the inhibitor AG-1343 by HIV-1 protease: conformationally flexible docking by evolutionary programming.
[24]
CommentsX-ray crystallography
JournalJ Am Chem Soc
Year1995
Volume117
Pages1181-2
AuthorsKim E.E, Baker CT, Dwyer MD, Murcko MA, Rao BG, Tung RD, Navia MA
TitleCrystal structure of HIV-1 protease in complex with VX-478, a potent and orally bioavailable inhibitor of the enzyme.
Related PDB1hpv
[25]
PubMed ID7665551
JournalJ Biol Chem
Year1995
Volume270
Pages21433-6
AuthorsChen Z, Li Y, Schock HB, Hall D, Chen E, Kuo LC
TitleThree-dimensional structure of a mutant HIV-1 protease displaying cross-resistance to all protease inhibitors in clinical trials.
[26]
CommentsX-ray crystallography
PubMed ID7650677
JournalJ Med Chem
Year1995
Volume38
Pages3246-52
AuthorsHoog SS, Zhao B, Winborne E, Fisher S, Green DW, DesJarlais RL, Newlander KA, Callahan JF, Moore ML, Huffman WF, et al
TitleA check on rational drug design: crystal structure of a complex of human immunodeficiency virus type 1 protease with a novel gamma-turn mimetic inhibitor.
Related PDB1hef
[27]
PubMed ID7796263
JournalNat Struct Biol
Year1995
Volume2
Pages274-80
AuthorsNicholson LK, Yamazaki T, Torchia DA, Grzesiek S, Bax A, Stahl SJ, Kaufman JD, Wingfield PT, Lam PY, Jadhav PK, et al
TitleFlexibility and function in HIV-1 protease.
[28]
PubMed ID8590019
JournalStructure
Year1995
Volume3
Pages581-90
AuthorsBaldwin ET, Bhat TN, Gulnik S, Liu B, Topol IA, Kiso Y, Mimoto T, Mitsuya H, Erickson JW
TitleStructure of HIV-1 protease with KNI-272, a tight-binding transition-state analog containing allophenylnorstatine.
[29]
CommentsX-ray crystallography
PubMed ID7613867
JournalStructure
Year1995
Volume3
Pages381-9
AuthorsPriestle JP, Fassler A, Rosel J, Tintelnot-Blomley M, Strop P, Grutter MG
TitleComparative analysis of the X-ray structures of HIV-1 and HIV-2 proteases in complex with CGP 53820, a novel pseudosymmetric inhibitor.
Related PDB1hih
[30]
PubMed ID8652592
JournalBiochemistry
Year1996
Volume35
Pages2482-8
AuthorsDavis DA, Dorsey K, Wingfield PT, Stahl SJ, Kaufman J, Fales HM, Levine RL
TitleRegulation of HIV-1 protease activity through cysteine modification.
[31]
CommentsX-ray crystallography
PubMed ID8718851
JournalBiochemistry
Year1996
Volume35
Pages10627-33
AuthorsHong L, Treharne A, Hartsuck JA, Foundling S, Tang J
TitleCrystal structures of complexes of a peptidic inhibitor with wild-type and two mutant HIV-1 proteases.
Related PDB1gnn,1gno
[32]
CommentsX-ray crystallography
PubMed ID8756683
JournalBiochemistry
Year1996
Volume35
Pages10279-86
AuthorsHoog SS, Towler EM, Zhao B, Doyle ML, Debouck C, Abdel-Meguid SS
TitleHuman immunodeficiency virus protease ligand specificity conferred by residues outside of the active site cavity.
Related PDB1tcx
[33]
PubMed ID8841139
JournalBiochemistry
Year1996
Volume35
Pages12933-44
AuthorsRose RB, Craik CS, Douglas NL, Stroud RM
TitleThree-dimensional structures of HIV-1 and SIV protease product complexes.
[34]
PubMed ID8756455
JournalBiochemistry
Year1996
Volume35
Pages9945-50
AuthorsWang YX, Freedberg DI, Yamazaki T, Wingfield PT, Stahl SJ, Kaufman JD, Kiso Y, Torchia DA
TitleSolution NMR evidence that the HIV-1 protease catalytic aspartyl groups have different ionization states in the complex formed with the asymmetric drug KNI-272.
[35]
CommentsX-ray crystallography
PubMed ID8807858
JournalChem Biol
Year1996
Volume3
Pages301-14
AuthorsHodge CN, Aldrich PE, Bacheler LT, Chang CH, Eyermann CJ, Garber S, Grubb M, Jackson DA, Jadhav PK, Korant B, Lam PY, Maurin MB, Meek JL, Otto MJ, Rayner MM, Reid C, Sharpe TR, Shum L, Winslow DL, Erickson-Viitanen S
TitleImproved cyclic urea inhibitors of the HIV-1 protease: synthesis, potency, resistance profile, human pharmacokinetics and X-ray crystal structure of DMP 450.
Related PDB1dmp
[36]
PubMed ID8621402
JournalJ Biol Chem
Year1996
Volume271
Pages5458-63
AuthorsSzeltner Z, Polgar L
TitleConformational stability and catalytic activity of HIV-1 protease are both enhanced at high salt concentration.
[37]
CommentsX-ray crystallography
PubMed ID8784449
JournalJ Med Chem
Year1996
Volume39
Pages3514-25
AuthorsLam PY, Ru Y, Jadhav PK, Aldrich PE, DeLucca GV, Eyermann CJ, Chang CH, Emmett G, Holler ER, Daneker WF, Li L, Confalone PN, McHugh RJ, Han Q, Li R, Markwalder JA, Seitz SP, Sharpe TR, Bacheler LT, Rayner MM, Klabe RM, Shum L, Winslow DL, Kornhauser DM, Hodge CN, et al
TitleCyclic HIV protease inhibitors: synthesis, conformational analysis, P2/P2' structure-activity relationship, and molecular recognition of cyclic ureas.
Related PDB1qbs
[38]
PubMed ID8667359
JournalJ Med Chem
Year1996
Volume39
Pages2156-69
AuthorsNugiel DA, Jacobs K, Kaltenbach RF, Worley T, Patel M, Meyer DT, Jadhav PK, De Lucca GV, Smyser TE, Klabe RM, Bacheler LT, Rayner MM, Seitz SP
TitlePreparation and structure-activity relationship of novel P1/P1'-substituted cyclic urea-based human immunodeficiency virus type-1 protease inhibitors.
[39]
PubMed ID8551523
JournalJ Mol Biol
Year1996
Volume255
Pages321-46
AuthorsSilva AM, Cachau RE, Sham HL, Erickson JW
TitleInhibition and catalytic mechanism of HIV-1 aspartic protease.
[40]
PubMed ID8901873
JournalNat Struct Biol
Year1996
Volume3
Pages946-50
AuthorsSmith R, Brereton IM, Chai RY, Kent SB
TitleIonization states of the catalytic residues in HIV-1 protease.
[41]
PubMed ID9390264
JournalPac Symp Biocomput
Year1996
Volume
Pages638-52
AuthorsVerkhivker GM
TitleEmpirical free energy calculations of human immunodeficiency virus type 1 protease crystallographic complexes. II. Knowledge-based ligand-protein interaction potentials applied to thermodynamic analysis of hydrophobic mutations.
[42]
PubMed ID8875645
JournalProtein Eng
Year1996
Volume9
Pages679-90
AuthorsWeber IT, Harrison RW
TitleMolecular mechanics calculations on HIV-1 protease with peptide substrates correlate with experimental data.
[43]
CommentsX-ray crystallography
JournalProtein Pept Lett
Year1996
Volume3
Pages399-406
AuthorsKervinen J, Thanki N, Zdanov A, Tino J, Barrish J, Pin FL, Colonno R, Riccardi K, Samanta H, Wlodawer A
TitleStructural Analysis of the Native and Drug-Resistant HIV-1 Proteinases Complexed with an Aminodiol Inhibitor.
Related PDB1odx
[44]
CommentsSTRUCTURE BY NMR OF 57-155.
Medline ID97022126
PubMed ID8868486
JournalProtein Sci
Year1996
Volume5
Pages495-506
AuthorsYamazaki T, Hinck AP, Wang YX, Nicholson LK, Torchia DA, Wingfield P, Stahl SJ, Kaufman JD, Chang CH, Domaille PJ, Lam PY
TitleThree-dimensional solution structure of the HIV-1 protease complexed with DMP323, a novel cyclic urea-type inhibitor, determined by nuclear magnetic resonance spectroscopy.
Related PDB1bve,1bvg
Related Swiss-protP04585
[45]
CommentsX-ray crystallography
PubMed ID9048541
JournalBiochemistry
Year1997
Volume36
Pages1573-80
AuthorsAla PJ, Huston EE, Klabe RM, McCabe DD, Duke JL, Rizzo CJ, Korant BD, DeLoskey RJ, Lam PY, Hodge CN, Chang CH
TitleMolecular basis of HIV-1 protease drug resistance: structural analysis of mutant proteases complexed with cyclic urea inhibitors.
Related PDB1mer,1mes,1met,1meu
[46]
PubMed ID9346283
JournalEur J Biochem
Year1997
Volume248
Pages313-22
AuthorsLange-Savage G, Berchtold H, Liesum A, Budt KH, Peyman A, Knolle J, Sedlacek J, Fabry M, Hilgenfeld R
TitleStructure of HOE/BAY 793 complexed to human immunodeficiency virus (HIV-1) protease in two different crystal forms--structure/function relationship and influence of crystal packing.
[47]
PubMed ID9188447
JournalJ Biol Chem
Year1997
Volume272
Pages15603-6
AuthorsVance JE, LeBlanc DA, Wingfield P, London RE
TitleConformational selectivity of HIV-1 protease cleavage of X-Pro peptide bonds and its implications.
[48]
CommentsX-ray crystallography
PubMed ID9083478
JournalJ Med Chem
Year1997
Volume40
Pages898-902
AuthorsBackbro K, Lowgren S, Osterlund K, Atepo J, Unge T, Hulten J, Bonham NM, Schaal W, Karlen A, Hallberg A
TitleUnexpected binding mode of a cyclic sulfamide HIV-1 protease inhibitor.
Related PDB1ajv,1ajx
[49]
CommentsX-ray crystallography
PubMed ID9003516
JournalJ Med Chem
Year1997
Volume40
Pages181-91
AuthorsJadhav PK, Ala P, Woerner FJ, Chang CH, Garber SS, Anton ED, Bacheler LT
TitleCyclic urea amides: HIV-1 protease inhibitors with low nanomolar potency against both wild type and protease inhibitor resistant mutants of HIV.
Related PDB1qbr,1qbt,1qbu
[50]
PubMed ID9258349
JournalJ Med Chem
Year1997
Volume40
Pages2440-4
AuthorsSmith AB 3rd, Hirschmann R, Pasternak A, Yao W, Sprengeler PA, Holloway MK, Kuo LC, Chen Z, Darke PL, Schleif WA
TitleAn orally bioavailable pyrrolinone inhibitor of HIV-1 protease: computational analysis and X-ray crystal structure of the enzyme complex.
[51]
PubMed ID9061782
JournalProteins
Year1997
Volume27
Pages184-94
AuthorsMiller M, Geller M, Gribskov M, Kent SB
TitleAnalysis of the structure of chemically synthesized HIV-1 protease complexed with a hexapeptide inhibitor. Part I: Crystallographic refinement of 2 A data.
[52]
CommentsX-ray crystallography
PubMed ID9757136
JournalActa Crystallogr D Biol Crystallogr
Year1998
Volume54
Pages1053-60
AuthorsMunshi S, Chen Z, Li Y, Olsen DB, Fraley ME, Hungate RW, Kuo LC
TitleRapid X-ray diffraction analysis of HIV-1 protease-inhibitor complexes: inhibitor exchange in single crystals of the bound enzyme.
Related PDB2bpv,2bpw,2bpx,2bpy,2bpz
[53]
PubMed ID9561200
JournalAdv Exp Med Biol
Year1998
Volume436
Pages59-63
AuthorsHong L, Zhang C, Hartsuck JA, Foundling S, Tang J
TitleX-ray crystallographic studies of the structure-function relationships of HIV-1 protease.
[54]
CommentsX-ray crystallography
PubMed ID9790666
JournalBiochemistry
Year1998
Volume37
Pages15042-9
AuthorsAla PJ, Huston EE, Klabe RM, Jadhav PK, Lam PY, Chang CH
TitleCounteracting HIV-1 protease drug resistance: structural analysis of mutant proteases complexed with XV638 and SD146, cyclic urea amides with broad specificities.
Related PDB1bv7,1bv9,1bwa,1bwb
[55]
CommentsX-ray crystallography
PubMed ID9485357
JournalBiochemistry
Year1998
Volume37
Pages2105-10
AuthorsLouis JM, Dyda F, Nashed NT, Kimmel AR, Davies DR
TitleHydrophilic peptides derived from the transframe region of Gag-Pol inhibit the HIV-1 protease.
Related PDB1a30
[56]
CommentsX-ray crystallography
PubMed ID9692985
JournalBiochemistry
Year1998
Volume37
Pages10928-36
AuthorsSwairjo MA, Towler EM, Debouck C, Abdel-Meguid SS
TitleStructural role of the 30's loop in determining the ligand specificity of the human immunodeficiency virus protease.
Related PDB1bdr
[57]
PubMed ID9860826
JournalBiochemistry
Year1998
Volume37
Pages17137-44
AuthorsTowler EM, Gulnik SV, Bhat TN, Xie D, Gustschina E, Sumpter TR, Robertson N, Jones C, Sauter M, Mueller-Lantzsch N, Debouck C, Erickson JW
TitleFunctional characterization of the protease of human endogenous retrovirus, K10: can it complement HIV-1 protease?
[58]
PubMed ID9881109
JournalBioorg Med Chem
Year1998
Volume6
Pages2185-92
AuthorsGupta SP, Babu MS, Sowmya S
TitleA quantitative structure-activity relationship study on some sulfolanes and arylthiomethanes acting as HIV-1 protease inhibitors.
[59]
PubMed ID9789740
JournalGen Physiol Biophys
Year1998
Volume17 Suppl 1
Pages3-6
AuthorsLescar J, Stouracova R, Riottot MM, Chitarra V, Brynda J, Fabry M, Horejsi M, Sedlacek J, Bentley GA
TitleStructural studies of HIV-1 protease-inhibiting antibodies.
[60]
CommentsX-ray crystallography
PubMed ID9575185
JournalJ Biol Chem
Year1998
Volume273
Pages12325-31
AuthorsAla PJ, DeLoskey RJ, Huston EE, Jadhav PK, Lam PY, Eyermann CJ, Hodge CN, Schadt MC, Lewandowski FA, Weber PC, McCabe DD, Duke JL, Chang CH
TitleMolecular recognition of cyclic urea HIV-1 protease inhibitors.
Related PDB1hwr
[61]
CommentsX-ray crystallography
PubMed ID9554878
JournalJ Med Chem
Year1998
Volume41
Pages1446-55
AuthorsJadhav PK, Woerner FJ, Lam PY, Hodge CN, Eyermann CJ, Man HW, Daneker WF, Bacheler LT, Rayner MM, Meek JL, Erickson-Viitanen S, Jackson DA, Calabrese JC, Schadt M, Chang CH
TitleNonpeptide cyclic cyanoguanidines as HIV-1 protease inhibitors: synthesis, structure-activity relationships, and X-ray crystal structure studies.
Related PDB1hvh
[62]
CommentsX-ray crystallography
PubMed ID9521105
JournalProtein Sci
Year1998
Volume7
Pages300-5
AuthorsHong L, Hartsuck JA, Foundling S, Ermolieff J, Tang J
TitleActive-site mobility in human immunodeficiency virus, type 1, protease as demonstrated by crystal structure of A28S mutant.
Related PDB1axa
[63]
CommentsX-RAY CRYSTALLOGRAPHY (2.0 ANGSTROMS) OF 57-155.
Medline ID99043699
PubMed ID9827997
JournalProtein Sci
Year1998
Volume7
Pages2314-23
AuthorsKervinen J, Lubkowski J, Zdanov A, Bhatt D, Dunn BM, Hui KY, Powell DJ, Kay J, Wlodawer A, Gustchina A
TitleToward a universal inhibitor of retroviral proteases: comparative analysis of the interactions of LP-130 complexed with proteases from HIV-1, FIV, and EIAV.
Related PDB1ody
Related Swiss-protP04585
[64]
PubMed ID9672038
JournalProteins
Year1998
Volume32
Pages7-16
AuthorsRick SW, Erickson JW, Burt SK
TitleReaction path and free energy calculations of the transition between alternate conformations of HIV-1 protease.
[65]
CommentsX-ray crystallography
PubMed ID10429209
JournalEur J Biochem
Year1999
Volume263
Pages238-45
AuthorsMahalingam B, Louis JM, Reed CC, Adomat JM, Krouse J, Wang YF, Harrison RW, Weber IT
TitleStructural and kinetic analysis of drug resistant mutants of HIV-1 protease.
Related PDB1dw6,1ebk
[66]
PubMed ID10438521
JournalJ Biol Chem
Year1999
Volume274
Pages23437-42
AuthorsLouis JM, Wondrak EM, Kimmel AR, Wingfield PT, Nashed NT
TitleProteolytic processing of HIV-1 protease precursor, kinetics and mechanism.
[67]
PubMed ID11000004
JournalJ Med Chem
Year2000
Volume43
Pages3495-504
AuthorsTyndall JD, Reid RC, Tyssen DP, Jardine DK, Todd B, Passmore M, March DR, Pattenden LK, Bergman DA, Alewood D, Hu SH, Alewood PF, Birch CJ, Martin JL, Fairlie DP
TitleSynthesis, stability, antiviral activity, and protease-bound structures of substrate-mimicking constrained macrocyclic inhibitors of HIV-1 protease.
[68]
CommentsX-ray crystallography
PubMed ID10651036
JournalProteins
Year2000
Volume38
Pages29-40
AuthorsLi M, Morris GM, Lee T, Laco GS, Wong CH, Olson AJ, Elder JH, Wlodawer A, Gustchina A
TitleStructural studies of FIV and HIV-1 proteases complexed with an efficient inhibitor of FIV protease.
Related PDB3tlh
[69]
PubMed ID10858137
JournalScience
Year2000
Volume288
Pages1590
AuthorsKent S, Marshall GR, Wlodawer A
TitleDetermining the 3D structure of HIV-1 protease.
[70]
PubMed ID11741592
JournalFEBS Lett
Year2001
Volume509
Pages218-24
AuthorsBhavesh NS, Panchal SC, Mittal R, Hosur RV
TitleNMR identification of local structural preferences in HIV-1 protease tethered heterodimer in 6 M guanidine hydrochloride.
[71]
CommentsX-ray crystallography
PubMed ID11170625
JournalJ Med Chem
Year2001
Volume44
Pages155-69
AuthorsSchaal W, Karlsson A, Ahlsen G, Lindberg J, Andersson HO, Danielson UH, Classon B, Unge T, Samuelsson B, Hulten J, Hallberg A, Karlen A
TitleSynthesis and comparative molecular field analysis (CoMFA) of symmetric and nonsymmetric cyclic sulfamide HIV-1 protease inhibitors.
Related PDB1g2k
[72]
PubMed ID11410934
JournalMed Res Rev
Year2001
Volume21
Pages348-53
AuthorsMager PP
TitleThe active site of HIV-1 protease.
[73]
CommentsX-ray crystallography
PubMed ID11340661
JournalProteins
Year2001
Volume43
Pages455-64
AuthorsMahalingam B, Louis JM, Hung J, Harrison RW, Weber IT
TitleStructural implications of drug-resistant mutants of HIV-1 protease: high-resolution crystal structures of the mutant protease/substrate analogue complexes.
Related PDB1fej,1ff0,1fff,1ffi,1fg6,1fg8,1fgc
[74]
CommentsX-ray crystallography
PubMed ID11170214
JournalProteins
Year2001
Volume43
Pages57-64
AuthorsPillai B, Kannan KK, Hosur MV
Title1.9 A x-ray study shows closed flap conformation in crystals of tethered HIV-1 PR.
Related PDB1g6l
[75]
PubMed ID11591344
JournalStructure
Year2001
Volume9
Pages887-95
AuthorsRezacova P, Lescar J, Brynda J, Fabry M, Horejsi M, Sedlacek J, Bentley GA
TitleStructural basis of HIV-1 and HIV-2 protease inhibition by a monoclonal antibody.
[76]
CommentsX-ray crystallography
PubMed ID12051725
JournalBiochem Biophys Res Commun
Year2002
Volume294
Pages395-401
AuthorsKumar M, Kannan KK, Hosur MV, Bhavesh NS, Chatterjee A, Mittal R, Hosur RV
TitleEffects of remote mutation on the autolysis of HIV-1 PR: X-ray and NMR investigations.
Related PDB1lv1
[77]
PubMed ID12034371
JournalBiochem Pharmacol
Year2002
Volume63
Pages1863-73
AuthorsLebon F, Boggetto N, Ledecq M, Durant F, Benatallah Z, Sicsic S, Lapouyade R, Kahn O, Mouithys-Mickalad A, Deby-Dupont G, Reboud-Ravaux M. Metal-organic compounds: a new approach for drug discovery
TitleN1-(4-methyl-2-pyridyl)-2,3,6-trimethoxybenzamide copper(II) complex as an inhibitor of human immunodeficiency virus 1 protease.
[78]
PubMed ID11802730
JournalBiochemistry
Year2002
Volume41
Pages1302-7
AuthorsPorter DJ, Hanlon MH, Furfine ES
TitleHIV-1 protease: characterization of a catalytically competent enzyme-substrate intermediate.
[79]
PubMed ID12124265
JournalBiophys J
Year2002
Volume83
Pages794-807
AuthorsTrylska J, Bala P, Geller M, Grochowski P
TitleMolecular dynamics simulations of the first steps of the reaction catalyzed by HIV-1 protease.
[80]
PubMed ID11906284
JournalJ Med Chem
Year2002
Volume45
Pages1432-8
AuthorsDohnalek J, Hasek J, Duskova J, Petrokova H, Hradilek M, Soucek M, Konvalinka J, Brynda J, Sedlacek J, Fabry M
TitleHydroxyethylamine isostere of an HIV-1 protease inhibitor prefers its amine to the hydroxy group in binding to catalytic aspartates. A synchrotron study of HIV-1 protease in complex with a peptidomimetic inhibitor.
[81]
PubMed ID12051929
JournalJ Mol Biol
Year2002
Volume319
Pages567-83
AuthorsPiana S, Carloni P, Parrinello M
TitleRole of conformational fluctuations in the enzymatic reaction of HIV-1 protease.
[82]
PubMed ID11771964
JournalJ Mol Biol
Year2002
Volume315
Pages21-52
AuthorsZoete V, Michielin O, Karplus M
TitleRelation between sequence and structure of HIV-1 protease inhibitor complexes: a model system for the analysis of protein flexibility.
[83]
PubMed ID11773409
JournalJ Virol
Year2002
Volume76
Pages1349-58
AuthorsYoshimura K, Kato R, Kavlick MF, Nguyen A, Maroun V, Maeda K, Hussain KA, Ghosh AK, Gulnik SV, Erickson JW, Mitsuya H
TitleA potent human immunodeficiency virus type 1 protease inhibitor, UIC-94003 (TMC-126), and selection of a novel (A28S) mutation in the protease active site.
[84]
CommentsX-ray crystallography
PubMed ID11790852
JournalProtein Sci
Year2002
Volume11
Pages418-29
AuthorsKing NM, Melnick L, Prabu-Jeyabalan M, Nalivaika EA, Yang SS, Gao Y, Nie X, Zepp C, Heefner DL, Schiffer CA
TitleLack of synergy for inhibitors targeting a multi-drug-resistant HIV-1 protease.
Related PDB1k6c,1k6p,1k6t,1k6v
[85]
PubMed ID12237461
JournalProtein Sci
Year2002
Volume11
Pages2393-402
AuthorsPiana S, Carloni P, Rothlisberger U
TitleDrug resistance in HIV-1 protease: Flexibility-assisted mechanism of compensatory mutations.
[86]
CommentsX-ray crystallography
PubMed ID12012342
JournalProteins
Year2002
Volume48
Pages107-16
AuthorsMahalingam B, Boross P, Wang YF, Louis JM, Fischer CC, Tozser J, Harrison RW, Weber IT
TitleCombining mutations in HIV-1 protease to understand mechanisms of resistance.
Related PDB1k1t,1k1u,1k2b,1k2c
[87]
PubMed ID12005435
JournalStructure
Year2002
Volume10
Pages369-81
AuthorsPrabu-Jeyabalan M, Nalivaika E, Schiffer CA
TitleSubstrate shape determines specificity of recognition for HIV-1 protease: analysis of crystal structures of six substrate complexes.
[88]
PubMed ID12534275
JournalBiochemistry
Year2003
Volume42
Pages631-8
AuthorsMuzammil S, Ross P, Freire E
TitleA major role for a set of non-active site mutations in the development of HIV-1 protease drug resistance.
[89]
PubMed ID12564936
JournalBiochemistry
Year2003
Volume42
Pages1326-33
AuthorsZhu Z, Schuster DI, Tuckerman ME
TitleMolecular dynamics study of the connection between flap closing and binding of fullerene-based inhibitors of the HIV-1 protease.
[90]
PubMed ID12675950
JournalBMC Struct Biol
Year2003
Volume3
Pages2
AuthorsJenwitheesuk E, Samudrala R
TitleImproved prediction of HIV-1 protease-inhibitor binding energies by molecular dynamics simulations.
[91]
PubMed ID12644464
JournalJ Biol Chem
Year2003
Volume278
Pages19980-5
AuthorsBhavesh NS, Sinha R, Mohan PM, Hosur RV
TitleNMR elucidation of early folding hierarchy in HIV-1 protease.
[92]
PubMed ID12933791
JournalJ Biol Chem
Year2003
Volume278
Pages43311-9
AuthorsIshima R, Torchia DA, Lynch SM, Gronenborn AM, Louis JM
TitleSolution structure of the mature HIV-1 protease monomer: insight into the tertiary fold and stability of a precursor.
[93]
PubMed ID12696052
JournalProteins
Year2003
Volume51
Pages409-22
AuthorsKurt N, Scott WR, Schiffer CA, Haliloglu T
TitleCooperative fluctuations of unliganded and substrate-bound HIV-1 protease: a structure-based analysis on a variety of conformations from crystallography and molecular dynamics simulations.
[94]
PubMed ID15317462
JournalJ Med Chem
Year2004
Volume47
Pages4507-16
AuthorsFornabaio M, Spyrakis F, Mozzarelli A, Cozzini P, Abraham DJ, Kellogg GE
TitleSimple, intuitive calculations of free energy of binding for protein-ligand complexes. 3. The free energy contribution of structural water molecules in HIV-1 protease complexes.
[95]
PubMed ID15184023
JournalJ Mol Biol
Year2004
Volume340
Pages67-79
AuthorsLevy Y, Caflisch A, Onuchic JN, Wolynes PG
TitleThe folding and dimerization of HIV-1 protease: evidence for a stable monomer from simulations.
[96]
PubMed ID15066436
JournalJ Mol Biol
Year2004
Volume338
Pages341-52
AuthorsTie Y, Boross PI, Wang YF, Gaddis L, Hussain AK, Leshchenko S, Ghosh AK, Louis JM, Harrison RW, Weber IT
TitleHigh resolution crystal structures of HIV-1 protease with a potent non-peptide inhibitor (UIC-94017) active against multi-drug-resistant clinical strains.
[97]
PubMed ID14990731
JournalJ Virol
Year2004
Volume78
Pages3123-32
AuthorsLogsdon BC, Vickrey JF, Martin P, Proteasa G, Koepke JI, Terlecky SR, Wawrzak Z, Winters MA, Merigan TC, Kovari LC
TitleCrystal structures of a multidrug-resistant human immunodeficiency virus type 1 protease reveal an expanded active-site cavity.
[98]
PubMed ID15289598
JournalProc Natl Acad Sci U S A
Year2004
Volume101
Pages11640-5
AuthorsFernandez A, Rogale K, Scott R, Scheraga HA
TitleInhibitor design by wrapping packing defects in HIV-1 proteins.
[99]
PubMed ID15044738
JournalProtein Sci
Year2004
Volume13
Pages1108-23
AuthorsPerryman AL, Lin JH, McCammon JA
TitleHIV-1 protease molecular dynamics of a wild-type and of the V82F/I84V mutant: possible contributions to drug resistance and a potential new target site for drugs.
[100]
PubMed ID14739332
JournalProtein Sci
Year2004
Volume13
Pages513-28
AuthorsTrylska J, Grochowski P, McCammon JA
TitleThe role of hydrogen bonding in the enzymatic reaction catalyzed by HIV-1 protease.

comments
The protein, POL polyprotein from HIV-1, is composed of the following enzymes, protease (E.C. 3.4.23.16), reverse transcriptase (E.C. 2.7.7.49), ribonuclease H (E.C. 3.1.26.4) and integrase.
This entry corresponds to the protease domain, which belongs to the peptidase family-A2.
According to the literature, this enzyme has got a similar catalytic mechanism to that of pepsin (D00436 in EzCatDB).

createdupdated
2004-03-052012-07-03


Copyright: Nozomi Nagano, JST & CBRC-AIST
Funded by PRESTO/Japan Science and Technology Corporation (JST) (December 2001 - November 2004)
Funded by Grant-in-Aid for Publication of Scientific Research Results/Japan Society for the Promotion of Science (JSPS) (April 2005 - March 2006)
Funded by Grant-in-Aid for Scientific Research (B)/Japan Society for the Promotion of Science (JSPS) (April 2005 - March 2008)
Funded by BIRD/Japan Science and Technology Corporation (JST) (September 2005 - September 2010)
Funded by BIRD/Japan Science and Technology Corporation (JST) (October 2007 - September 2010)
Funded by Grant-in-Aid for Publication of Scientific Research Results/Japan Society for the Promotion of Science (JSPS) (April 2011 - March 2012)

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