Structure of PDB 4m8y Chain A Binding Site BS02

Receptor Information
>4m8y Chain A (length=100) Species: 11676 (Human immunodeficiency virus 1) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
PQITLWQRPFVTVKIAGQLMEALLDTGADDTILEEEMSLPGRWTPKVVGG
IGGFMKVRQYDQILVEICGHKVIGTVLVGPTPANIIGRNLLTQIGCTLNF
Ligand information
Ligand IDKGQ
InChIInChI=1S/C33H49N2O12PS/c1-6-45-48(38,46-7-2)22-44-26-10-8-24(9-11-26)18-29(34-33(37)47-31-21-43-32-28(31)16-17-42-32)30(36)20-35(19-23(3)4)49(39,40)27-14-12-25(41-5)13-15-27/h8-15,23,28-32,36H,6-7,16-22H2,1-5H3,(H,34,37)/t28-,29-,30+,31-,32+/m0/s1
InChIKeyFCLYPCIMVVLLRN-FXSYQQGGSA-N
SMILES
SoftwareSMILES
CACTVS 3.341CCO[P](=O)(COc1ccc(C[C@H](NC(=O)O[C@H]2CO[C@H]3OCC[C@@H]23)[C@H](O)CN(CC(C)C)[S](=O)(=O)c4ccc(OC)cc4)cc1)OCC
OpenEye OEToolkits 1.5.0CCOP(=O)(COc1ccc(cc1)CC(C(CN(CC(C)C)S(=O)(=O)c2ccc(cc2)OC)O)NC(=O)OC3COC4C3CCO4)OCC
ACDLabs 10.04O=P(OCC)(OCC)COc1ccc(cc1)CC(NC(=O)OC2COC3OCCC23)C(O)CN(CC(C)C)S(=O)(=O)c4ccc(OC)cc4
CACTVS 3.341CCO[P](=O)(COc1ccc(C[CH](NC(=O)O[CH]2CO[CH]3OCC[CH]23)[CH](O)CN(CC(C)C)[S](=O)(=O)c4ccc(OC)cc4)cc1)OCC
OpenEye OEToolkits 1.5.0CCOP(=O)(COc1ccc(cc1)C[C@@H]([C@@H](C[N@](CC(C)C)S(=O)(=O)c2ccc(cc2)OC)O)NC(=O)O[C@H]3CO[C@@H]4[C@H]3CCO4)OCC
FormulaC33 H49 N2 O12 P S
NameDIETHYL ({4-[(2S,3R)-2-({[(3R,3AS,6AR)-HEXAHYDROFURO[2,3-B]FURAN-3-YLOXY]CARBONYL}AMINO)-3-HYDROXY-4-{ISOBUTYL[(4-METHOXYPHENYL)SULFONYL]AMINO}BUTYL]PHENOXY}METHYL)PHOSPHONATE
ChEMBLCHEMBL1233845
DrugBank
ZINCZINC000024880759
PDB chain4m8y Chain A Residue 202 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB4m8y GS-8374, a prototype phosphonate-containing inhibitor of HIV-1 protease, effectively inhibits protease mutants with amino acid insertions.
Resolution2.22 Å
Binding residue
(original residue number in PDB)		D25 G27 A28 D30 V48 G49 G50 P82
Binding residue
(residue number reindexed from 1)		D25 G27 A28 D30 V48 G49 G50 P82
Annotation score1
Binding affinityMOAD: Ki=0.11nM
PDBbind-CN: -logKd/Ki=9.96,Ki=0.11nM
Enzymatic activity
Catalytic site (original residue number in PDB) D25 T26 G27
Catalytic site (residue number reindexed from 1) D25 T26 G27
Enzyme Commision number 3.1.26.13: retroviral ribonuclease H.
Gene Ontology
Molecular Function
GO:0004190 aspartic-type endopeptidase activity
Biological Process
GO:0006508 proteolysis

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Molecular Function
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Biological Process
External links
PDB RCSB:4m8y, PDBe:4m8y, PDBj:4m8y
PDBsum4m8y
PubMed24371077
UniProtQ90JJ9

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