Structure of PDB 2qi7 Chain A Binding Site BS01

Receptor Information
>2qi7 Chain A (length=99) Species: 11676 (Human immunodeficiency virus 1) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
PQITLWKRPLVTIRIGGQLKEALLDTGADDTVLEEMNLPGKWKPKMIGGI
GGFIKVRQYDQIPIEICGHKAIGTVLVGPTPVNIIGRNLLTQIGCTLNF
Ligand information
Ligand IDMZ9
InChIInChI=1S/C28H40N2O6S/c1-5-21(3)19-30(37(34,35)25-15-13-24(36-4)14-16-25)20-27(32)26(18-22-10-8-7-9-11-22)29-28(33)17-12-23(31)6-2/h7-11,13-16,21,26-27,32H,5-6,12,17-20H2,1-4H3,(H,29,33)/t21-,26-,27+/m0/s1
InChIKeyJJMPZKDTRWEIEO-NJTBCWBZSA-N
SMILES
SoftwareSMILES
ACDLabs 10.04O=C(CC)CCC(=O)NC(Cc1ccccc1)C(O)CN(S(=O)(=O)c2ccc(OC)cc2)CC(C)CC
OpenEye OEToolkits 1.5.0CC[C@H](C)C[N@@](C[C@H]([C@H](Cc1ccccc1)NC(=O)CCC(=O)CC)O)S(=O)(=O)c2ccc(cc2)OC
OpenEye OEToolkits 1.5.0CCC(C)CN(CC(C(Cc1ccccc1)NC(=O)CCC(=O)CC)O)S(=O)(=O)c2ccc(cc2)OC
CACTVS 3.341CC[CH](C)CN(C[CH](O)[CH](Cc1ccccc1)NC(=O)CCC(=O)CC)[S](=O)(=O)c2ccc(OC)cc2
CACTVS 3.341CC[C@H](C)CN(C[C@@H](O)[C@H](Cc1ccccc1)NC(=O)CCC(=O)CC)[S](=O)(=O)c2ccc(OC)cc2
FormulaC28 H40 N2 O6 S
NameN-[(1S,2R)-1-BENZYL-2-HYDROXY-3-{[(4-METHOXYPHENYL)SULFONYL][(2S)-2-METHYLBUTYL]AMINO}PROPYL]-4-OXOHEXANAMIDE
ChEMBL
DrugBank
ZINCZINC000043151755
PDB chain2qi7 Chain B Residue 200 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB2qi7 HIV-1 protease inhibitors from inverse design in the substrate envelope exhibit subnanomolar binding to drug-resistant variants.
Resolution1.85 Å
Binding residue
(original residue number in PDB)		D25 G27 D29 G48 G49 I50 V82
Binding residue
(residue number reindexed from 1)		D25 G27 D29 G48 G49 I50 V82
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=10.21,Ki=0.062nM
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 2.7.7.-
2.7.7.49: RNA-directed DNA polymerase.
2.7.7.7: DNA-directed DNA polymerase.
3.1.-.-
3.1.13.2: exoribonuclease H.
3.1.26.13: retroviral ribonuclease H.
3.4.23.16: HIV-1 retropepsin.
Gene Ontology
Molecular Function
GO:0004190 aspartic-type endopeptidase activity
Biological Process
GO:0006508 proteolysis

View graph for
Molecular Function
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Biological Process
External links
PDB RCSB:2qi7, PDBe:2qi7, PDBj:2qi7
PDBsum2qi7
PubMed18412349
UniProtP03369|POL_HV1A2 Gag-Pol polyprotein (Gene Name=gag-pol)

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