Structure of PDB 2qi0 Chain B Binding Site BS01

Receptor Information
>2qi0 Chain B (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 IDMZ3
InChIInChI=1S/C30H31FN2O5S2/c1-21-26(14-7-15-27(21)31)30(35)32-28(17-22-9-4-3-5-10-22)29(34)20-33(19-24-12-8-16-39-24)40(36,37)25-13-6-11-23(18-25)38-2/h3-16,18,28-29,34H,17,19-20H2,1-2H3,(H,32,35)/t28-,29+/m0/s1
InChIKeyAXUYLLZCOSCKTG-URLMMPGGSA-N
SMILES
SoftwareSMILES
CACTVS 3.341COc1cccc(c1)[S](=O)(=O)N(C[CH](O)[CH](Cc2ccccc2)NC(=O)c3cccc(F)c3C)Cc4sccc4
CACTVS 3.341COc1cccc(c1)[S](=O)(=O)N(C[C@@H](O)[C@H](Cc2ccccc2)NC(=O)c3cccc(F)c3C)Cc4sccc4
OpenEye OEToolkits 1.5.0Cc1c(cccc1F)C(=O)N[C@@H](Cc2ccccc2)[C@@H](C[N@](Cc3cccs3)S(=O)(=O)c4cccc(c4)OC)O
ACDLabs 10.04O=S(=O)(N(Cc1sccc1)CC(O)C(NC(=O)c2cccc(F)c2C)Cc3ccccc3)c4cccc(OC)c4
OpenEye OEToolkits 1.5.0Cc1c(cccc1F)C(=O)NC(Cc2ccccc2)C(CN(Cc3cccs3)S(=O)(=O)c4cccc(c4)OC)O
FormulaC30 H31 F N2 O5 S2
NameN-[(1S,2R)-1-BENZYL-2-HYDROXY-3-{[(3-METHOXYPHENYL)SULFONYL](2-THIENYLMETHYL)AMINO}PROPYL]-3-FLUORO-2-METHYLBENZAMIDE
ChEMBLCHEMBL475279
DrugBank
ZINCZINC000016052445
PDB chain2qi0 Chain B Residue 200 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB2qi0 HIV-1 protease inhibitors from inverse design in the substrate envelope exhibit subnanomolar binding to drug-resistant variants.
Resolution2.1 Å
Binding residue
(original residue number in PDB)		D25 A28 D30 I47 G49 I50 P81 V82 I84
Binding residue
(residue number reindexed from 1)		D25 A28 D30 I47 G49 I50 P81 V82 I84
Annotation score1
Binding affinityMOAD: Ki=42nM
PDBbind-CN: -logKd/Ki=7.38,Ki=42nM
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

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Molecular Function
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Biological Process
External links
PDB RCSB:2qi0, PDBe:2qi0, PDBj:2qi0
PDBsum2qi0
PubMed18412349
UniProtP03369|POL_HV1A2 Gag-Pol polyprotein (Gene Name=gag-pol)

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