Structure of PDB 3gi5 Chain B Binding Site BS01

Receptor Information
>3gi5 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 IDK62
InChIInChI=1S/C33H37N3O9S/c1-21(2)17-35(46(41,42)26-12-13-29-30(16-26)44-20-43-29)18-28(38)27(14-23-8-5-4-6-9-23)34-32(39)31-19-36(33(40)45-31)25-11-7-10-24(15-25)22(3)37/h4-13,15-16,21,27-28,31,38H,14,17-20H2,1-3H3,(H,34,39)/t27-,28+,31-/m0/s1
InChIKeyGNJDFMNCMAQPGN-QXIHQKPUSA-N
SMILES
SoftwareSMILES
CACTVS 3.341CC(C)CN(C[C@@H](O)[C@H](Cc1ccccc1)NC(=O)[C@@H]2CN(C(=O)O2)c3cccc(c3)C(C)=O)[S](=O)(=O)c4ccc5OCOc5c4
OpenEye OEToolkits 1.5.0CC(C)C[N@@](C[C@H]([C@H](Cc1ccccc1)NC(=O)[C@@H]2CN(C(=O)O2)c3cccc(c3)C(=O)C)O)S(=O)(=O)c4ccc5c(c4)OCO5
CACTVS 3.341CC(C)CN(C[CH](O)[CH](Cc1ccccc1)NC(=O)[CH]2CN(C(=O)O2)c3cccc(c3)C(C)=O)[S](=O)(=O)c4ccc5OCOc5c4
ACDLabs 10.04O=C(c1cc(ccc1)N5C(=O)OC(C(=O)NC(Cc2ccccc2)C(O)CN(CC(C)C)S(=O)(=O)c3ccc4OCOc4c3)C5)C
OpenEye OEToolkits 1.5.0CC(C)CN(CC(C(Cc1ccccc1)NC(=O)C2CN(C(=O)O2)c3cccc(c3)C(=O)C)O)S(=O)(=O)c4ccc5c(c4)OCO5
FormulaC33 H37 N3 O9 S
Name(5S)-3-(3-Acetylphenyl)-N-[(1S,2R)-3-[(1,3-benzodioxol-5-ylsulfonyl)(2-methylpropyl)amino]-2-hydroxy-1-(phenylmethyl)pr opyl]-2-oxo-5-oxazolidinecarboxamide;
(5S)-3-(3-acetylphenyl)-N-{(1S,2R)-3-[(1,3-benzodioxol-5-ylsulfonyl)(2-methylpropyl)amino]-1-benzyl-2-hydroxypropyl}-2- oxo-1,3-oxazolidine-5-carboxamide
ChEMBLCHEMBL220078
DrugBank
ZINCZINC000043315966
PDB chain3gi5 Chain A Residue 200 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB3gi5 Evaluating the substrate-envelope hypothesis: structural analysis of novel HIV-1 protease inhibitors designed to be robust against drug resistance.
Resolution1.8 Å
Binding residue
(original residue number in PDB)
D25 A28 D30 P81 V82
Binding residue
(residue number reindexed from 1)
D25 A28 D30 P81 V82
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=11.22,Ki=6pM
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:3gi5, PDBe:3gi5, PDBj:3gi5
PDBsum3gi5
PubMed20237088
UniProtP03369|POL_HV1A2 Gag-Pol polyprotein (Gene Name=gag-pol)

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