Structure of PDB 3gi6 Chain A Binding Site BS01

Receptor Information
>3gi6 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 IDD78
InChIInChI=1S/C32H36F3N3O7S/c1-21(2)18-37(46(42,43)26-14-12-25(44-3)13-15-26)19-28(39)27(16-22-8-5-4-6-9-22)36-30(40)29-20-38(31(41)45-29)24-11-7-10-23(17-24)32(33,34)35/h4-15,17,21,27-29,39H,16,18-20H2,1-3H3,(H,36,40)/t27-,28+,29-/m0/s1
InChIKeyDDUYAVRQCCSESZ-NHKHRBQYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0CC(C)CN(CC(C(Cc1ccccc1)NC(=O)C2CN(C(=O)O2)c3cccc(c3)C(F)(F)F)O)S(=O)(=O)c4ccc(cc4)OC
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(F)(F)F)O)S(=O)(=O)c4ccc(cc4)OC
CACTVS 3.341COc1ccc(cc1)[S](=O)(=O)N(CC(C)C)C[C@@H](O)[C@H](Cc2ccccc2)NC(=O)[C@@H]3CN(C(=O)O3)c4cccc(c4)C(F)(F)F
CACTVS 3.341COc1ccc(cc1)[S](=O)(=O)N(CC(C)C)C[CH](O)[CH](Cc2ccccc2)NC(=O)[CH]3CN(C(=O)O3)c4cccc(c4)C(F)(F)F
ACDLabs 10.04O=C4OC(C(=O)NC(Cc1ccccc1)C(O)CN(CC(C)C)S(=O)(=O)c2ccc(OC)cc2)CN4c3cccc(c3)C(F)(F)F
FormulaC32 H36 F3 N3 O7 S
Name(5S)-N-[(1S,2R)-2-Hydroxy-3-[[(4-methoxyphenyl)sulfonyl](2-methylpropyl)amino]-1-(phenylmethyl)propyl]-2-oxo-3-[3-(trif luoromethyl)phenyl]-5-oxazolidinecarboxamide;
(5S)-N-[(1S,2R)-1-benzyl-2-hydroxy-3-{[(4-methoxyphenyl)sulfonyl](2-methylpropyl)amino}propyl]-2-oxo-3-[3-(trifluoromet hyl)phenyl]-1,3-oxazolidine-5-carboxamide
ChEMBLCHEMBL382400
DrugBank
ZINCZINC000049778301
PDB chain3gi6 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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PDB3gi6 Evaluating the substrate-envelope hypothesis: structural analysis of novel HIV-1 protease inhibitors designed to be robust against drug resistance.
Resolution1.84 Å
Binding residue
(original residue number in PDB)		D25 G27 D29 G48 G49 I50
Binding residue
(residue number reindexed from 1)		D25 G27 D29 G48 G49 I50
Annotation score1
Binding affinityMOAD: Ki=0.006nM
PDBbind-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:3gi6, PDBe:3gi6, PDBj:3gi6
PDBsum3gi6
PubMed20237088
UniProtP03369|POL_HV1A2 Gag-Pol polyprotein (Gene Name=gag-pol)

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