Structure of PDB 3o9i Chain A Binding Site BS01

Receptor Information
>3o9i 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 IDA61
InChIInChI=1S/C30H39N3O7S2/c1-3-20(4-2)16-33(42(36,37)22-10-11-24-28(15-22)41-19-31-24)17-26(34)25(14-21-8-6-5-7-9-21)32-30(35)40-27-18-39-29-23(27)12-13-38-29/h5-11,15,19-20,23,25-27,29,34H,3-4,12-14,16-18H2,1-2H3,(H,32,35)/t23-,25-,26+,27-,29+/m0/s1
InChIKeyRAFDIRILGICCDS-OPUPNEDUSA-N
SMILES
SoftwareSMILES
CACTVS 3.370CCC(CC)CN(C[CH](O)[CH](Cc1ccccc1)NC(=O)O[CH]2CO[CH]3OCC[CH]23)[S](=O)(=O)c4ccc5ncsc5c4
OpenEye OEToolkits 1.7.0CCC(CC)CN(CC(C(Cc1ccccc1)NC(=O)OC2COC3C2CCO3)O)S(=O)(=O)c4ccc5c(c4)scn5
OpenEye OEToolkits 1.7.0CCC(CC)C[N@@](C[C@H]([C@H](Cc1ccccc1)NC(=O)O[C@H]2CO[C@@H]3[C@H]2CCO3)O)S(=O)(=O)c4ccc5c(c4)scn5
ACDLabs 12.01O=C(OC1C2CCOC2OC1)NC(Cc3ccccc3)C(O)CN(CC(CC)CC)S(=O)(=O)c4ccc5ncsc5c4
CACTVS 3.370CCC(CC)CN(C[C@@H](O)[C@H](Cc1ccccc1)NC(=O)O[C@H]2CO[C@H]3OCC[C@@H]23)[S](=O)(=O)c4ccc5ncsc5c4
FormulaC30 H39 N3 O7 S2
Name(3R,3aS,6aR)-hexahydrofuro[2,3-b]furan-3-yl {(1S,2R)-3-[(1,3-benzothiazol-6-ylsulfonyl)(2-ethylbutyl)amino]-1-benzyl-2-hydroxypropyl}carbamate
ChEMBL
DrugBank
ZINCZINC000098208629
PDB chain3o9i 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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PDB3o9i Substrate envelope-designed potent HIV-1 protease inhibitors to avoid drug resistance.
Resolution1.45 Å
Binding residue
(original residue number in PDB)		D25 G27 A28 D29 D30 G48 I50 I84
Binding residue
(residue number reindexed from 1)		D25 G27 A28 D29 D30 G48 I50 I84
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=11.82,Ki=1.5pM
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:3o9i, PDBe:3o9i, PDBj:3o9i
PDBsum3o9i
PubMed24012370
UniProtP03369|POL_HV1A2 Gag-Pol polyprotein (Gene Name=gag-pol)

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