Structure of PDB 3h5b Chain B Binding Site BS01

Receptor Information
>3h5b Chain B (length=99) Species: 11686 (Human immunodeficiency virus type 1 (BRU ISOLATE)) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
PQITLWKRPLVTIKIGGQLKEALLDTGADDTVIEEMSLPGRWKPKMIGGI
GGFIKVRQYDQIIIEIAGHKAIGTVLVGPTPVNIIGRNLLTQIGATLNF
Ligand information
Ligand ID031
InChIInChI=1S/C30H39N3O8S/c1-39-23-8-10-25(11-9-23)42(37,38)33(18-22-7-12-29(35)31-22)19-27(34)26(15-20-5-3-2-4-6-20)32-30(36)41-24-16-21-13-14-40-28(21)17-24/h2-6,8-11,21-22,24,26-28,34H,7,12-19H2,1H3,(H,31,35)(H,32,36)/t21-,22+,24+,26-,27+,28+/m0/s1
InChIKeyRPIALZPTIFOQGC-CXLNPQPMSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0COc1ccc(cc1)S(=O)(=O)[N@@](C[C@H]2CCC(=O)N2)C[C@H]([C@H](Cc3ccccc3)NC(=O)O[C@@H]4C[C@@H]5CCO[C@@H]5C4)O
ACDLabs 10.04O=C1NC(CC1)CN(S(=O)(=O)c2ccc(OC)cc2)CC(O)C(NC(=O)OC4CC3C(OCC3)C4)Cc5ccccc5
OpenEye OEToolkits 1.5.0COc1ccc(cc1)S(=O)(=O)N(CC2CCC(=O)N2)CC(C(Cc3ccccc3)NC(=O)OC4CC5CCOC5C4)O
CACTVS 3.341COc1ccc(cc1)[S](=O)(=O)N(C[C@@H](O)[C@H](Cc2ccccc2)NC(=O)O[C@@H]3C[C@@H]4CCO[C@@H]4C3)C[C@H]5CCC(=O)N5
CACTVS 3.341COc1ccc(cc1)[S](=O)(=O)N(C[CH](O)[CH](Cc2ccccc2)NC(=O)O[CH]3C[CH]4CCO[CH]4C3)C[CH]5CCC(=O)N5
FormulaC30 H39 N3 O8 S
Name(3aS,5R,6aR)-hexahydro-2H-cyclopenta[b]furan-5-yl [(1S,2R)-1-benzyl-2-hydroxy-3-([(4-methoxyphenyl)sulfonyl]{[(2R)-5-oxopyrrolidin-2-yl]methyl}amino)propyl]carbamate
ChEMBLCHEMBL502946
DrugBank
ZINCZINC000006717049
PDB chain3h5b Chain B Residue 404 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB3h5b Design of HIV-1 protease inhibitors with pyrrolidinones and oxazolidinones as novel P1'-ligands to enhance backbone-binding interactions with protease: synthesis, biological evaluation, and protein-ligand X-ray studies.
Resolution1.29 Å
Binding residue
(original residue number in PDB)		D125 G127 A128 D130 P181 I184
Binding residue
(residue number reindexed from 1)		D25 G27 A28 D30 P81 I84
Annotation score1
Binding affinityMOAD: Ki=0.099nM
PDBbind-CN: -logKd/Ki=10.00,Ki=0.099nM
Enzymatic activity
Catalytic site (original residue number in PDB) D125 T126 G127
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:3h5b, PDBe:3h5b, PDBj:3h5b
PDBsum3h5b
PubMed19473017
UniProtP03367|POL_HV1BR Gag-Pol polyprotein (Gene Name=gag-pol)

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