Structure of PDB 1bdr Chain B Binding Site BS01

Receptor Information
>1bdr 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]
PQITLWQRPLVTIKIGGQLKEALLDTGADDSVVAGIELPGRWKPKMIGGI
GGFIKVRQYDQILIEICGHKAIGTVLVGPTPVNIIGRNLLTQIGCTLNF
Ligand information
Ligand IDIM1
InChIInChI=1S/C31H42N4O4/c1-21(2)27(28-32-16-17-33-28)35-29(37)24(18-22-12-8-6-9-13-22)20-26(36)25(19-23-14-10-7-11-15-23)34-30(38)39-31(3,4)5/h6-17,21,24-27,36H,18-20H2,1-5H3,(H,32,33)(H,34,38)(H,35,37)/t24-,25+,26+,27+/m1/s1
InChIKeyQAHXABIFJPGWDD-WKAQUBQDSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0CC(C)[C@@H](c1[nH]ccn1)NC(=O)[C@H](Cc2ccccc2)C[C@@H]([C@H](Cc3ccccc3)NC(=O)OC(C)(C)C)O
ACDLabs 10.04O=C(NC(c1nccn1)C(C)C)C(Cc2ccccc2)CC(O)C(NC(=O)OC(C)(C)C)Cc3ccccc3
OpenEye OEToolkits 1.5.0CC(C)C(c1[nH]ccn1)NC(=O)C(Cc2ccccc2)CC(C(Cc3ccccc3)NC(=O)OC(C)(C)C)O
CACTVS 3.341CC(C)[CH](NC(=O)[CH](C[CH](O)[CH](Cc1ccccc1)NC(=O)OC(C)(C)C)Cc2ccccc2)c3[nH]ccn3
CACTVS 3.341CC(C)[C@H](NC(=O)[C@@H](C[C@H](O)[C@H](Cc1ccccc1)NC(=O)OC(C)(C)C)Cc2ccccc2)c3[nH]ccn3
FormulaC31 H42 N4 O4
Name(2R,4S,5S,1'S)-2-PHENYLMETHYL-4-HYDROXY-5-(TERT-BUTOXYCARBONYL)AMINO-6-PHENYL HEXANOYL-N-(1'-IMIDAZO-2-YL)-2'-METHYLPROPANAMIDE
ChEMBL
DrugBank
ZINCZINC000003922930
PDB chain1bdr Chain B Residue 400 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB1bdr Structural role of the 30's loop in determining the ligand specificity of the human immunodeficiency virus protease.
Resolution2.8 Å
Binding residue
(original residue number in PDB)		D25 G27 A28 D29 G48 G49 I50 V82
Binding residue
(residue number reindexed from 1)		D25 G27 A28 D29 G48 G49 I50 V82
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=6.68,Ki=0.21uM
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:1bdr, PDBe:1bdr, PDBj:1bdr
PDBsum1bdr
PubMed9692985
UniProtP04587|POL_HV1B5 Gag-Pol polyprotein (Gene Name=gag-pol)

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