Structure of PDB 1bdr Chain A Binding Site BS01

Receptor Information
>1bdr 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]
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 G48 G49 V82
Binding residue
(residue number reindexed from 1)		D25 G27 G48 G49 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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