Structure of PDB 1b6k Chain B Binding Site BS01

Receptor Information
>1b6k 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]
PQITLWKRPLVTIRIGGQLKEALLDTGADDTVIEEMNLPGKWKPKMIGGI
GGFIKVRQYDQIPVEIAGHKAIGTVLVGPTPVNIIGRNLLTQIGATLNF
Ligand information
Ligand IDPI5
InChIInChI=1S/C37H53N5O7/c1-5-24(4)33-36(47)38-17-7-19-49-28-15-11-26(12-16-28)21-30(35(46)41-33)39-22-31(44)29(20-25-9-13-27(43)14-10-25)40-37(48)34(23(2)3)42-18-6-8-32(42)45/h9-16,23-24,29-31,33-34,39,43-44H,5-8,17-22H2,1-4H3,(H,38,47)(H,40,48)(H,41,46)/t24-,29-,30-,31+,33-,34-/m0/s1
InChIKeyWGWWDGLTNADWNS-HKERLIEGSA-N
SMILES
SoftwareSMILES
CACTVS 3.341CC[CH](C)[CH]1NC(=O)[CH](Cc2ccc(OCCCNC1=O)cc2)NC[CH](O)[CH](Cc3ccc(O)cc3)NC(=O)[CH](C(C)C)N4CCCC4=O
ACDLabs 10.04O=C1N(CCC1)C(C(=O)NC(Cc2ccc(O)cc2)C(O)CNC4C(=O)NC(C(=O)NCCCOc3ccc(cc3)C4)C(C)CC)C(C)C
CACTVS 3.341CC[C@H](C)[C@@H]1NC(=O)[C@H](Cc2ccc(OCCCNC1=O)cc2)NC[C@@H](O)[C@H](Cc3ccc(O)cc3)NC(=O)[C@H](C(C)C)N4CCCC4=O
OpenEye OEToolkits 1.5.0CCC(C)C1C(=O)NCCCOc2ccc(cc2)CC(C(=O)N1)NCC(C(Cc3ccc(cc3)O)NC(=O)C(C(C)C)N4CCCC4=O)O
OpenEye OEToolkits 1.5.0CC[C@H](C)[C@H]1C(=O)NCCCOc2ccc(cc2)C[C@@H](C(=O)N1)NC[C@H]([C@H](Cc3ccc(cc3)O)NC(=O)[C@H](C(C)C)N4CCCC4=O)O
FormulaC37 H53 N5 O7
NameN-[3-(8-SEC-BUTYL-7,10-DIOXO-2-OXA-6,9-DIAZA-BICYCLO[11.2.2]HEPTADECA-1(16),13(17),14- TRIEN-11-YLAMINO)-2-HYDROXY-1-(4-HYDROXY-BENZYL)-PROPYL]-3-METHYL-2- (2-OXO-PYRROLIDIN-1-YL)-BUTYRAMIDE;
MACROCYCLIC PEPTIDOMIMETIC INHIBITOR 5
ChEMBL
DrugBank
ZINCZINC000058632560
PDB chain1b6k Chain A Residue 201 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB1b6k Molecular recognition of macrocyclic peptidomimetic inhibitors by HIV-1 protease.
Resolution1.85 Å
Binding residue
(original residue number in PDB)		D125 G127 A128 D129 G148 V182
Binding residue
(residue number reindexed from 1)		D25 G27 A28 D29 G48 V82
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=8.74,Ki=1.8nM
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

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:1b6k, PDBe:1b6k, PDBj:1b6k
PDBsum1b6k
PubMed10387041
UniProtP03369|POL_HV1A2 Gag-Pol polyprotein (Gene Name=gag-pol)

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