Structure of PDB 3dck Chain B Binding Site BS01

Receptor Information
>3dck 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]
PQITLWKRPLVTIRIGGQLKEALLNTGADDTVIEELNLPGCWKPKLIGGI
GGFIKVRQYDQIPVEIAGHKAIGTVLVGPTPVNIIGRNLLTQIGATLNF
Ligand information
Ligand IDKVI
InChIInChI=1S/C36H66N10O9/c1-7-10-13-23(32(52)45-26(16-17-28(37)50)33(53)44-25(31(38)51)15-12-18-41-36(39)40)19-27(49)24(14-11-8-2)43-34(54)29(20(4)9-3)46-35(55)30(21(5)47)42-22(6)48/h20-21,23-26,29-30,47H,7-19H2,1-6H3,(H2,37,50)(H2,38,51)(H,42,48)(H,43,54)(H,44,53)(H,45,52)(H,46,55)(H4,39,40,41)/t20-,21+,23+,24-,25-,26-,29-,30-/m0/s1
InChIKeyARYLRJRVHGPIHO-XPRREXDTSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.6[H]/N=C(/N)\NCCC[C@@H](C(=O)N)NC(=O)[C@H](CCC(=O)N)NC(=O)[C@H](CCCC)CC(=O)[C@H](CCCC)NC(=O)[C@H]([C@@H](C)CC)NC(=O)[C@H]([C@@H](C)O)NC(=O)C
OpenEye OEToolkits 1.7.6CCCCC(CC(=O)C(CCCC)NC(=O)C(C(C)CC)NC(=O)C(C(C)O)NC(=O)C)C(=O)NC(CCC(=O)N)C(=O)NC(CCCNC(=N)N)C(=O)N
CACTVS 3.385CCCC[C@H](CC(=O)[C@H](CCCC)NC(=O)[C@@H](NC(=O)[C@@H](NC(C)=O)[C@@H](C)O)[C@@H](C)CC)C(=O)N[C@@H](CCC(N)=O)C(=O)N[C@@H](CCCNC(N)=N)C(N)=O
ACDLabs 12.01O=C(NC(C(=O)NC(C(=O)CC(C(=O)NC(C(=O)NC(C(=O)N)CCCNC(=[N@H])N)CCC(=O)N)CCCC)CCCC)C(C)CC)C(NC(=O)C)C(O)C
CACTVS 3.385CCCC[CH](CC(=O)[CH](CCCC)NC(=O)[CH](NC(=O)[CH](NC(C)=O)[CH](C)O)[CH](C)CC)C(=O)N[CH](CCC(N)=O)C(=O)N[CH](CCCNC(N)=N)C(N)=O
FormulaC36 H66 N10 O9
Name
ChEMBL
DrugBank
ZINCZINC000098209091
PDB chain3dck Chain B Residue 101 [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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PDB3dck Crystal structure of chemically synthesized HIV-1 protease and a ketomethylene isostere inhibitor based on the p2/NC cleavage site
Resolution1.8 Å
Binding residue
(original residue number in PDB)		N25 G27 A28 D29 D30 I47 G48 P81
Binding residue
(residue number reindexed from 1)		N25 G27 A28 D29 D30 I47 G48 P81
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) N25 T26 G27
Catalytic site (residue number reindexed from 1) N25 T26 G27
Enzyme Commision number 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:3dck, PDBe:3dck, PDBj:3dck
PDBsum3dck
PubMed18657969
UniProtO38732

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