Structure of PDB 2j9k Chain B Binding Site BS01

Receptor Information
>2j9k 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]
PQITLWKRPLVTIRIGGQLKEALLDTGADDTVIEELNLPGKWKPKLIGGI
GGFIKVRQYDQIPVEIAGHKAIGTVLVGPTPVNIIGRNLLTQIGATLNF
Ligand information
Ligand ID2NC
InChIInChI=1S/C35H67N11O8/c1-7-10-13-23(43-33(53)28(20(4)9-3)46-34(54)29(21(5)47)42-22(6)48)19-41-25(14-11-8-2)31(51)45-26(16-17-27(36)49)32(52)44-24(30(37)50)15-12-18-40-35(38)39/h20-21,23-26,28-29,41,47H,7-19H2,1-6H3,(H2,36,49)(H2,37,50)(H,42,48)(H,43,53)(H,44,52)(H,45,51)(H,46,54)(H4,38,39,40)/p+1/t20-,21+,23-,24-,25-,26-,28-,29-/m0/s1
InChIKeyMQPXOVRKKPPKFZ-QYKDHROSSA-O
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.5CCCCC(CNC(CCCC)C(=O)NC(CCC(=O)N)C(=O)NC(CCCNC(=[NH2+])N)C(=O)N)NC(=O)C(C(C)CC)NC(=O)C(C(C)O)NC(=O)C
CACTVS 3.385CCCC[CH](CN[CH](CCCC)C(=O)N[CH](CCC(N)=O)C(=O)N[CH](CCCNC(N)=[NH2+])C(N)=O)NC(=O)[CH](NC(=O)[CH](NC(C)=O)[CH](C)O)[CH](C)CC
ACDLabs 12.01O=C(NC(C(=O)NC(CCCC)CNC(C(=O)NC(C(=O)NC(C(=O)N)CCCNC(=[NH2+])\\N)CCC(=O)N)CCCC)C(C)CC)C(NC(=O)C)C(O)C
CACTVS 3.385CCCC[C@@H](CN[C@@H](CCCC)C(=O)N[C@@H](CCC(N)=O)C(=O)N[C@@H](CCCNC(N)=[NH2+])C(N)=O)NC(=O)[C@@H](NC(=O)[C@@H](NC(C)=O)[C@@H](C)O)[C@@H](C)CC
OpenEye OEToolkits 1.7.5CCCC[C@@H](CN[C@@H](CCCC)C(=O)N[C@@H](CCC(=O)N)C(=O)N[C@@H](CCCNC(=[NH2+])N)C(=O)N)NC(=O)[C@H]([C@@H](C)CC)NC(=O)[C@H]([C@@H](C)O)NC(=O)C
FormulaC35 H68 N11 O8
NameN-{(2S)-2-[(N-acetyl-L-threonyl-L-isoleucyl)amino]hexyl}-L-norleucyl-L-glutaminyl-N~5~-[amino(iminio)methyl]-L-ornithinamide;
p2/NC
ChEMBL
DrugBank
ZINC
PDB chain2j9k Chain A Residue 0 [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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PDB2j9k Insights from Atomic-Resolution X-Ray Structures of Chemically Synthesized HIV-1 Protease in Complex with Inhibitors.
Resolution1.2 Å
Binding residue
(original residue number in PDB)		D25 G27 A28 D29 D30 G48 I84
Binding residue
(residue number reindexed from 1)		D25 G27 A28 D29 D30 G48 I84
Annotation score1
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
View graph for
Biological Process
External links
PDB RCSB:2j9k, PDBe:2j9k, PDBj:2j9k
PDBsum2j9k
PubMed17869270
UniProtP03369|POL_HV1A2 Gag-Pol polyprotein (Gene Name=gag-pol)

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