Structure of PDB 3nxn Chain A Binding Site BS01

Receptor Information
>3nxn Chain A (length=203) Species: 11685 (HIV-1 M:B_ARV2/SF2) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
PQITLWKRPLVTIRIGGQLKEALLDTGADDTVIEELNLPGCWKPKLIGGI
GGFIKVRQYDQIPVEIAGHKAIGTVLVGPTPVNIIGRNLLTQIGATLNFC
GGGGPQITLWKRPLVTIRIGGQLKEALLDTGADDTVIEELNLPGCWKPKL
IGGIGGFIKVRQYDQIPVEIAGHKAIGTVLVGPTPVNIIGRNLLTQIGAT
LNF
Ligand information
Ligand IDKVS
InChIInChI=1S/C36H68N10O10/c1-7-10-13-23(31(51)44-25(16-17-27(37)49)32(52)43-24(30(38)50)14-12-18-41-35(39)40)19-36(55,56)26(15-11-8-2)45-33(53)28(20(4)9-3)46-34(54)29(21(5)47)42-22(6)48/h20-21,23-26,28-29,47,55-56H,7-19H2,1-6H3,(H2,37,49)(H2,38,50)(H,42,48)(H,43,52)(H,44,51)(H,45,53)(H,46,54)(H4,39,40,41)/t20-,21+,23+,24-,25-,26-,28-,29-/m0/s1
InChIKeyGHZIZWOGRIROFP-WZGNFWQUSA-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([C@H](CCCC)NC(=O)[C@H]([C@@H](C)CC)NC(=O)[C@H]([C@@H](C)O)NC(=O)C)(O)O
CACTVS 3.385CCCC[C@H](CC(O)(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 12.01C(=O)(C)NC(C(NC(C(=O)NC(C(O)(CC(C(NC(C(NC(C(N)=O)CCCN/C(N)=N)=O)CCC(N)=O)=O)CCCC)O)CCCC)C(C)CC)=O)C(C)O
CACTVS 3.385CCCC[CH](CC(O)(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
OpenEye OEToolkits 1.7.6CCCCC(CC(C(CCCC)NC(=O)C(C(C)CC)NC(=O)C(C(C)O)NC(=O)C)(O)O)C(=O)NC(CCC(=O)N)C(=O)NC(CCCNC(=N)N)C(=O)N
FormulaC36 H68 N10 O10
NameN~2~-[(2R,5S)-5-({(2S,3S)-2-[(N-acetyl-L-threonyl)amino]-3-methylpent-4-enoyl}amino)-2-butyl-4,4-dihydroxynonanoyl]-L-glutaminyl-L-argininamide
ChEMBL
DrugBank
ZINC
PDB chain3nxn Chain A Residue 204 [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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PDB3nxn Protein conformational dynamics in the mechanism of HIV-1 protease catalysis.
Resolution1.8 Å
Binding residue
(original residue number in PDB)		R8 D25 G27 A28 D29 G48 I84 D129 G131 A132 D133 D134 I151 G152
Binding residue
(residue number reindexed from 1)		R8 D25 G27 A28 D29 G48 I84 D129 G131 A132 D133 D134 I151 G152
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:3nxn, PDBe:3nxn, PDBj:3nxn
PDBsum3nxn
PubMed22158985
UniProtP03369|POL_HV1A2 Gag-Pol polyprotein (Gene Name=gag-pol)

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