Structure of PDB 3iaw Chain A Binding Site BS01

Receptor Information
>3iaw 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
IGGIAGFIKVRQYDQIPVEIAGHKAIGTVLVGPTPVNIIGRNLLTQIGAT
LNF
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 chain3iaw 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

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB3iaw Protein conformational dynamics in the mechanism of HIV-1 protease catalysis.
Resolution1.61 Å
Binding residue
(original residue number in PDB)		D25 G27 D29 G48 G49 I50 P81 L127 D129 G131 A132 D133 D134 I151 G152 I154 P185
Binding residue
(residue number reindexed from 1)		D25 G27 D29 G48 G49 I50 P81 L127 D129 G131 A132 D133 D134 I151 G152 I154 P185
Annotation score1
Binding affinityMOAD: Kd=1.57uM
PDBbind-CN: -logKd/Ki=5.80,Kd=1.57uM
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:3iaw, PDBe:3iaw, PDBj:3iaw
PDBsum3iaw
PubMed22158985
UniProtP03369|POL_HV1A2 Gag-Pol polyprotein (Gene Name=gag-pol)

[Back to BioLiP]