Structure of PDB 3zsq Chain B Binding Site BS02

Receptor Information
>3zsq Chain B (length=149) Species: 12721 (Human immunodeficiency virus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SPGIWQLDCTHLEGKVILVAVHVASGYIEAEVIPAETGQETAYFLLKLAG
RWPVKTVHTDNGSNFTSTTVKAACWWAGIKQEDGIPYNPQSQGVIESMNK
ELKKIIGQVRDQAEHLKTAVQMAVFIHNHKRKGYSAGERIVDIIATDIQ
Ligand information
Ligand IDO4N
InChIInChI=1S/C31H34N2O6/c1-4-8-26(21-11-14-24(37-3)15-12-21)32-30(34)25-10-7-6-9-22(25)18-33(17-5-2)19-23-13-16-27-29(39-20-38-27)28(23)31(35)36/h5-7,9-16,26H,2,4,8,17-20H2,1,3H3,(H,32,34)(H,35,36)/t26-/m0/s1
InChIKeyBMRIMVDVHSTXPF-SANMLTNESA-N
SMILES
SoftwareSMILES
CACTVS 3.385CCC[CH](NC(=O)c1ccccc1CN(CC=C)Cc2ccc3OCOc3c2C(O)=O)c4ccc(OC)cc4
OpenEye OEToolkits 1.9.2CCC[C@@H](c1ccc(cc1)OC)NC(=O)c2ccccc2CN(CC=C)Cc3ccc4c(c3C(=O)O)OCO4
OpenEye OEToolkits 1.9.2CCCC(c1ccc(cc1)OC)NC(=O)c2ccccc2CN(CC=C)Cc3ccc4c(c3C(=O)O)OCO4
CACTVS 3.385CCC[C@H](NC(=O)c1ccccc1CN(CC=C)Cc2ccc3OCOc3c2C(O)=O)c4ccc(OC)cc4
ACDLabs 12.01O=C(NC(c1ccc(OC)cc1)CCC)c2ccccc2CN(C/C=C)Cc3ccc4OCOc4c3C(=O)O
FormulaC31 H34 N2 O6
Name5-[[[2-[[(1S)-1-(4-METHOXYPHENYL)BUTYL]CARBAMOYL]PHENYL]METHYL-PROP-2-ENYL-AMINO]METHYL]-1,3-BENZODIOXOLE-4-CARBOXYLIC ACID
ChEMBL
DrugBank
ZINCZINC000098209253
PDB chain3zsq Chain B Residue 1213 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB3zsq Small Molecule Inhibitors of the Ledgf Site of Human Immunodeficiency Virus Integrase Identified by Fragment Screening and Structure Based Design.
Resolution1.7 Å
Binding residue
(original residue number in PDB)		Q168 A169 E170 H171 T174
Binding residue
(residue number reindexed from 1)		Q112 A113 E114 H115 T118
Annotation score1
Binding affinityMOAD: Kd=10.9uM
PDBbind-CN: -logKd/Ki=4.96,Kd=10.9uM
Enzymatic activity
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:0003676 nucleic acid binding
Biological Process
GO:0015074 DNA integration

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:3zsq, PDBe:3zsq, PDBj:3zsq
PDBsum3zsq
PubMed22808106
UniProtP12497|POL_HV1N5 Gag-Pol polyprotein (Gene Name=gag-pol)

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