Structure of PDB 3zsw Chain B Binding Site BS01

Receptor Information
>3zsw 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 IDZSW
InChIInChI=1S/C28H34N2O7/c1-4-14-30(15-19-8-6-7-9-22(19)27(33)29-18(3)5-2)16-20-10-12-23-26(25(20)28(34)35)36-17-21(37-23)11-13-24(31)32/h4,6-10,12,18,21H,1,5,11,13-17H2,2-3H3,(H,29,33)(H,31,32)(H,34,35)/p+1/t18-,21+/m1/s1
InChIKeyAGZZKFCNWHLQQG-NQIIRXRSSA-O
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.7CC[C@@H](C)NC(=O)c1ccccc1C[NH+](CC=C)Cc2ccc3c(c2C(=O)O)OC[C@@H](O3)CCC(=O)O
CACTVS 3.385CC[CH](C)NC(=O)c1ccccc1C[NH+](CC=C)Cc2ccc3O[CH](CCC(O)=O)COc3c2C(O)=O
OpenEye OEToolkits 2.0.7CCC(C)NC(=O)c1ccccc1C[NH+](CC=C)Cc2ccc3c(c2C(=O)O)OCC(O3)CCC(=O)O
CACTVS 3.385CC[C@@H](C)NC(=O)c1ccccc1C[NH+](CC=C)Cc2ccc3O[C@@H](CCC(O)=O)COc3c2C(O)=O
FormulaC28 H35 N2 O7
Name(R)-[2-[[(2R)-butan-2-yl]carbamoyl]phenyl]methyl-[[(2S)-5-carboxy-2-(2-carboxyethyl)-2,3-dihydro-1,4-benzodioxin-6-yl]methyl]-prop-2-enyl-azanium
ChEMBL
DrugBank
ZINC
PDB chain3zsw Chain A Residue 308 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB3zsw Small Molecule Inhibitors of the Ledgf Site of Human Immunodeficiency Virus Integrase Identified by Fragment Screening and Structure Based Design.
Resolution1.8 Å
Binding residue
(original residue number in PDB)		Q95 E96 Y99
Binding residue
(residue number reindexed from 1)		Q39 E40 Y43
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=2.70,Kd>2000uM
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
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Biological Process
External links
PDB RCSB:3zsw, PDBe:3zsw, PDBj:3zsw
PDBsum3zsw
PubMed22808106
UniProtP12497|POL_HV1N5 Gag-Pol polyprotein (Gene Name=gag-pol)

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