Structure of PDB 3zt1 Chain B Binding Site BS02

Receptor Information
>3zt1 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 IDOM1
InChIInChI=1S/C25H24N2O6/c1-31-19-9-6-16(7-10-19)12-27-24(28)20-5-3-2-4-17(20)13-26-14-18-8-11-21-23(33-15-32-21)22(18)25(29)30/h2-11,26H,12-15H2,1H3,(H,27,28)(H,29,30)/p+1
InChIKeyKFDRXOMFDTWNBI-UHFFFAOYSA-O
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.9.2COc1ccc(cc1)CNC(=O)c2ccccc2C[NH2+]Cc3ccc4c(c3C(=O)O)OCO4
CACTVS 3.385COc1ccc(CNC(=O)c2ccccc2C[NH2+]Cc3ccc4OCOc4c3C(O)=O)cc1
ACDLabs 12.01O=C(NCc1ccc(OC)cc1)c2ccccc2C[NH2+]Cc3ccc4OCOc4c3C(=O)O
FormulaC25 H25 N2 O6
Name(4-CARBOXY-1,3-BENZODIOXOL-5-YL)METHYL-[[2-[(4-METHOXYPHENYL)METHYLCARBAMOYL]PHENYL]METHYL]AZANIUM
ChEMBL
DrugBank
ZINC
PDB chain3zt1 Chain B Residue 1216 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB3zt1 Small Molecule Inhibitors of the Ledgf Site of Human Immunodeficiency Virus Integrase Identified by Fragment Screening and Structure Based Design.
Resolution1.75 Å
Binding residue
(original residue number in PDB)		Q168 A169 E170 H171 T174 M178
Binding residue
(residue number reindexed from 1)		Q112 A113 E114 H115 T118 M122
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:3zt1, PDBe:3zt1, PDBj:3zt1
PDBsum3zt1
PubMed22808106
UniProtP12497|POL_HV1N5 Gag-Pol polyprotein (Gene Name=gag-pol)

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