Structure of PDB 4o55 Chain A Binding Site BS01

Receptor Information
>4o55 Chain A (length=141) Species: 11698 (Human immunodeficiency virus type 1 (NEW YORK-5 ISOLATE)) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
CSPGIWQLDCTHLEGKVILVAVHVASGYIEAEVIPAETGQETAYFLLKLA
GRWPVKTVHTDNGSNFTSTTVKAACWWAGIKQEFGESMNKELKKIIGQVR
DQAEHLKTAVQMAVFIHNKKRKGGGYSAGERIVDIIATDIQ
Ligand information
Ligand IDLF9
InChIInChI=1S/C26H26ClN3O3/c1-14-20(16-9-7-6-8-10-16)21(23(25(31)32)33-26(3,4)5)15(2)28-22(14)24-29-18-12-11-17(27)13-19(18)30-24/h6-13,23H,1-5H3,(H,29,30)(H,31,32)/t23-/m0/s1
InChIKeyCTTJHLOYHQRQKO-QHCPKHFHSA-N
SMILES
SoftwareSMILES
CACTVS 3.385Cc1nc(c(C)c(c2ccccc2)c1[CH](OC(C)(C)C)C(O)=O)c3[nH]c4ccc(Cl)cc4n3
ACDLabs 12.01O=C(O)C(OC(C)(C)C)c2c(c1ccccc1)c(c(nc2C)c4nc3cc(Cl)ccc3n4)C
OpenEye OEToolkits 1.7.6Cc1c(c(c(nc1c2[nH]c3ccc(cc3n2)Cl)C)C(C(=O)O)OC(C)(C)C)c4ccccc4
OpenEye OEToolkits 1.7.6Cc1c(c(c(nc1c2[nH]c3ccc(cc3n2)Cl)C)[C@@H](C(=O)O)OC(C)(C)C)c4ccccc4
CACTVS 3.385Cc1nc(c(C)c(c2ccccc2)c1[C@H](OC(C)(C)C)C(O)=O)c3[nH]c4ccc(Cl)cc4n3
FormulaC26 H26 Cl N3 O3
Name(2S)-tert-butoxy[6-(5-chloro-1H-benzimidazol-2-yl)-2,5-dimethyl-4-phenylpyridin-3-yl]ethanoic acid
ChEMBL
DrugBank
ZINCZINC000098209108
PDB chain4o55 Chain A Residue 301 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB4o55 A New Class of Multimerization Selective Inhibitors of HIV-1 Integrase.
Resolution2.24 Å
Binding residue
(original residue number in PDB)		Q95 T124 T125 A128 A129
Binding residue
(residue number reindexed from 1)		Q40 T69 T70 A73 A74
Annotation score1
Binding affinityMOAD: ic50=5.03uM
PDBbind-CN: -logKd/Ki=5.30,IC50=5.03uM
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:4o55, PDBe:4o55, PDBj:4o55
PDBsum4o55
PubMed24874515
UniProtP12497|POL_HV1N5 Gag-Pol polyprotein (Gene Name=gag-pol)

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