Structure of PDB 4cj4 Chain A Binding Site BS01

Receptor Information
>4cj4 Chain A (length=148) Species: 11676 (Human immunodeficiency virus 1) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SPGIWQLDCTHLEGKVILVAVHVASGYIEAEVIPAETGQETAYFLLKLAG
RWPVKTVHTDNGSNFTSTTVKAACWWAGIKQEDGIPYNPQSQGVIESMNK
ELKKIIGQVRDQAEHLKTAVQMAVFIHNHKRGYSAGERIVDIIATDIQ
Ligand information
Ligand IDS3G
InChIInChI=1S/C21H24N2O5/c1-13(2)9-14(11-23-20(24)15-5-7-22-8-6-15)10-16-3-4-17-19(28-12-27-17)18(16)21(25)26/h3-8,13-14H,9-12H2,1-2H3,(H,23,24)(H,25,26)/t14-/m0/s1
InChIKeyMNUFCQCGIBAEIV-AWEZNQCLSA-N
SMILES
SoftwareSMILES
CACTVS 3.385CC(C)C[CH](CNC(=O)c1ccncc1)Cc2ccc3OCOc3c2C(O)=O
CACTVS 3.385CC(C)C[C@H](CNC(=O)c1ccncc1)Cc2ccc3OCOc3c2C(O)=O
ACDLabs 12.01O=C(O)c1c(ccc2OCOc12)CC(CC(C)C)CNC(=O)c3ccncc3
OpenEye OEToolkits 1.9.2CC(C)CC(Cc1ccc2c(c1C(=O)O)OCO2)CNC(=O)c3ccncc3
OpenEye OEToolkits 1.9.2CC(C)C[C@@H](Cc1ccc2c(c1C(=O)O)OCO2)CNC(=O)c3ccncc3
FormulaC21 H24 N2 O5
Name5-[(2S)-4-methyl-2-[(pyridin-4-ylcarbonylamino)methyl]pentyl]-1,3-benzodioxole-4-carboxylic acid
ChEMBL
DrugBank
ZINCZINC000095920996
PDB chain4cj4 Chain A Residue 1217 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB4cj4 Interrogating HIV Integrase for Compounds that Bind- a Sampl Challenge.
Resolution1.8 Å
Binding residue
(original residue number in PDB)		A169 E170 H171 T174 M178
Binding residue
(residue number reindexed from 1)		A113 E114 H115 T118 M122
Annotation score1
Binding affinityMOAD: Kd=432uM
PDBbind-CN: -logKd/Ki=3.36,Kd=432uM
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:4cj4, PDBe:4cj4, PDBj:4cj4
PDBsum4cj4
PubMed24532034
UniProtP12497|POL_HV1N5 Gag-Pol polyprotein (Gene Name=gag-pol)

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