Structure of PDB 4cef Chain A Binding Site BS02

Receptor Information
>4cef Chain A (length=149) 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
ELKKIIGQVRDQAEHLKTAVQMAVFIHNHKRKGYSAGERIVDIIATDIQ
Ligand information
Ligand IDD0T
InChIInChI=1S/C29H30N2O7/c1-31(16-20-9-5-6-10-23(20)28(34)30-15-19-7-3-2-4-8-19)17-21-11-13-24-27(26(21)29(35)36)37-18-22(38-24)12-14-25(32)33/h2-11,13,22H,12,14-18H2,1H3,(H,30,34)(H,32,33)(H,35,36)/t22-/m0/s1
InChIKeyRDFKANMJCXGBBA-QFIPXVFZSA-N
SMILES
SoftwareSMILES
ACDLabs 12.01O=C(NCc1ccccc1)c2ccccc2CN(C)Cc4ccc3OC(COc3c4C(=O)O)CCC(=O)O
CACTVS 3.385CN(Cc1ccccc1C(=O)NCc2ccccc2)Cc3ccc4O[CH](CCC(O)=O)COc4c3C(O)=O
OpenEye OEToolkits 1.7.6CN(Cc1ccccc1C(=O)NCc2ccccc2)Cc3ccc4c(c3C(=O)O)OCC(O4)CCC(=O)O
CACTVS 3.385CN(Cc1ccccc1C(=O)NCc2ccccc2)Cc3ccc4O[C@@H](CCC(O)=O)COc4c3C(O)=O
OpenEye OEToolkits 1.7.6CN(Cc1ccccc1C(=O)NCc2ccccc2)Cc3ccc4c(c3C(=O)O)OC[C@@H](O4)CCC(=O)O
FormulaC29 H30 N2 O7
Name(2S)-2-(3-hydroxy-3-oxopropyl)-6-[[methyl-[[2-[(phenylmethyl)carbamoyl]phenyl]methyl]amino]methyl]-2,3-dihydro-1,4-benzodioxine-5-carboxylic acid
ChEMBL
DrugBank
ZINCZINC000098208779
PDB chain4cef Chain B Residue 1215 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB4cef Interrogating HIV Integrase for Compounds that Bind- a Sampl Challenge.
Resolution1.7 Å
Binding residue
(original residue number in PDB)		Q95 E96 Y99 A129
Binding residue
(residue number reindexed from 1)		Q39 E40 Y43 A73
Annotation score1
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:4cef, PDBe:4cef, PDBj:4cef
PDBsum4cef
PubMed24532034
UniProtP12497|POL_HV1N5 Gag-Pol polyprotein (Gene Name=gag-pol)

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