Structure of PDB 4cf2 Chain B Binding Site BS01

Receptor Information
>4cf2 Chain B (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 ID3GM
InChIInChI=1S/C26H30N2O7/c27-11-3-6-22(29)28-20-13-15-4-1-2-5-18(15)19(20)12-16-7-9-21-25(24(16)26(32)33)34-14-17(35-21)8-10-23(30)31/h1-2,4-5,7,9,17,19-20H,3,6,8,10-14,27H2,(H,28,29)(H,30,31)(H,32,33)/t17-,19+,20-/m0/s1
InChIKeyUEGSVADLZPXOAG-SXLOBPIMSA-N
SMILES
SoftwareSMILES
CACTVS 3.385NCCCC(=O)N[C@H]1Cc2ccccc2[C@H]1Cc3ccc4O[C@@H](CCC(O)=O)COc4c3C(O)=O
ACDLabs 12.01O=C(O)c2c(ccc1OC(COc12)CCC(=O)O)CC4c3ccccc3CC4NC(=O)CCCN
OpenEye OEToolkits 1.9.2c1ccc2c(c1)C[C@@H]([C@@H]2Cc3ccc4c(c3C(=O)O)OC[C@@H](O4)CCC(=O)O)NC(=O)CCCN
OpenEye OEToolkits 1.9.2c1ccc2c(c1)CC(C2Cc3ccc4c(c3C(=O)O)OCC(O4)CCC(=O)O)NC(=O)CCCN
CACTVS 3.385NCCCC(=O)N[CH]1Cc2ccccc2[CH]1Cc3ccc4O[CH](CCC(O)=O)COc4c3C(O)=O
FormulaC26 H30 N2 O7
Name(2s)-6-[[(1r,2s)-2-(4-azanylbutanoylamino)-2,3-dihydro-1h-inden-1-yl]methyl]-2-(3-hydroxy-3-oxopropyl)-2,3-dihydro-1,4-benzodioxine-5-carboxylic acid
ChEMBL
DrugBank
ZINCZINC000095920903
PDB chain4cf2 Chain A Residue 1213 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB4cf2 Interrogating HIV Integrase for Compounds that Bind- a Sampl Challenge.
Resolution1.95 Å
Binding residue
(original residue number in PDB)		E96 Y99 A129 W132
Binding residue
(residue number reindexed from 1)		E40 Y43 A73 W76
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:4cf2, PDBe:4cf2, PDBj:4cf2
PDBsum4cf2
PubMed24532034
UniProtP12497|POL_HV1N5 Gag-Pol polyprotein (Gene Name=gag-pol)

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