Structure of PDB 4cf0 Chain B Binding Site BS01

Receptor Information
>4cf0 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 IDO5U
InChIInChI=1S/C28H34N2O7/c29-13-5-1-2-8-24(31)30-22-15-17-6-3-4-7-20(17)21(22)14-18-9-11-23-27(26(18)28(34)35)36-16-19(37-23)10-12-25(32)33/h3-4,6-7,9,11,19,21-22H,1-2,5,8,10,12-16,29H2,(H,30,31)(H,32,33)(H,34,35)/t19-,21-,22+/m1/s1
InChIKeyJSZOFYHIMWWVMH-FCEUIQTBSA-N
SMILES
SoftwareSMILES
ACDLabs 12.01O=C(O)c2c(ccc1OC(COc12)CCC(=O)O)CC4c3ccccc3CC4NC(=O)CCCCCN
OpenEye OEToolkits 1.9.2c1ccc2c(c1)CC(C2Cc3ccc4c(c3C(=O)O)OCC(O4)CCC(=O)O)NC(=O)CCCCCN
CACTVS 3.385NCCCCCC(=O)N[CH]1Cc2ccccc2[CH]1Cc3ccc4O[CH](CCC(O)=O)COc4c3C(O)=O
CACTVS 3.385NCCCCCC(=O)N[C@H]1Cc2ccccc2[C@H]1Cc3ccc4O[C@H](CCC(O)=O)COc4c3C(O)=O
OpenEye OEToolkits 1.9.2c1ccc2c(c1)C[C@@H]([C@@H]2Cc3ccc4c(c3C(=O)O)OC[C@H](O4)CCC(=O)O)NC(=O)CCCCCN
FormulaC28 H34 N2 O7
Name(2R)-6-[[(1R,2S)-2-(6-azanylhexanoylamino)-2,3-dihydro-1H-inden-1-yl]methyl]-2-(3-hydroxy-3-oxopropyl)-2,3-dihydro-1,4-benzodioxine-5-carboxylic acid
ChEMBL
DrugBank
ZINCZINC000098209255
PDB chain4cf0 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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PDB4cf0 Interrogating HIV Integrase for Compounds that Bind- a Sampl Challenge.
Resolution1.85 Å
Binding residue
(original residue number in PDB)		Q95 E96 Y99 W132
Binding residue
(residue number reindexed from 1)		Q39 E40 Y43 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:4cf0, PDBe:4cf0, PDBj:4cf0
PDBsum4cf0
PubMed24532034
UniProtP12497|POL_HV1N5 Gag-Pol polyprotein (Gene Name=gag-pol)

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