Structure of PDB 4cgj Chain B Binding Site BS01

Receptor Information
>4cgj 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 IDNZL
InChIInChI=1S/C24H28N2O5/c25-11-5-1-2-8-21(27)26-19-13-15-6-3-4-7-17(15)18(19)12-16-9-10-20-23(31-14-30-20)22(16)24(28)29/h3-4,6-7,9-10,18-19H,1-2,5,8,11-14,25H2,(H,26,27)(H,28,29)/t18-,19-/m0/s1
InChIKeySSXWUTMSZZTPIE-OALUTQOASA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.9.2c1ccc2c(c1)CC(C2Cc3ccc4c(c3C(=O)O)OCO4)NC(=O)CCCCCN
OpenEye OEToolkits 1.9.2c1ccc2c(c1)C[C@@H]([C@H]2Cc3ccc4c(c3C(=O)O)OCO4)NC(=O)CCCCCN
CACTVS 3.385NCCCCCC(=O)N[C@H]1Cc2ccccc2[C@@H]1Cc3ccc4OCOc4c3C(O)=O
ACDLabs 12.01O=C(NC2Cc1ccccc1C2Cc3ccc4OCOc4c3C(=O)O)CCCCCN
CACTVS 3.385NCCCCCC(=O)N[CH]1Cc2ccccc2[CH]1Cc3ccc4OCOc4c3C(O)=O
FormulaC24 H28 N2 O5
Name5-[[(1S,2S)-2-(6-azanylhexanoylamino)-2,3-dihydro-1H-inden-1-yl]methyl]-1,3-benzodioxole-4-carboxylic acid
ChEMBL
DrugBank
ZINCZINC000095920905
PDB chain4cgj Chain A Residue 1216 [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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PDB4cgj Interrogating HIV Integrase for Compounds that Bind- a Sampl Challenge.
Resolution2.15 Å
Binding residue
(original residue number in PDB)		Q95 A129
Binding residue
(residue number reindexed from 1)		Q39 A73
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=2.84,Kd=1460uM
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:4cgj, PDBe:4cgj, PDBj:4cgj
PDBsum4cgj
PubMed24532034
UniProtP12497|POL_HV1N5 Gag-Pol polyprotein (Gene Name=gag-pol)

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