Structure of PDB 3nf9 Chain B Binding Site BS01

Receptor Information
>3nf9 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 IDCD9
InChIInChI=1S/C17H12ClNO5/c18-11-3-1-9-5-14(20)19(12(9)6-11)7-10-2-4-13-16(24-8-23-13)15(10)17(21)22/h1-4,6H,5,7-8H2,(H,21,22)
InChIKeyXVKFXTJLVSDWCE-UHFFFAOYSA-N
SMILES
SoftwareSMILES
ACDLabs 12.01Clc1ccc2c(c1)N(C(=O)C2)Cc3ccc4OCOc4c3C(=O)O
OpenEye OEToolkits 1.7.0c1cc2c(cc1Cl)N(C(=O)C2)Cc3ccc4c(c3C(=O)O)OCO4
CACTVS 3.370OC(=O)c1c(CN2C(=O)Cc3ccc(Cl)cc23)ccc4OCOc14
FormulaC17 H12 Cl N O5
Name5-[(6-chloro-2-oxo-2,3-dihydro-1H-indol-1-yl)methyl]-1,3-benzodioxole-4-carboxylic acid
ChEMBL
DrugBank
ZINCZINC000066166929
PDB chain3nf9 Chain B Residue 213 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB3nf9 Structural basis for a new mechanism of inhibition of HIV-1 integrase identified by fragment screening and structure-based design
Resolution1.95 Å
Binding residue
(original residue number in PDB)		V77 V79 G82 V150 I151 S153 M154 E157 H183
Binding residue
(residue number reindexed from 1)		V21 V23 G26 V94 I95 S97 M98 E101 H127
Annotation score1
Binding affinityMOAD: ic50=290uM
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

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Molecular Function
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Biological Process
External links
PDB RCSB:3nf9, PDBe:3nf9, PDBj:3nf9
PDBsum3nf9
PubMed21602613
UniProtP12497|POL_HV1N5 Gag-Pol polyprotein (Gene Name=gag-pol)

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