Structure of PDB 5x9o Chain A Binding Site BS01

Receptor Information

>5x9o Chain A (length=130) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]

LYFQGADSCIQFTRHASDVLLNLNRLRSRDILTDVVIVVSREQFRAHKTV
LMACSGLFYSIFTDQLKCNLSVINLDPEINPEGFCILLDFMYTSRLNLRE
GNIMAVMATAMYLQMEHVVDTCRKFIKASE

Ligand information

InChI=1S/C13H9ClN4O3/c14-9-6-8(18(20)21)2-4-10(9)15-7-1-3-11-12(5-7)17-13(19)16-11/h1-6,15H,(H2,16,17,19)

LBXJVISQYZQJLT-UHFFFAOYSA-N

SMILES

Software	SMILES
CACTVS 3.385	[O-][N+](=O)c1ccc(Nc2ccc3NC(=O)Nc3c2)c(Cl)c1
OpenEye OEToolkits 2.0.6	c1cc2c(cc1Nc3ccc(cc3Cl)[N+](=O)[O-])NC(=O)N2

Formula

C13 H9 Cl N4 O3

Name

5-[(2-chloranyl-4-nitro-phenyl)amino]-1,3-dihydrobenzimidazol-2-one

ZINC000020666675

PDB chain

5x9o Chain A Residue 801 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]

Receptor-Ligand Complex Structure

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PDB	5x9o Discovery of a novel B-cell lymphoma 6 (BCL6)-corepressor interaction inhibitor by utilizing structure-based drug design
Resolution	1.58 Å
Binding residue (original residue number in PDB)	N21 R24 L25 R28
Binding residue (residue number reindexed from 1)	N22 R25 L26 R29
Annotation score	1
Binding affinity	MOAD: Kd=5uM PDBbind-CN: -logKd/Ki=5.30,Kd=5uM BindingDB: Kd=5000nM

Enzymatic activity

Enzyme Commision number

External links

PDB	RCSB:5x9o, PDBe:5x9o, PDBj:5x9o
PDBsum	5x9o
PubMed	28760529
UniProt	P41182\|BCL6_HUMAN B-cell lymphoma 6 protein (Gene Name=BCL6)

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