Structure of PDB 5raq Chain A Binding Site BS01

Receptor Information

>5raq Chain A (length=340) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]

SMTSHSWLCDGRLLCLHDPSNKNNWKIFRECWKQGQPVLVSGVHKKLKSE
LWKPEAFSQEFGDQDVDLVNCRNCAIISDVKVRDFWDGFEIICKRLRSED
GQPMVLKLKDWPPGEDFRDMMPTRFEDLMENLPLPEYTKRDGRLNLASRL
PSYFVRPDLGPKMYNAYGLITAEDRRVGTTNLHLDVSDAVNVMVYVGIPI
GEGAHDEEVLKTIDEGDADEVTKERIHDHKEKPGALWHIYAAKDAEKIRE
LLRKVGEEQGQENPPDHDPIHDQSWYLDQTLRKRLYEEYGVQGWAIVQFL
GDAVFIPAGAPHQVHNLYSCIKVAEDFVSPEHVKHCFRLT

Ligand information

Ligand ID

S5J

InChI

InChI=1S/C13H17N3O/c1-17-13-5-3-2-4-12(13)16-10-8-15(7-6-14)9-11-16/h2-5H,7-11H2,1H3

InChIKey

CMNAMTJQXKKSGP-UHFFFAOYSA-N

SMILES

Software	SMILES
CACTVS 3.385 OpenEye OEToolkits 2.0.6	COc1ccccc1N2CCN(CC2)CC#N

Formula

C13 H17 N3 O

Name

2-[4-(2-methoxyphenyl)piperazin-1-yl]ethanenitrile

PDB chain

5raq Chain A Residue 1801 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]

Receptor-Ligand Complex Structure

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Structure summary

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PDB	5raq PanDDA analysis group deposition of Human JMJD1B screened against the DSPL Fragment Library
Resolution	1.85 Å
Binding residue (original residue number in PDB)	S1383 H1394 S1418 E1608
Binding residue (residue number reindexed from 1)	S6 H17 S41 E231
Annotation score	1

Enzymatic activity

Enzyme Commision number

1.14.11.65: [histone H3]-dimethyl-L-lysine(9) demethylase.

Gene Ontology

	Molecular Function
GO:0032454	histone H3K9 demethylase activity

View graph for
Molecular Function

External links

PDB	RCSB:5raq, PDBe:5raq, PDBj:5raq
PDBsum	5raq
PubMed
UniProt	Q7LBC6\|KDM3B_HUMAN Lysine-specific demethylase 3B (Gene Name=KDM3B)

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