Structure of PDB 5rb4 Chain A Binding Site BS01

Receptor Information

>5rb4 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

A6Z

InChI

InChI=1S/C12H14ClN3/c13-11-2-1-3-12(10-11)16-8-6-15(5-4-14)7-9-16/h1-3,10H,5-9H2/p+1

InChIKey

BIGOTGAMVFQWPQ-UHFFFAOYSA-O

SMILES

Software	SMILES
OpenEye OEToolkits 2.0.6	c1cc(cc(c1)Cl)N2CC[NH+](CC2)CC#N
CACTVS 3.385	Clc1cccc(c1)N2CC[NH+](CC2)CC#N

Formula

C12 H15 Cl N3

Name

2-[4-(3-chlorophenyl)piperazin-1-ium-1-yl]ethanenitrile

ChEMBL

DrugBank

ZINC

PDB chain

5rb4 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	5rb4 PanDDA analysis group deposition of Human JMJD1B screened against the DSPL Fragment Library
Resolution	1.55 Å
Binding residue (original residue number in PDB)	I1603 H1606 E1608 P1610 Y1695
Binding residue (residue number reindexed from 1)	I226 H229 E231 P233 Y318
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:5rb4, PDBe:5rb4, PDBj:5rb4
PDBsum	5rb4
PubMed
UniProt	Q7LBC6\|KDM3B_HUMAN Lysine-specific demethylase 3B (Gene Name=KDM3B)

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