Structure of PDB 5rar Chain A Binding Site BS01

Receptor Information
>5rar 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 IDS9D
InChIInChI=1S/C13H14N4O/c1-7-14-13(15-8-1)18-11-4-2-10(3-5-11)12-6-9-16-17-12/h1-5,7-8,12,16-17H,6,9H2/t12-/m0/s1
InChIKeyIZVIOVJMKGPYAR-LBPRGKRZSA-N
SMILES
SoftwareSMILES
CACTVS 3.385C1C[C@H](NN1)c2ccc(Oc3ncccn3)cc2
OpenEye OEToolkits 2.0.6c1cnc(nc1)Oc2ccc(cc2)C3CCNN3
OpenEye OEToolkits 2.0.6c1cnc(nc1)Oc2ccc(cc2)[C@@H]3CCNN3
CACTVS 3.385C1C[CH](NN1)c2ccc(Oc3ncccn3)cc2
FormulaC13 H14 N4 O
Name2-[4-[(3~{S})-pyrazolidin-3-yl]phenoxy]pyrimidine
ChEMBL
DrugBank
ZINC
PDB chain5rar Chain A Residue 1801 [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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PDB5rar PanDDA analysis group deposition of Human JMJD1B screened against the DSPL Fragment Library
Resolution1.47 Å
Binding residue
(original residue number in PDB)		M1379 S1381 N1398 N1400 N1401
Binding residue
(residue number reindexed from 1)		M2 S4 N21 N23 N24
Annotation score1
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:5rar, PDBe:5rar, PDBj:5rar
PDBsum5rar
PubMed
UniProtQ7LBC6|KDM3B_HUMAN Lysine-specific demethylase 3B (Gene Name=KDM3B)

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