Structure of PDB 5raa Chain A Binding Site BS01

Receptor Information

>5raa Chain A (length=340) Species: 9606 (Homo sapiens)

SMTSHSWLCDGRLLCLHDPSNKNNWKIFRECWKQGQPVLVSGVHKKLKSE
LWKPEAFSQEFGDQDVDLVNCRNCAIISDVKVRDFWDGFEIICKRLRSED
GQPMVLKLKDWPPGEDFRDMMPTRFEDLMENLPLPEYTKRDGRLNLASRL
PSYFVRPDLGPKMYNAYGLITAEDRRVGTTNLHLDVSDAVNVMVYVGIPI
GEGAHDEEVLKTIDEGDADEVTKERIHDHKEKPGALWHIYAAKDAEKIRE
LLRKVGEEQGQENPPDHDPIHDQSWYLDQTLRKRLYEEYGVQGWAIVQFL
GDAVFIPAGAPHQVHNLYSCIKVAEDFVSPEHVKHCFRLT

Ligand information

• Ligand ID: S3Y
• InChI: InChI=1S/C9H12ClN3O/c10-7-1-3-9(4-2-7)13-5-8(6-14)11-12-13/h1-4,8,11-12,14H,5-6H2
• InChIKey: JIARGTWLSPJECI-UHFFFAOYSA-N
• SMILES:
  OpenEye OEToolkits 2.0.7: c1cc(ccc1N2C[C@@H](NN2)CO)Cl
  CACTVS 3.385: OC[C@H]1CN(NN1)c2ccc(Cl)cc2
  OpenEye OEToolkits 2.0.7: c1cc(ccc1N2CC(NN2)CO)Cl
  ACDLabs 12.01: C(O)C1NNN(C1)c2ccc(cc2)Cl
  CACTVS 3.385: OC[CH]1CN(NN1)c2ccc(Cl)cc2
• Formula: C9 H12 Cl N3 O
• Name: [(4S)-1-(4-chlorophenyl)-1,2,3-triazolidin-4-yl]methanol
• PDB chain: 5raa Chain A Residue 1801

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5raa PanDDA analysis group deposition of Human JMJD1B screened against the DSPL Fragment Library
• Resolution: 1.57 Å
• Binding residue (original residue number in PDB): S1381 N1398
• Binding residue (residue number reindexed from 1): S4 N21
• 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

External links

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