Structure of PDB 6ydv Chain AAA Binding Site BS01

Receptor Information

>6ydv Chain AAA (length=340) Species: 9606 (Homo sapiens)

SMTSHSWLCDGRLLCLHDPSNKNNWKIFRECWKQGQPVLVSGVHKKLKSE
LWKPEAFSQEFGDQDVDLVNCRNCAIISDVKVRDFWDGFEIICKRLRSED
GQPMVLKLKDWPPGEDFRDMMPTRFEDLMENLPLPEYTKRDGRLNLASRL
PSYFVRPDLGPKMYNAYGLITAEDRRVGTTNLHLDVSDAVNVMVYVGIPI
GEGAHDEEVLKTIDEGDADEVTKERIHDHKEKPGALWHIYAAKDAEKIRE
LLRKVGEEQGQENPPDHDPIHDQSWYLDQTLRKRLYEEYGVQGWAIVQFL
GDAVFIPAGAPHQVHNLYSCIKVAEDFVSPEHVKHCFRLT

Ligand information

• Ligand ID: ONQ
• InChI: InChI=1S/C10H12N2O3/c1-15-8-4-2-7(3-5-8)10(14)12-6-9(11)13/h2-5H,6H2,1H3,(H2,11,13)(H,12,14)
• InChIKey: ZKADLOGPYJUFCB-UHFFFAOYSA-N
• SMILES:
  OpenEye OEToolkits 2.0.7: COc1ccc(cc1)C(=O)NCC(=O)N
  CACTVS 3.385: COc1ccc(cc1)C(=O)NCC(N)=O
• Formula: C10 H12 N2 O3
• Name: ~{N}-(2-azanyl-2-oxidanylidene-ethyl)-4-methoxy-benzamide
• ZINC: ZINC000000040120
• PDB chain: 6ydv Chain AAA Residue 1801

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6ydv Crystal Structure of the Jmjc Domain of Human JMJD1B in complex with FM001511a from the DSPL fragment library
• Resolution: 2.07 Å
• Binding residue (original residue number in PDB): C1386 R1389 Q1669 G1670 W1671 A1672
• Binding residue (residue number reindexed from 1): C9 R12 Q292 G293 W294 A295
• 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:6ydv, PDBe:6ydv, PDBj:6ydv
• PDBsum: 6ydv
• UniProt: A4FUT8