Structure of PDB 2w2i Chain A Binding Site BS01

Receptor Information

>2w2i Chain A (length=305) Species: 9606 (Homo sapiens)

HTIMTFYPTMEEFADFNTYVAYMESQGAHQAGLAKVIPPKEWKARQMYDD
IEDILIATPLQQVTSGQGGVFTQYHKKKKAMRVGQYRRLANSKKYQTPPH
QNFADLEQRYWKSHPGNPPIYGADISGSLFEESTKQWNLGHLGTILDLLE
QECGVVIEGVNTPYLYFGMWKTTFAWHTEDMDLYSINYLHFGEPKTWYVV
PPEHGQHLERLARELFPDISAFLRHKVALISPTVLKENGIPFNCMTQEAG
EFMVTFPYGYHAGFNHGFNCAEAINFATPRWIDYGKMAVTFSMDPFVRIV
QPESY

Ligand information

• Ligand ID: PD2
• InChI: InChI=1S/C7H5NO4/c9-6(10)4-1-2-8-5(3-4)7(11)12/h1-3H,(H,9,10)(H,11,12)
• InChIKey: MJIVRKPEXXHNJT-UHFFFAOYSA-N
• SMILES:
  CACTVS 3.341: OC(=O)c1ccnc(c1)C(O)=O
  ACDLabs 10.04: O=C(O)c1nccc(C(=O)O)c1
  OpenEye OEToolkits 1.5.0: c1cnc(cc1C(=O)O)C(=O)O
• Formula: C7 H5 N O4
• Name: PYRIDINE-2,4-DICARBOXYLIC ACID
• ChEMBL: CHEMBL316034
• ZINC: ZINC000000391915
• PDB chain: 2w2i Chain A Residue 602

Receptor-Ligand Complex Structure

Structure summary

• PDB: 2w2i Structural and Evolutionary Basis for the Dual Substrate Selectivity of Human Kdm4 Histone Demethylase Family.
• Resolution: 2.1 Å
• Binding residue (original residue number in PDB): Y133 F186 H189 E191 K207 W209 K242 H277
• Binding residue (residue number reindexed from 1): Y121 F174 H177 E179 K195 W197 K226 H261
• Annotation score: 1
• Binding affinity: PDBbind-CN: -logKd/Ki=6.04,Ki=914nM
  BindingDB: IC50=1400nM,Ki=914000nM

Enzymatic activity

• Catalytic site (original residue number in PDB): G171 Y178 H189 E191 H277 A289
• Catalytic site (residue number reindexed from 1): G159 Y166 H177 E179 H261 A273
• Enzyme Commision number: 1.14.11.66: [histone H3]-trimethyl-L-lysine(9) demethylase.

External links

• PDB: RCSB:2w2i, PDBe:2w2i, PDBj:2w2i
• PDBsum: 2w2i
• PubMed: 21914792
• UniProt: B2RXH2|KDM4E_HUMAN Lysine-specific demethylase 4E (Gene Name=KDM4E)