Structure of PDB 5a7q Chain A Binding Site BS03

Receptor Information

>5a7q Chain A (length=351) Species: 9606 (Homo sapiens)

SESETLNPSARIMTFYPTMEEFRNFSRYIAYIESQGAHRAGLAKVVPPKE
WKPRASYDDIDDLVIPAPIQQLVTGQSGLFTQYNIQKKAMTVREFRKIAN
SDKYCTPRYSEFEELERKYWKNLTFNPPIYGADVNGTLYEKHVDEWNIGR
LRTILDLVEKESGITIEGVNTPYLYFGMWKTSFAWHTEDMDLYSINYLHF
GEPKSWYSVPPEHGKRLERLAKGFFPGSAQSCEAFLRHKMTLISPLMLKK
YGIPFDKVTQEAGEFMITFPYGYHAGFNHGFNCAESTNFATRRWIEYGKQ
AVLCSCRKDMVKISMDVFVRKFQPERYKLWKAGKDNTVIDHTLPTPEAAE
F

Ligand information

• Ligand ID: KCH
• InChI: InChI=1S/C12H10N2O3/c13-8-1-2-11(15)9(6-8)10-5-7(12(16)17)3-4-14-10/h1-6,15H,13H2,(H,16,17)
• InChIKey: BJCZMMOGTXVENP-UHFFFAOYSA-N
• SMILES:
  CACTVS 3.385: Nc1ccc(O)c(c1)c2cc(ccn2)C(O)=O
  OpenEye OEToolkits 1.7.6: c1cc(c(cc1N)c2cc(ccn2)C(=O)O)O
• Formula: C12 H10 N2 O3
• Name: 2-(5-azanyl-2-oxidanyl-phenyl)pyridine-4-carboxylic acid
• ChEMBL: CHEMBL3775869
• ZINC: ZINC000263620269
• PDB chain: 5a7q Chain A Residue 1356

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5a7q Docking and Linking of Fragments to Discover Jumonji Histone Demethylase Inhibitors.
• Resolution: 2.0 Å
• Binding residue (original residue number in PDB): Y132 F185 H188 E190 K206 W208 K241 H276
• Binding residue (residue number reindexed from 1): Y130 F183 H186 E188 K204 W206 K239 H274
• Annotation score: 1

Enzymatic activity

• Catalytic site (original residue number in PDB): G170 Y177 H188 E190 H276 S288
• Catalytic site (residue number reindexed from 1): G168 Y175 H186 E188 H274 S286
• Enzyme Commision number: 1.14.11.66: [histone H3]-trimethyl-L-lysine(9) demethylase.
  1.14.11.69: [histone H3]-trimethyl-L-lysine(36) demethylase.

External links

• PDB: RCSB:5a7q, PDBe:5a7q, PDBj:5a7q
• PDBsum: 5a7q
• PubMed: 26699912
• UniProt: O75164|KDM4A_HUMAN Lysine-specific demethylase 4A (Gene Name=KDM4A)