Structure of PDB 5a7n Chain B Binding Site BS03

Receptor Information

>5a7n Chain B (length=346) Species: 9606 (Homo sapiens)

LNPSARIMTFYPTMEEFRNFSRYIAYIESQGAHRAGLAKVVPPKEWKPRA
SYDDIDDLVIPAPIQQLVTGQSGLFTQYNIQKKAMTVREFRKIANSDKYC
TPRYSEFEELERKYWKNLTFNPPIYGADVNGTLYEKHVDEWNIGRLRTIL
DLVEKESGITIEGVNTPYLYFGMWKTSFAWHTEDMDLYSINYLHFGEPKS
WYSVPPEHGKRLERLAKGFFPGSAQSCEAFLRHKMTLISPLMLKKYGIPF
DKVTQEAGEFMITFPYGYHAGFNHGFNCAESTNFATRRWIEYGKQAVLCS
CRKDMVKISMDVFVRKFQPERYKLWKAGKDNTVIDHTLPTPEAAEF

Ligand information

• Ligand ID: VAO
• InChI: InChI=1S/C13H8N2O3/c14-7-8-1-2-12(16)10(5-8)11-6-9(13(17)18)3-4-15-11/h1-6,16H,(H,17,18)
• InChIKey: NARDFYYIAAFALG-UHFFFAOYSA-N
• SMILES:
  CACTVS 3.385: OC(=O)c1ccnc(c1)c2cc(ccc2O)C#N
  OpenEye OEToolkits 1.7.6: c1cc(c(cc1C#N)c2cc(ccn2)C(=O)O)O
• Formula: C13 H8 N2 O3
• Name: 2-(5-cyano-2-oxidanyl-phenyl)pyridine-4-carboxylic acid
• ChEMBL: CHEMBL3774693
• ZINC: ZINC000263620778
• PDB chain: 5a7n Chain B Residue 4001

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5a7n Docking and Linking of Fragments to Discover Jumonji Histone Demethylase Inhibitors.
• Resolution: 2.39 Å
• Binding residue (original residue number in PDB): Y132 F185 H188 E190 K206 W208 K241 H276
• Binding residue (residue number reindexed from 1): Y125 F178 H181 E183 K199 W201 K234 H269
• 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): G163 Y170 H181 E183 H269 S281
• 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:5a7n, PDBe:5a7n, PDBj:5a7n
• PDBsum: 5a7n
• PubMed: 26699912
• UniProt: O75164|KDM4A_HUMAN Lysine-specific demethylase 4A (Gene Name=KDM4A)