Structure of PDB 5a7w Chain A Binding Site BS01

Receptor Information

>5a7w Chain A (length=345) Species: 9606 (Homo sapiens)

NPSARIMTFYPTMEEFRNFSRYIAYIESQGAHRAGLAKVVPPKEWKPRAS
YDDIDDLVIPAPIQQLVTGQSGLFTQYNIQKKAMTVREFRKIANSDKYCT
PRYSEFEELERKYWKNLTFNPPIYGADVNGTLYEKHVDEWNIGRLRTILD
LVEKESGITIEGVNTPYLYFGMWKTSFAWHTEDMDLYSINYLHFGEPKSW
YSVPPEHGKRLERLAKGFFPGSAQSCEAFLRHKMTLISPLMLKKYGIPFD
KVTQEAGEFMITFPYGYHAGFNHGFNCAESTNFATRRWIEYGKQAVLCSC
RKDMVKISMDVFVRKFQPERYKLWKAGKDNTVIDHTLPTPEAAEF

Ligand information

• Ligand ID: 35M
• InChI: InChI=1S/C19H14N2O5/c22-14-4-1-11(2-5-14)18(24)21-13-3-6-17(23)15(10-13)16-9-12(19(25)26)7-8-20-16/h1-10,22-23H,(H,21,24)(H,25,26)
• InChIKey: MXKVATSZRALAIN-UHFFFAOYSA-N
• SMILES:
  CACTVS 3.385: OC(=O)c1ccnc(c1)c2cc(NC(=O)c3ccc(O)cc3)ccc2O
  OpenEye OEToolkits 1.7.6: c1cc(ccc1C(=O)Nc2ccc(c(c2)c3cc(ccn3)C(=O)O)O)O
• Formula: C19 H14 N2 O5
• Name: 2-[5-[(4-hydroxyphenyl)carbonylamino]-2-oxidanyl-phenyl]pyridine-4-carboxylic acid
• ChEMBL: CHEMBL3775262
• ZINC: ZINC000263620772
• PDB chain: 5a7w Chain A Residue 1355

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5a7w Docking and Linking of Fragments to Discover Jumonji Histone Demethylase Inhibitors.
• Resolution: 2.27 Å
• Binding residue (original residue number in PDB): N86 Y132 F185 H188 E190 K206 W208 K241 H276
• Binding residue (residue number reindexed from 1): N78 Y124 F177 H180 E182 K198 W200 K233 H268
• 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): G162 Y169 H180 E182 H268 S280
• 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:5a7w, PDBe:5a7w, PDBj:5a7w
• PDBsum: 5a7w
• PubMed: 26699912
• UniProt: O75164|KDM4A_HUMAN Lysine-specific demethylase 4A (Gene Name=KDM4A)