Structure of PDB 5a80 Chain A Binding Site BS02

Receptor Information

>5a80 Chain A (length=351) Species: 9606 (Homo sapiens)

ESETLNPSARIMTFYPTMEEFRNFSRYIAYIESQGAHRAGLAKVVPPKEW
KPRASYDDIDDLVIPAPIQQLVTGQSGLFTQYNIQKKAMTVREFRKIANS
DKYCTPRYSEFEELERKYWKNLTFNPPIYGADVNGTLYEKHVDEWNIGRL
RTILDLVEKESGITIEGVNTPYLYFGMWKTSFAWHTEDMDLYSINYLHFG
EPKSWYSVPPEHGKRLERLAKGFFPGSAQSCEAFLRHKMTLISPLMLKKY
GIPFDKVTQEAGEFMITFPYGYHAGFNHGFNCAESTNFATRRWIEYGKQA
VLCSCRKDMVKISMDVFVRKFQPERYKLWKAGKDNTVIDHTLPTPEAAEF
L

Ligand information

• Ligand ID: 9CJ
• InChI: InChI=1S/C21H18N2O5/c1-28-16-4-2-3-13(9-16)10-20(25)23-15-5-6-19(24)17(12-15)18-11-14(21(26)27)7-8-22-18/h2-9,11-12,24H,10H2,1H3,(H,23,25)(H,26,27)
• InChIKey: QSWJSOQQNWMPME-UHFFFAOYSA-N
• SMILES:
  CACTVS 3.385: COc1cccc(CC(=O)Nc2ccc(O)c(c2)c3cc(ccn3)C(O)=O)c1
  OpenEye OEToolkits 1.7.6: COc1cccc(c1)CC(=O)Nc2ccc(c(c2)c3cc(ccn3)C(=O)O)O
• Formula: C21 H18 N2 O5
• Name: 2-[5-[2-(3-methoxyphenyl)ethanoylamino]-2-oxidanyl-phenyl]pyridine-4-carboxylic acid
• ChEMBL: CHEMBL3775272
• ZINC: ZINC000263620950
• PDB chain: 5a80 Chain A Residue 1357

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5a80 Docking and Linking of Fragments to Discover Jumonji Histone Demethylase Inhibitors.
• Resolution: 2.28 Å
• Binding residue (original residue number in PDB): Y132 F185 H188 E190 K206 W208 H240 K241 H276
• Binding residue (residue number reindexed from 1): Y129 F182 H185 E187 K203 W205 H237 K238 H273
• 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): G167 Y174 H185 E187 H273 S285
• 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:5a80, PDBe:5a80, PDBj:5a80
• PDBsum: 5a80
• PubMed: 26699912
• UniProt: O75164|KDM4A_HUMAN Lysine-specific demethylase 4A (Gene Name=KDM4A)