Structure of PDB 5f2w Chain A Binding Site BS03

Receptor Information

>5f2w Chain A (length=341) Species: 9606 (Homo sapiens)

NPSARIMTFYPTMEEFRNFSRYIAYIESQGAHRAGLAKVVPPKEWKPRAS
YDDIDDLVIPAPIQQLVTGQSGLFTQYNIQKKAMTVREFRKIANSDKYCT
PRYSEFEELERKYWKNLTFNPPIYGADVNGTLYEKHVDEWNIGRLRTILD
LVEKESGITIEGVNTPYLYFGMWKTSFAWHTEDMDLYSINYLHFGEPKSW
YSVPPEHGKRLERLAKGFFPGSAQSCEAFLRHKMTLISPLMLKKYGIPFD
KVTQEAGEFMITFPYGYHAGFNHGFNCAESTNFATRRWIEYGKQAVLCSV
KISMDVFVRKFQPERYKLWKAGKDNTVIDHTLPTPEAAEFL

Ligand information

• Ligand ID: 5UP
• InChI: InChI=1S/C9H8N4OS/c10-8(14)5-1-2-12-6(3-5)7-4-15-9(11)13-7/h1-4H,(H2,10,14)(H2,11,13)
• InChIKey: YCMAFYWOEDTAQB-UHFFFAOYSA-N
• SMILES:
  OpenEye OEToolkits 2.0.4: c1cnc(cc1C(=O)N)c2csc(n2)N
  CACTVS 3.385: NC(=O)c1ccnc(c1)c2csc(N)n2
• Formula: C9 H8 N4 O S
• Name: 2-(2-azanyl-1,3-thiazol-4-yl)pyridine-4-carboxamide
• ChEMBL: CHEMBL3775782
• ZINC: ZINC000263621254
• PDB chain: 5f2w Chain A Residue 403

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5f2w 8-Substituted Pyrido[3,4-d]pyrimidin-4(3H)-one Derivatives As Potent, Cell Permeable, KDM4 (JMJD2) and KDM5 (JARID1) Histone Lysine Demethylase Inhibitors.
• Resolution: 2.6 Å
• Binding residue (original residue number in PDB): Y132 F185 H188 E190 K206 W208 K241 H276
• Binding residue (residue number reindexed from 1): Y124 F177 H180 E182 K198 W200 K233 H268
• Annotation score: 1
• Binding affinity: PDBbind-CN: -logKd/Ki=3.98,IC50=104.2uM
  BindingDB: IC50=104200nM

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:5f2w, PDBe:5f2w, PDBj:5f2w
• PDBsum: 5f2w
• PubMed: 26741168
• UniProt: O75164|KDM4A_HUMAN Lysine-specific demethylase 4A (Gene Name=KDM4A)