Structure of PDB 5f32 Chain C Binding Site BS03

Receptor Information

>5f32 Chain C (length=350) Species: 9606 (Homo sapiens)

ETLNPSARIMTFYPTMEEFRNFSRYIAYIESQGAHRAGLAKVVPPKEWKP
RASYDDIDDLVIPAPIQQLVTGQSGLFTQYNIQKKAMTVREFRKIANSDK
YCTPRYSEFEELERKYWKNLTFNPPIYGADVNGTLYEKHVDEWNIGRLRT
ILDLVEKESGITIEGVNTPYLYFGMWKTSFAWHTEDMDLYSINYLHFGEP
KSWYSVPPEHGKRLERLAKGFFPGSAQSCEAFLRHKMTLISPLMLKKYGI
PFDKVTQEAGEFMITFPYGYHAGFNHGFNCAESTNFATRRWIEYGKQAVL
CSCRKDMVKISMDVFVRKFQPERYKLWKAGKDNTVIDHTLPTPEAAEFLK

Ligand information

• Ligand ID: 5V7
• InChI: InChI=1S/C10H7N5OS/c11-10-15-6(3-17-10)8-7-5(1-2-12-8)9(16)14-4-13-7/h1-4H,(H2,11,15)(H,13,14,16)
• InChIKey: JEHSMTZNFSEDBY-UHFFFAOYSA-N
• SMILES:
  OpenEye OEToolkits 2.0.4: c1cnc(c2c1C(=O)NC=N2)c3csc(n3)N
  CACTVS 3.385: Nc1scc(n1)c2nccc3C(=O)NC=Nc23
• Formula: C10 H7 N5 O S
• Name: 8-(2-azanyl-1,3-thiazol-4-yl)-3~{H}-pyrido[3,4-d]pyrimidin-4-one
• ChEMBL: CHEMBL3774798
• ZINC: ZINC000263620595
• PDB chain: 5f32 Chain C Residue 403

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5f32 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: 2.05 Å
• Binding residue (original residue number in PDB): Y132 Y177 F185 H188 E190 K206 W208 K241 H276
• Binding residue (residue number reindexed from 1): Y127 Y172 F180 H183 E185 K201 W203 K236 H271
• Annotation score: 1
• Binding affinity: MOAD: ic50=11.5uM
  BindingDB: IC50=11500nM

Enzymatic activity

• Catalytic site (original residue number in PDB): G170 Y177 H188 E190 H276 S288
• Catalytic site (residue number reindexed from 1): G165 Y172 H183 E185 H271 S283
• 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:5f32, PDBe:5f32, PDBj:5f32
• PDBsum: 5f32
• PubMed: 26741168
• UniProt: O75164|KDM4A_HUMAN Lysine-specific demethylase 4A (Gene Name=KDM4A)