Structure of PDB 5anq Chain A Binding Site BS01

Receptor Information

>5anq Chain A (length=350) Species: 9606 (Homo sapiens)

SESETLNPSARIMTFYPTMEEFRNFSRYIAYIESQGAHRAGLAKVVPPKE
WKPRASYDDIDDLVIPAPIQQLVTGQSGLFTQYNIQKKAMTVREFRKIAN
SDKYCTPRYSEFEELERKYWKNLTFNPPIYGADVNGTLYEKHVDEWNIGR
LRTILDLVEKESGITIEGVNTPYLYFGMWKTSFAWHTEDMDLYSINYLHF
GEPKSWYSVPPEHGKRLERLAKGFFPGSAQSCEAFLRHKMTLISPLMLKK
YGIPFDKVTQEAGEFMITFPYGYHAGFNHGFNCAESTNFATRRWIEYGKQ
AVLCSCRKDMVKISMDVFVRKFQPERYKLWKAGKDNTVIDHTLPTPEAAE

Ligand information

• Ligand ID: 5YQ
• InChI: InChI=1S/C16H13N5O2/c22-15(23)12-3-6-18-14(8-12)13-4-7-19-16(21-13)20-10-11-2-1-5-17-9-11/h1-9H,10H2,(H,22,23)(H,19,20,21)
• InChIKey: YUSWODBVCDCVMS-UHFFFAOYSA-N
• SMILES:
  OpenEye OEToolkits 1.7.6: c1cc(cnc1)CNc2nccc(n2)c3cc(ccn3)C(=O)O
  CACTVS 3.385: OC(=O)c1ccnc(c1)c2ccnc(NCc3cccnc3)n2
• Formula: C16 H13 N5 O2
• Name: 2-{2-[(pyridin-3-ylmethyl)amino]pyrimidin-4-yl}pyridine-4-carboxylic acid
• ZINC: ZINC000071721256
• PDB chain: 5anq Chain A Residue 1353

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5anq Substituted 2-(2-Aminopyrimidin-4-Yl)Pyridine-4-Carboxylates as Potent Inhibitors of Jumonjic Domain-Containing Histone Demethylases.
• Resolution: 2.0 Å
• Binding residue (original residue number in PDB): Y132 G170 V171 F185 H188 E190 D191 K206 W208 K241 H276
• Binding residue (residue number reindexed from 1): Y130 G168 V169 F183 H186 E188 D189 K204 W206 K239 H274
• Annotation score: 1
• Binding affinity: MOAD: ic50=3.98uM

Enzymatic activity

• Catalytic site (original residue number in PDB): G170 Y177 H188 E190 H276 S288
• Catalytic site (residue number reindexed from 1): G168 Y175 H186 E188 H274 S286
• 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:5anq, PDBe:5anq, PDBj:5anq
• PDBsum: 5anq
• PubMed: 26971619
• UniProt: O75164|KDM4A_HUMAN Lysine-specific demethylase 4A (Gene Name=KDM4A)