Structure of PDB 3pdq Chain B Binding Site BS02

Receptor Information

>3pdq Chain B (length=348) Species: 9606 (Homo sapiens)

TLNPSARIMTFYPTMEEFRNFSRYIAYIESQGAHRAGLAKVVPPKEWKPR
ASYDDIDDLVIPAPIQQLVTGQSGLFTQYNIQKKAMTVREFRKIANSDKY
CTPRYSEFEELERKYWKNLTFNPPIYGADVNGTLYEKHVDEWNIGRLRTI
LDLVEKESGITIEGVNTPYLYFGMWKTSFAWHTEDMDLYSINYLHFGEPK
SWYSVPPEHGKRLERLAKGFFPGSAQSCEAFLRHKMTLISPLMLKKYGIP
FDKVTQEAGEFMITFPYGYHAGFNHGFNCAESTNFATRRWIEYGKQAVLC
SCRKDMVKISMDVFVRKFQPERYKLWKAGKDNTVIDHTLPTPEAAEFL

Ligand information

• Ligand ID: KC6
• InChI: InChI=1S/C14H14N4O3/c15-3-6-18-13(19)9-1-4-16-11(7-9)12-8-10(14(20)21)2-5-17-12/h1-2,4-5,7-8H,3,6,15H2,(H,18,19)(H,20,21)
• InChIKey: RTGDPYNAIULBPL-UHFFFAOYSA-N
• SMILES:
  CACTVS 3.370: NCCNC(=O)c1ccnc(c1)c2cc(ccn2)C(O)=O
  ACDLabs 12.01: O=C(O)c2ccnc(c1nccc(C(=O)NCCN)c1)c2
  OpenEye OEToolkits 1.7.0: c1cnc(cc1C(=O)NCCN)c2cc(ccn2)C(=O)O
• Formula: C14 H14 N4 O3
• Name: 4'-[(2-aminoethyl)carbamoyl]-2,2'-bipyridine-4-carboxylic acid
• ChEMBL: CHEMBL1615036
• ZINC: ZINC000064754819
• PDB chain: 3pdq Chain B Residue 503

Receptor-Ligand Complex Structure

Structure summary

• PDB: 3pdq Inhibition of histone demethylases by 4-carboxy-2,2'-bipyridyl compounds
• Resolution: 1.989 Å
• Binding residue (original residue number in PDB): Y132 D135 F185 H188 E190 K206 W208 K241 H276
• Binding residue (residue number reindexed from 1): Y126 D129 F179 H182 E184 K200 W202 K235 H270
• Annotation score: 1
• Binding affinity: MOAD: ic50=0.18uM

Enzymatic activity

• Catalytic site (original residue number in PDB): G170 Y177 H188 E190 H276 S288
• Catalytic site (residue number reindexed from 1): G164 Y171 H182 E184 H270 S282
• 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:3pdq, PDBe:3pdq, PDBj:3pdq
• PDBsum: 3pdq
• PubMed: 21412984
• UniProt: O75164|KDM4A_HUMAN Lysine-specific demethylase 4A (Gene Name=KDM4A)