Structure of PDB 3pdq Chain A Binding Site BS02

Receptor Information
>3pdq Chain A (length=353) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SESETLNPSARIMTFYPTMEEFRNFSRYIAYIESQGAHRAGLAKVVPPKE
WKPRASYDDIDDLVIPAPIQQLVTGQSGLFTQYNIQKKAMTVREFRKIAN
SDKYCTPRYSEFEELERKYWKNLTFNPPIYGADVNGTLYEKHVDEWNIGR
LRTILDLVEKESGITIEGVNTPYLYFGMWKTSFAWHTEDMDLYSINYLHF
GEPKSWYSVPPEHGKRLERLAKGFFPGSAQSCEAFLRHKMTLISPLMLKK
YGIPFDKVTQEAGEFMITFPYGYHAGFNHGFNCAESTNFATRRWIEYGKQ
AVLCSCRKDMVKISMDVFVRKFQPERYKLWKAGKDNTVIDHTLPTPEAAE
FLK
Ligand information
Ligand IDKC6
InChIInChI=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)
InChIKeyRTGDPYNAIULBPL-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.370NCCNC(=O)c1ccnc(c1)c2cc(ccn2)C(O)=O
ACDLabs 12.01O=C(O)c2ccnc(c1nccc(C(=O)NCCN)c1)c2
OpenEye OEToolkits 1.7.0c1cnc(cc1C(=O)NCCN)c2cc(ccn2)C(=O)O
FormulaC14 H14 N4 O3
Name4'-[(2-aminoethyl)carbamoyl]-2,2'-bipyridine-4-carboxylic acid
ChEMBLCHEMBL1615036
DrugBank
ZINCZINC000064754819
PDB chain3pdq Chain A Residue 503 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB3pdq Inhibition of histone demethylases by 4-carboxy-2,2'-bipyridyl compounds
Resolution1.989 Å
Binding residue
(original residue number in PDB)		Y132 D135 Y177 F185 H188 E190 K206 W208 K241 H276
Binding residue
(residue number reindexed from 1)		Y130 D133 Y175 F183 H186 E188 K204 W206 K239 H274
Annotation score1
Binding affinityMOAD: ic50=0.18uM
PDBbind-CN: -logKd/Ki=6.74,IC50=180nM
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:3pdq, PDBe:3pdq, PDBj:3pdq
PDBsum3pdq
PubMed21412984
UniProtO75164|KDM4A_HUMAN Lysine-specific demethylase 4A (Gene Name=KDM4A)

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