Structure of PDB 5f5i Chain A Binding Site BS02

Receptor Information
>5f5i Chain A (length=349) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
ESETLNPSARIMTFYPTMEEFRNFSRYIAYIESQGAHRAGLAKVVPPKEW
KPRASYDDIDDLVIPAPIQQLVTGQSGLFTQYNIQKKAMTVREFRKIANS
DKYCTPRYSEFEELERKYWKNLTFNPPIYGADVNGTLYEKHVDEWNIGRL
RTILDLVEKESGITIEGVNTPYLYFGMWKTSFAWHTEDMDLYSINYLHFG
EPKSWYSVPPEHGKRLERLAKGFFPGSAQSCEAFLRHKMTLISPLMLKKY
GIPFDKVTQEAGEFMITFPYGYHAGFNHGFNCAESTNFATRRWIEYGKQA
VLCSCRKDMVKISMDVFVRKFQPERYKLWKAGKDNTVIDHTLPTPEAAE
Ligand information
Ligand ID5V1
InChIInChI=1S/C14H14N2O2/c17-14(18)12-6-7-16-13(8-12)10-15-9-11-4-2-1-3-5-11/h1-8,15H,9-10H2,(H,17,18)
InChIKeyIBSVWTKUXPGZFI-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.4c1ccc(cc1)CNCc2cc(ccn2)C(=O)O
CACTVS 3.385OC(=O)c1ccnc(CNCc2ccccc2)c1
FormulaC14 H14 N2 O2
Name2-[[(phenylmethyl)amino]methyl]pyridine-4-carboxylic acid
ChEMBLCHEMBL3775995
DrugBank
ZINCZINC000212614687
PDB chain5f5i Chain A Residue 504 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB5f5i 8-Substituted Pyrido[3,4-d]pyrimidin-4(3H)-one Derivatives As Potent, Cell Permeable, KDM4 (JMJD2) and KDM5 (JARID1) Histone Lysine Demethylase Inhibitors.
Resolution2.63 Å
Binding residue
(original residue number in PDB)		Y132 G170 Y175 Y177 F185 H188 E190 K206 W208 S288
Binding residue
(residue number reindexed from 1)		Y129 G167 Y172 Y174 F182 H185 E187 K203 W205 S285
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=6.02,IC50=0.95uM
Enzymatic activity
Catalytic site (original residue number in PDB) G170 Y177 H188 E190 H276 S288
Catalytic site (residue number reindexed from 1) G167 Y174 H185 E187 H273 S285
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:5f5i, PDBe:5f5i, PDBj:5f5i
PDBsum5f5i
PubMed26741168
UniProtO75164|KDM4A_HUMAN Lysine-specific demethylase 4A (Gene Name=KDM4A)

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