Structure of PDB 5f37 Chain C Binding Site BS03

Receptor Information
>5f37 Chain C (length=349) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
ETLNPSARIMTFYPTMEEFRNFSRYIAYIESQGAHRAGLAKVVPPKEWKP
RASYDDIDDLVIPAPIQQLVTGQSGLFTQYNIQKKAMTVREFRKIANSDK
YCTPRYSEFEELERKYWKNLTFNPPIYGADVNGTLYEKHVDEWNIGRLRT
ILDLVEKESGITIEGVNTPYLYFGMWKTSFAWHTEDMDLYSINYLHFGEP
KSWYSVPPEHGKRLERLAKGFFPGSAQSCEAFLRHKMTLISPLMLKKYGI
PFDKVTQEAGEFMITFPYGYHAGFNHGFNCAESTNFATRRWIEYGKQAVL
CSCRKDMVKISMDVFVRKFQPERYKLWKAGKDNTVIDHTLPTPEAAEFL
Ligand information
Ligand IDN5J
InChIInChI=1S/C7H5N3O/c11-7-5-1-2-8-3-6(5)9-4-10-7/h1-4H,(H,9,10,11)
InChIKeyQMOPAFMMLWUTKI-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.6c1cncc2c1C(=O)NC=N2
CACTVS 3.385O=C1NC=Nc2cnccc12
FormulaC7 H5 N3 O
Name3H-pyrido[3,4-d]pyrimidin-4-one
ChEMBLCHEMBL3770256
DrugBank
ZINCZINC000020981109
PDB chain5f37 Chain C Residue 403 [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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PDB5f37 8-Substituted Pyrido[3,4-d]pyrimidin-4(3H)-one Derivatives As Potent, Cell Permeable, KDM4 (JMJD2) and KDM5 (JARID1) Histone Lysine Demethylase Inhibitors.
Resolution2.22 Å
Binding residue
(original residue number in PDB)		Y132 Y177 F185 H188 K206 W208 K241 H276
Binding residue
(residue number reindexed from 1)		Y127 Y172 F180 H183 K201 W203 K236 H271
Annotation score1
Binding affinityMOAD: ic50=1.7uM
BindingDB: IC50=1700nM
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:5f37, PDBe:5f37, PDBj:5f37
PDBsum5f37
PubMed26741168
UniProtO75164|KDM4A_HUMAN Lysine-specific demethylase 4A (Gene Name=KDM4A)

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