Structure of PDB 5f37 Chain A Binding Site BS03

Receptor Information
>5f37 Chain A (length=350) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SETLNPSARIMTFYPTMEEFRNFSRYIAYIESQGAHRAGLAKVVPPKEWK
PRASYDDIDDLVIPAPIQQLVTGQSGLFTQYNIQKKAMTVREFRKIANSD
KYCTPRYSEFEELERKYWKNLTFNPPIYGADVNGTLYEKHVDEWNIGRLR
TILDLVEKESGITIEGVNTPYLYFGMWKTSFAWHTEDMDLYSINYLHFGE
PKSWYSVPPEHGKRLERLAKGFFPGSAQSCEAFLRHKMTLISPLMLKKYG
IPFDKVTQEAGEFMITFPYGYHAGFNHGFNCAESTNFATRRWIEYGKQAV
LCSCRKDMVKISMDVFVRKFQPERYKLWKAGKDNTVIDHTLPTPEAAEFL
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 A 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)		Y128 Y173 F181 H184 K202 W204 K237 H272
Annotation score1
Binding affinityMOAD: ic50=1.7uM
PDBbind-CN: -logKd/Ki=5.77,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) G166 Y173 H184 E186 H272 S284
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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