Structure of PDB 5f39 Chain B Binding Site BS03

Receptor Information
>5f39 Chain B (length=344) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SARIMTFYPTMEEFRNFSRYIAYIESQGAHRAGLAKVVPPKEWKPRASYD
DIDDLVIPAPIQQLVTGQSGLFTQYNIQKKAMTVREFRKIANSDKYCTPR
YSEFEELERKYWKNLTFNPPIYGADVNGTLYEKHVDEWNIGRLRTILDLV
EKESGITIEGVNTPYLYFGMWKTSFAWHTEDMDLYSINYLHFGEPKSWYS
VPPEHGKRLERLAKGFFPGSAQSCEAFLRHKMTLISPLMLKKYGIPFDKV
TQEAGEFMITFPYGYHAGFNHGFNCAESTNFATRRWIEYGKQAVLCSCRK
DMVKISMDVFVRKFQPERYKLWKAGKDNTVIDHTLPTPEAAEFL
Ligand information
Ligand ID5UB
InChIInChI=1S/C10H6N4OS/c15-10-6-1-2-11-9(7-3-16-5-14-7)8(6)12-4-13-10/h1-5H,(H,12,13,15)
InChIKeyOBJLYJZXQQXIFV-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.4c1cnc(c2c1C(=O)NC=N2)c3cscn3
CACTVS 3.385O=C1NC=Nc2c1ccnc2c3cscn3
FormulaC10 H6 N4 O S
Name8-(1,3-thiazol-4-yl)-3~{H}-pyrido[3,4-d]pyrimidin-4-one
ChEMBLCHEMBL3775636
DrugBank
ZINCZINC000263620826
PDB chain5f39 Chain B 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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PDB5f39 8-Substituted Pyrido[3,4-d]pyrimidin-4(3H)-one Derivatives As Potent, Cell Permeable, KDM4 (JMJD2) and KDM5 (JARID1) Histone Lysine Demethylase Inhibitors.
Resolution2.65 Å
Binding residue
(original residue number in PDB)		Y132 Y177 F185 H188 E190 K206 W208 K241 H276
Binding residue
(residue number reindexed from 1)		Y122 Y167 F175 H178 E180 K196 W198 K231 H266
Annotation score1
Binding affinityBindingDB: IC50=8000nM
Enzymatic activity
Catalytic site (original residue number in PDB) G170 Y177 H188 E190 H276 S288
Catalytic site (residue number reindexed from 1) G160 Y167 H178 E180 H266 S278
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:5f39, PDBe:5f39, PDBj:5f39
PDBsum5f39
PubMed26741168
UniProtO75164|KDM4A_HUMAN Lysine-specific demethylase 4A (Gene Name=KDM4A)

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