Structure of PDB 5f3c Chain B Binding Site BS03

Receptor Information
>5f3c Chain B (length=337) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
PSARIMTFYPTMEEFRNFSRYIAYIESQGAHRAGLAKVVPPKEWKPRASY
DDIDDLVIPAPIQQLVTGQSGLFTQYNIQKKAMTVREFRKIANSDKYCTP
RYSEFEELERKYWKNLTFNPPIYGADVNGTLYEKHVDEWNIGRLRTILDL
VEGVNTPYLYFGMWKTSFAWHTEDMDLYSINYLHFGEPKSWYSVPPEHGK
RLERLAKGFFPGSAQSCEAFLRHKMTLISPLMLKKYGIPFDKVTQEAGEF
MITFPYGYHAGFNHGFNCAESTNFATRRWIEYGKQAVLCSCRKDMVKISM
DVFVRKFQPERYKLWKAGKDNTVIDHTLPTPEAAEFL
Ligand information
Ligand ID5U8
InChIInChI=1S/C20H19FN6O/c1-26(11-14-2-4-16(21)5-3-14)9-7-15-10-25-27(12-15)19-18-17(6-8-22-19)20(28)24-13-23-18/h2-6,8,10,12-13H,7,9,11H2,1H3,(H,23,24,28)
InChIKeyNLGUSOLKPNWPKR-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.385CN(CCc1cnn(c1)c2nccc3C(=O)NC=Nc23)Cc4ccc(F)cc4
OpenEye OEToolkits 2.0.4CN(CCc1cnn(c1)c2c3c(ccn2)C(=O)NC=N3)Cc4ccc(cc4)F
FormulaC20 H19 F N6 O
Name8-[4-[2-[(4-fluorophenyl)methyl-methyl-amino]ethyl]pyrazol-1-yl]-3~{H}-pyrido[3,4-d]pyrimidin-4-one
ChEMBLCHEMBL3774747
DrugBank
ZINCZINC000263620798
PDB chain5f3c 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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PDB5f3c 8-Substituted Pyrido[3,4-d]pyrimidin-4(3H)-one Derivatives As Potent, Cell Permeable, KDM4 (JMJD2) and KDM5 (JARID1) Histone Lysine Demethylase Inhibitors.
Resolution2.06 Å
Binding residue
(original residue number in PDB)		Y132 D135 G170 Y177 F185 H188 E190 K206 W208 K241 H276
Binding residue
(residue number reindexed from 1)		Y123 D126 G153 Y160 F168 H171 E173 K189 W191 K224 H259
Annotation score1
Binding affinityMOAD: ic50=0.9uM
BindingDB: IC50=900nM
Enzymatic activity
Catalytic site (original residue number in PDB) G170 Y177 H188 E190 H276 S288
Catalytic site (residue number reindexed from 1) G153 Y160 H171 E173 H259 S271
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:5f3c, PDBe:5f3c, PDBj:5f3c
PDBsum5f3c
PubMed26741168
UniProtO75164|KDM4A_HUMAN Lysine-specific demethylase 4A (Gene Name=KDM4A)

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