Structure of PDB 5f3e Chain B Binding Site BS03

Receptor Information
>5f3e Chain B (length=335) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
TLNPSARIMTFYPTMEEFRNFSRYIAYIESQGAHRAGLAKVVPPKEWKPR
ASYDDIDDLVIPAPIQQLVTGQSGLFTQYNIQKKAMTVREFRKIANSDKY
CTPRYSEFEELERKYWKNLTFNPPIYGADVNGTLYEKHVDEWNIGRLRTI
LDLVVNTPYLYFGMWKTSFAWHTEDMDLYSINYLHFGEPKSWYSVPPEHG
KRLERLAKGFFPGSAQSCEAFLRHKMTLISPLMLKKYGIPFDKVTQEAGE
FMITFPYGYHAGFNHGFNCAESTNFATRRWIEYGKQAVLCSCRMVKISMD
VFVRKFQPERYKLWKAGKDNTVIDHTLPTPEAAEF
Ligand information
Ligand ID5UO
InChIInChI=1S/C23H23ClN6O/c24-19-3-1-17(2-4-19)18-7-11-29(12-8-18)10-6-16-13-28-30(14-16)22-21-20(5-9-25-22)23(31)27-15-26-21/h1-5,9,13-15,18H,6-8,10-12H2,(H,26,27,31)
InChIKeySQDIBEJSOSAPGF-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.4c1cc(ccc1C2CCN(CC2)CCc3cnn(c3)c4c5c(ccn4)C(=O)NC=N5)Cl
CACTVS 3.385Clc1ccc(cc1)C2CCN(CC2)CCc3cnn(c3)c4nccc5C(=O)NC=Nc45
FormulaC23 H23 Cl N6 O
Name8-[4-[2-[4-(4-chlorophenyl)piperidin-1-yl]ethyl]pyrazol-1-yl]-3~{H}-pyrido[3,4-d]pyrimidin-4-one
ChEMBLCHEMBL3775977
DrugBank
ZINCZINC000263621056
PDB chain5f3e 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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PDB5f3e 8-Substituted Pyrido[3,4-d]pyrimidin-4(3H)-one Derivatives As Potent, Cell Permeable, KDM4 (JMJD2) and KDM5 (JARID1) Histone Lysine Demethylase Inhibitors.
Resolution2.16 Å
Binding residue
(original residue number in PDB)		Y132 D135 Y175 Y177 F185 H188 E190 K206 W208 H276
Binding residue
(residue number reindexed from 1)		Y126 D129 Y159 Y161 F169 H172 E174 K190 W192 H260
Annotation score1
Binding affinityMOAD: ic50=0.138uM
BindingDB: IC50=138nM
Enzymatic activity
Catalytic site (original residue number in PDB) Y177 H188 E190 H276 S288
Catalytic site (residue number reindexed from 1) Y161 H172 E174 H260 S272
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:5f3e, PDBe:5f3e, PDBj:5f3e
PDBsum5f3e
PubMed26741168
UniProtO75164|KDM4A_HUMAN Lysine-specific demethylase 4A (Gene Name=KDM4A)

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