Structure of PDB 5f3g Chain D Binding Site BS03

Receptor Information
>5f3g Chain D (length=339) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SARIMTFYPTMEEFRNFSRYIAYIESQGAHRAGLAKVVPPKEWKPRASYD
DIDDLVIPAPIQQLVTGQSGLFTQYNIQKKAMTVREFRKIANSDKYCTPR
YSEFEELERKYWKNLTFNPPIYGADVNGTLYEKHVDEWNIGRLRTILDLV
EKESGITIVNTPYLYFGMWKTSFAWHTEDMDLYSINYLHFGEPKSWYSVP
PEHGKRLERLAKGFFPGSAQSCEAFLRHKMTLISPLMLKKYGIPFDKVTQ
EAGEFMITFPYGYHAGFNHGFNCAESTNFATRRWIEYGKQAVLCSCMVKI
SMDVFVRKFQPERYKLWKAGKDNTVIDHTLPTPEAAEFL
Ligand information
Ligand ID5UL
InChIInChI=1S/C24H25ClN6O/c25-20-3-1-17(2-4-20)13-18-6-10-30(11-7-18)12-8-19-14-29-31(15-19)23-22-21(5-9-26-23)24(32)28-16-27-22/h1-5,9,14-16,18H,6-8,10-13H2,(H,27,28,32)
InChIKeyMIHKHZZRKYZHJU-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.4c1cc(ccc1CC2CCN(CC2)CCc3cnn(c3)c4c5c(ccn4)C(=O)NC=N5)Cl
CACTVS 3.385Clc1ccc(CC2CCN(CC2)CCc3cnn(c3)c4nccc5C(=O)NC=Nc45)cc1
FormulaC24 H25 Cl N6 O
Name8-[4-[2-[4-[(4-chlorophenyl)methyl]piperidin-1-yl]ethyl]pyrazol-1-yl]-3~{H}-pyrido[3,4-d]pyrimidin-4-one
ChEMBLCHEMBL3775899
DrugBank
ZINCZINC000263620742
PDB chain5f3g Chain D 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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PDB5f3g 8-Substituted Pyrido[3,4-d]pyrimidin-4(3H)-one Derivatives As Potent, Cell Permeable, KDM4 (JMJD2) and KDM5 (JARID1) Histone Lysine Demethylase Inhibitors.
Resolution2.5 Å
Binding residue
(original residue number in PDB)		Y132 Y177 F185 H188 K206 W208 K241 H276
Binding residue
(residue number reindexed from 1)		Y122 Y165 F173 H176 K194 W196 K229 H264
Annotation score1
Binding affinityMOAD: ic50=0.126uM
BindingDB: IC50=126nM
Enzymatic activity
Catalytic site (original residue number in PDB) Y177 H188 E190 H276 S288
Catalytic site (residue number reindexed from 1) Y165 H176 E178 H264 S276
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:5f3g, PDBe:5f3g, PDBj:5f3g
PDBsum5f3g
PubMed26741168
UniProtO75164|KDM4A_HUMAN Lysine-specific demethylase 4A (Gene Name=KDM4A)

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