Structure of PDB 5f3i Chain C Binding Site BS03

Receptor Information
>5f3i Chain C (length=342) 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
TQEAGEFMITFPYGYHAGFNHGFNCAESTNFATRRWIEYGKQAVLCSCRM
VKISMDVFVRKFQPERYKLWKAGKDNTVIDHTLPTPEAAEFL
Ligand information
Ligand ID5UJ
InChIInChI=1S/C23H22Cl2N6O/c24-18-9-17(10-19(25)11-18)16-3-7-30(8-4-16)6-2-15-12-29-31(13-15)22-21-20(1-5-26-22)23(32)28-14-27-21/h1,5,9-14,16H,2-4,6-8H2,(H,27,28,32)
InChIKeyRLRGPZGIQMEBLC-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.385Clc1cc(Cl)cc(c1)C2CCN(CC2)CCc3cnn(c3)c4nccc5C(=O)NC=Nc45
OpenEye OEToolkits 2.0.4c1cnc(c2c1C(=O)NC=N2)n3cc(cn3)CCN4CCC(CC4)c5cc(cc(c5)Cl)Cl
FormulaC23 H22 Cl2 N6 O
Name8-[4-[2-[4-[3,5-bis(chloranyl)phenyl]piperidin-1-yl]ethyl]pyrazol-1-yl]-3~{H}-pyrido[3,4-d]pyrimidin-4-one
ChEMBLCHEMBL3775894
DrugBank
ZINCZINC000263620975
PDB chain5f3i Chain C 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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PDB5f3i 8-Substituted Pyrido[3,4-d]pyrimidin-4(3H)-one Derivatives As Potent, Cell Permeable, KDM4 (JMJD2) and KDM5 (JARID1) Histone Lysine Demethylase Inhibitors.
Resolution2.24 Å
Binding residue
(original residue number in PDB)		Y132 E169 Y177 F185 H188 E190 D191 K206 W208 K241 H276 V313
Binding residue
(residue number reindexed from 1)		Y122 E159 Y167 F175 H178 E180 D181 K196 W198 K231 H266 V301
Annotation score1
Binding affinityMOAD: ic50=0.08uM
BindingDB: IC50=80nM
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:5f3i, PDBe:5f3i, PDBj:5f3i
PDBsum5f3i
PubMed26741168
UniProtO75164|KDM4A_HUMAN Lysine-specific demethylase 4A (Gene Name=KDM4A)

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