Structure of PDB 5f3i Chain A Binding Site BS03

Receptor Information
>5f3i Chain A (length=342) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
ETLNPSARIMTFYPTMEEFRNFSRYIAYIESQGAHRAGLAKVVPPKEWKP
RASYDDIDDLVIPAPIQQLVTGQSGLFTQYNIQKKAMTVREFRKIANSDK
YCTPRYSEFEELERKYWKNLTFNPPIYGADVNGTLYEKHVDEWNIGRLRT
ILDLVEKGVNTPYLYFGMWKTSFAWHTEDMDLYSINYLHFGEPKSWYSVP
PEHGKRLERLAKGFFPGSAQSCEAFLRHKMTLISPLMLKKYGIPFDKVTQ
EAGEFMITFPYGYHAGFNHGFNCAESTNFATRRWIEYGKQAVLCSCRKMV
KISMDVFVRKFQPERYKLWKAGKDNTVIDHTLPTPEAAEFLK
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 A 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 Y177 F185 H188 E190 K206 W208 K241 H276
Binding residue
(residue number reindexed from 1)		Y127 Y165 F173 H176 E178 K194 W196 K229 H264
Annotation score1
Binding affinityMOAD: ic50=0.08uM
PDBbind-CN: -logKd/Ki=7.10,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) G158 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:5f3i, PDBe:5f3i, PDBj:5f3i
PDBsum5f3i
PubMed26741168
UniProtO75164|KDM4A_HUMAN Lysine-specific demethylase 4A (Gene Name=KDM4A)

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