Structure of PDB 6h4o Chain A Binding Site BS03

Receptor Information
>6h4o Chain A (length=338) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
LNPSARIMTFYPTMEEFRNFSRYIAYIESQGAHRAGLAKVVPPKEWKPRA
SYDDIDDLVIPAPIQQLVTGQSGLFTQYNIQKKAMTVREFRKIANSDKYC
TPRYSEFEELERKYWKNLTFNPPIYGADVNGTLYEKHVDEWNIGRLRTIL
DLVEGVNTPYLYFGMWKTSFAWHTEDMDLYSINYLHFGEPKSWYSVPPEH
GKRLERLAKGFFPGSAQSCEAFLRHKMTLISPLMLKKYGIPFDKVTQEAG
EFMITFPYGYHAGFNHGFNCAESTNFATRRWIEYGKQAVLCSCRKMVKIS
MDVFVRKFQPERYKLWKAGKDNTVIDHTLPTPEAAEFL
Ligand information
Ligand IDFQH
InChIInChI=1S/C24H23F3N6O/c25-24(26,27)19-3-1-2-18(12-19)17-6-10-32(11-7-17)9-5-16-13-31-33(14-16)22-21-20(4-8-28-22)23(34)30-15-29-21/h1-4,8,12-15,17H,5-7,9-11H2,(H,29,30,34)
InChIKeyZBLHURFMYIWFIY-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.6c1cc(cc(c1)C(F)(F)F)C2CCN(CC2)CCc3cnn(c3)c4c5c(ccn4)C(=O)NC=N5
CACTVS 3.385FC(F)(F)c1cccc(c1)C2CCN(CC2)CCc3cnn(c3)c4nccc5C(=O)NC=Nc45
FormulaC24 H23 F3 N6 O
Name8-[4-[2-[4-[3-(trifluoromethyl)phenyl]piperidin-1-yl]ethyl]pyrazol-1-yl]-3~{H}-pyrido[3,4-d]pyrimidin-4-one
ChEMBLCHEMBL3775548
DrugBank
ZINCZINC000653730611
PDB chain6h4o 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

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB6h4o C8-substituted pyrido[3,4-d]pyrimidin-4(3H)-ones: Studies towards the identification of potent, cell penetrant Jumonji C domain containing histone lysine demethylase 4 subfamily (KDM4) inhibitors, compound profiling in cell-based target engagement assays.
Resolution2.25 Å
Binding residue
(original residue number in PDB)		Y132 Y177 F185 H188 E190 K206 W208 K241 H276
Binding residue
(residue number reindexed from 1)		Y125 Y162 F170 H173 E175 K191 W193 K226 H261
Annotation score1
Binding affinityMOAD: ic50=0.128uM
PDBbind-CN: -logKd/Ki=6.89,IC50=0.128uM
BindingDB: IC50=128nM
Enzymatic activity
Catalytic site (original residue number in PDB) G170 Y177 H188 E190 H276 S288
Catalytic site (residue number reindexed from 1) G155 Y162 H173 E175 H261 S273
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:6h4o, PDBe:6h4o, PDBj:6h4o
PDBsum6h4o
PubMed31158747
UniProtO75164|KDM4A_HUMAN Lysine-specific demethylase 4A (Gene Name=KDM4A)

[Back to BioLiP]