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BioLiP

Structure of PDB 6h4t Chain C Binding Site BS03

Receptor Information
>6h4t Chain C (length=338) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
PSARIMTFYPTMEEFRNFSRYIAYIESQGAHRAGLAKVVPPKEWKPRASY
DDIDDLVIPAPIQQLVTGQSGLFTQYNIQKKAMTVREFRKIANSDKYCTP
RYSEFEELERKYWKNLTFNPPIYGADVNGTLYEKHVDEWNIGRLRTILDL
VEKESEGVNTPYLYFGMWKTSFAWHTEDMDLYSINYLHFGEPKSWYSVPP
EHGKRLERLAKGFFPGSAQSCEAFLRHKMTLISPLMLKKYGIPFDKVTQE
AGEFMITFPYGYHAGFNHGFNCAESTNFATRRWIEYGKQAVLCSCRVKIS
MDVFVRKFQPERYKLWKAGKDNTVIDHTLPTPEAAEFL
Ligand information
Ligand IDFOW
InChIInChI=1S/C25H26N6O/c32-24-20-6-11-26-23(22(20)27-17-28-24)31-16-18(15-29-31)7-12-30-13-9-25(10-14-30)8-5-19-3-1-2-4-21(19)25/h1-4,6,11,15-17H,5,7-10,12-14H2,(H,27,28,32)
InChIKeyAVFIHINZEZRGBL-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.6c1ccc2c(c1)CCC23CCN(CC3)CCc4cnn(c4)c5c6c(ccn5)C(=O)NC=N6
CACTVS 3.385O=C1NC=Nc2c1ccnc2n3cc(CCN4CCC5(CC4)CCc6ccccc56)cn3
FormulaC25 H26 N6 O
Name8-[4-(2-spiro[1,2-dihydroindene-3,4'-piperidine]-1'-ylethyl)pyrazol-1-yl]-3~{H}-pyrido[3,4-d]pyrimidin-4-one
ChEMBLCHEMBL4449500
DrugBank
ZINC
PDB chain6h4t 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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PDB6h4t 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.
Resolution2.38 Å
Binding residue
(original residue number in PDB)		Y132 Y177 F185 H188 E190 K206 W208 H276
Binding residue
(residue number reindexed from 1)		Y123 Y164 F172 H175 E177 K193 W195 H263
Annotation score1
Binding affinityMOAD: Ki=0.004uM
BindingDB: IC50=423nM,EC50=4700nM,Ki=4.0nM
Enzymatic activity
Catalytic site (original residue number in PDB) G170 Y177 H188 E190 H276 S288
Catalytic site (residue number reindexed from 1) G157 Y164 H175 E177 H263 S275
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:6h4t, PDBe:6h4t, PDBj:6h4t
PDBsum6h4t
PubMed31158747
UniProtO75164|KDM4A_HUMAN Lysine-specific demethylase 4A (Gene Name=KDM4A)

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