Structure of PDB 6h4t Chain D Binding Site BS03

Receptor Information
>6h4t Chain D (length=342) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SETLNPSARIMTFYPTMEEFRNFSRYIAYIESQGAHRAGLAKVVPPKEWK
PRASYDDIDDLVIPAPIQQLVTGQSGLFTQYNIQKKAMTVREFRKIANSD
KYCTPRYSEFEELERKYWKNLTFNPPIYGADVNGTLYEKHVDEWNIGRLR
TILDLVEKEGVNTPYLYFGMWKTSFAWHTEDMDLYSINYLHFGEPKSWYS
VPPEHGKRLERLAKGFFPGSAQSCEAFLRHKMTLISPLMLKKYGIPFDKV
TQEAGEFMITFPYGYHAGFNHGFNCAESTNFATRRWIEYGKQAVLCSCDM
VKISMDVFVRKFQPERYKLWKAGKDNTVIDHTLPTPEAAEFL
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 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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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 D135 Y175 Y177 F185 H188 E190 K206 W208 K241 H276
Binding residue
(residue number reindexed from 1)		Y128 D131 Y165 Y167 F175 H178 E180 K196 W198 K231 H266
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) 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:6h4t, PDBe:6h4t, PDBj:6h4t
PDBsum6h4t
PubMed31158747
UniProtO75164|KDM4A_HUMAN Lysine-specific demethylase 4A (Gene Name=KDM4A)

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