Structure of PDB 6h4q Chain D Binding Site BS03

Receptor Information
>6h4q Chain D (length=344) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
NPSARIMTFYPTMEEFRNFSRYIAYIESQGAHRAGLAKVVPPKEWKPRAS
YDDIDDLVIPAPIQQLVTGQSGLFTQYNIQKKAMTVREFRKIANSDKYCT
PRYSEFEELERKYWKNLTFNPPIYGADVNGTLYEKHVDEWNIGRLRTILD
LVEKESGITIEGVNTPYLYFGMWKTSFAWHTEDMDLYSINYLHFGEPKSW
YSVPPEHGKRLERLAKGFFPGSAQSCEAFLRHKMTLISPLMLKKYGIPFD
KVTQEAGEFMITFPYGYHAGFNHGFNCAESTNFATRRWIEYGKQAVLCSC
RMVKISMDVFVRKFQPERYKLWKAGKDNTVIDHTLPTPEAAEFL
Ligand information
Ligand IDFO2
InChIInChI=1S/C16H18N6O/c1-21-6-3-11(4-7-21)12-8-20-22(9-12)15-14-13(2-5-17-15)16(23)19-10-18-14/h2,5,8-11H,3-4,6-7H2,1H3,(H,18,19,23)
InChIKeyWDLBUONJQGHSKT-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.6CN1CCC(CC1)c2cnn(c2)c3c4c(ccn3)C(=O)NC=N4
CACTVS 3.385CN1CCC(CC1)c2cnn(c2)c3nccc4C(=O)NC=Nc34
FormulaC16 H18 N6 O
Name8-[4-(1-methylpiperidin-4-yl)pyrazol-1-yl]-3~{H}-pyrido[3,4-d]pyrimidin-4-one
ChEMBLCHEMBL4483780
DrugBank
ZINC
PDB chain6h4q 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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PDB6h4q 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.
Resolution2.31 Å
Binding residue
(original residue number in PDB)		Y132 G170 Y177 F185 H188 E190 D191 K206 W208 K241 H276
Binding residue
(residue number reindexed from 1)		Y124 G162 Y169 F177 H180 E182 D183 K198 W200 K233 H268
Annotation score1
Binding affinityMOAD: ic50=2.06uM
BindingDB: IC50=2060nM
Enzymatic activity
Catalytic site (original residue number in PDB) G170 Y177 H188 E190 H276 S288
Catalytic site (residue number reindexed from 1) G162 Y169 H180 E182 H268 S280
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:6h4q, PDBe:6h4q, PDBj:6h4q
PDBsum6h4q
PubMed31158747
UniProtO75164|KDM4A_HUMAN Lysine-specific demethylase 4A (Gene Name=KDM4A)

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