Structure of PDB 6h4u Chain B Binding Site BS03

Receptor Information
>6h4u Chain B (length=348) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
ETLNPSARIMTFYPTMEEFRNFSRYIAYIESQGAHRAGLAKVVPPKEWKP
RASYDDIDDLVIPAPIQQLVTGQSGLFTQYNIQKKAMTVREFRKIANSDK
YCTPRYSEFEELERKYWKNLTFNPPIYGADVNGTLYEKHVDEWNIGRLRT
ILDLVEKESGITIEGVNTPYLYFGMWKTSFAWHTEDMDLYSINYLHFGEP
KSWYSVPPEHGKRLERLAKGFFPGSAQSCEAFLRHKMTLISPLMLKKYGI
PFDKVTQEAGEFMITFPYGYHAGFNHGFNCAESTNFATRRWIEYGKQAVL
CSCRKDMVKISMDVFVRKFQPERYKLWKAGKDNTVIDHTLPTPEAAEF
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 chain6h4u Chain B 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]
PDB6h4u 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.
Resolution2.21 Å
Binding residue
(original residue number in PDB)		Y132 Y175 Y177 F185 H188 E190 K206 W208
Binding residue
(residue number reindexed from 1)		Y127 Y170 Y172 F180 H183 E185 K201 W203
Annotation score1
Binding affinityBindingDB: IC50=2060nM
Enzymatic activity
Catalytic site (original residue number in PDB) G170 Y177 H188 E190 H276 S288
Catalytic site (residue number reindexed from 1) G165 Y172 H183 E185 H271 S283
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:6h4u, PDBe:6h4u, PDBj:6h4u
PDBsum6h4u
PubMed31158747
UniProtO75164|KDM4A_HUMAN Lysine-specific demethylase 4A (Gene Name=KDM4A)

[Back to BioLiP]