Structure of PDB 6h4u Chain A Binding Site BS03

Receptor Information
>6h4u Chain A (length=341) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
LNPSARIMTFYPTMEEFRNFSRYIAYIESQGAHRAGLAKVVPPKEWKPRA
SYDDIDDLVIPAPIQQLVTGQSGLFTQYNIQKKAMTVREFRKIANSDKYC
TPRYSEFEELERKYWKNLTFNPPIYGADVNGTLYEKHVDEWNIGRLRTIL
DLVEKESEGVNTPYLYFGMWKTSFAWHTEDMDLYSINYLHFGEPKSWYSV
PPEHGKRLERLAKGFFPGSAQSCEAFLRHKMTLISPLMLKKYGIPFDKVT
QEAGEFMITFPYGYHAGFNHGFNCAESTNFATRRWIEYGKQAVLCSCRDM
VKISMDVFVRKFQPERYKLWKAGKDNTVIDHTLPTPEAAEF
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 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]
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 D135 Y177 F185 H188 E190 K206 W208 H276
Binding residue
(residue number reindexed from 1)		Y125 D128 Y166 F174 H177 E179 K195 W197 H265
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=6.16,IC50=0.693uM
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) G159 Y166 H177 E179 H265 S277
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]