Structure of PDB 6h4y Chain B Binding Site BS03

Receptor Information
>6h4y Chain B (length=341) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
ETLNPSARIMTFYPTMEEFRNFSRYIAYIESQGAHRAGLAKVVPPKEWKP
RASYDDIDDLVIPAPIQQLVTGQSGLFTQYNIQKKAMTVREFRKIANSDK
YCTPRYSEFEELERKYWKNLTFNPPIYGADVNGTLYEKHVDEWNIGRLRT
ILDLVEGVNTPYLYFGMWKTSFAWHTEDMDLYSINYLHFGEPKSWYSVPP
EHGKRLERLAKGFFPGSAQSCEAFLRHKMTLISPLMLKKYGIPFDKVTQE
AGEFMITFPYGYHAGFNHGFNCAESTNFATRRWIEYGKQAVLCSCRKDMV
KISMDVFVRKFQPERYKLWKAGKDNTVIDHTLPTPEAAEFL
Ligand information
Ligand IDFO8
InChIInChI=1S/C29H35N7O2/c37-29-26-5-10-30-28(27(26)31-21-32-29)36-20-23(19-33-36)7-12-34-13-8-25(9-14-34)24-3-1-22(2-4-24)6-11-35-15-17-38-18-16-35/h1-5,10,19-21,25H,6-9,11-18H2,(H,31,32,37)
InChIKeyNLYFSJWBMSCWSU-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.6c1cc(ccc1CCN2CCOCC2)C3CCN(CC3)CCc4cnn(c4)c5c6c(ccn5)C(=O)NC=N6
CACTVS 3.385O=C1NC=Nc2c(nccc12)n3cc(CCN4CCC(CC4)c5ccc(CCN6CCOCC6)cc5)cn3
FormulaC29 H35 N7 O2
Name8-[4-[2-[4-[4-(2-morpholin-4-ylethyl)phenyl]piperidin-1-yl]ethyl]pyrazol-1-yl]-3~{H}-pyrido[3,4-d]pyrimidin-4-one
ChEMBLCHEMBL4466130
DrugBank
ZINC
PDB chain6h4y 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

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PDB6h4y 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 Y175 Y177 F185 H188 E190 K206 W208 H276
Binding residue
(residue number reindexed from 1)		Y127 Y162 Y164 F172 H175 E177 K193 W195 H263
Annotation score1
Binding affinityMOAD: ic50=0.077uM
BindingDB: IC50=77nM
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:6h4y, PDBe:6h4y, PDBj:6h4y
PDBsum6h4y
PubMed31158747
UniProtO75164|KDM4A_HUMAN Lysine-specific demethylase 4A (Gene Name=KDM4A)

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