Structure of PDB 6h4x Chain A Binding Site BS03

Receptor Information
>6h4x Chain A (length=340) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
ETLNPSARIMTFYPTMEEFRNFSRYIAYIESQGAHRAGLAKVVPPKEWKP
RASYDDIDDLVIPAPIQQLVTGQSGLFTQYNIQKKAMTVREFRKIANSDK
YCTPRYSEFEELERKYWKNLTFNPPIYGADVNGTLYEKHVDEWNIGRLRT
ILDLVEEGVNTPYLYFGMWKTSFAWHTEDMDLYSINYLHFGEPKSWYSVP
PEHGKRLERLAKGFFPGSAQSCEAFLRHKMTLISPLMLKKYGIPFDKVTQ
EAGEFMITFPYGYHAGFNHGFNCAESTNFATRRWIEYGKQAVLCSCRMVK
ISMDVFVRKFQPERYKLWKAGKDNTVIDHTLPTPEAAEFL
Ligand information
Ligand IDFNQ
InChIInChI=1S/C28H27N7O/c36-28-25-7-12-30-27(26(25)31-19-32-28)35-18-20(16-33-35)8-13-34-14-9-23(10-15-34)21-3-5-22(6-4-21)24-2-1-11-29-17-24/h1-7,11-12,16-19,23H,8-10,13-15H2,(H,31,32,36)
InChIKeyJRDMCDIQZVMPPB-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.6c1cc(cnc1)c2ccc(cc2)C3CCN(CC3)CCc4cnn(c4)c5c6c(ccn5)C(=O)NC=N6
CACTVS 3.385O=C1NC=Nc2c1ccnc2n3cc(CCN4CCC(CC4)c5ccc(cc5)c6cccnc6)cn3
FormulaC28 H27 N7 O
Name8-[4-[2-[4-(4-pyridin-3-ylphenyl)piperidin-1-yl]ethyl]pyrazol-1-yl]-3~{H}-pyrido[3,4-d]pyrimidin-4-one
ChEMBLCHEMBL4559561
DrugBank
ZINC
PDB chain6h4x 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

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PDB6h4x 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.
Resolution2.34 Å
Binding residue
(original residue number in PDB)		Y132 Y177 F185 H188 E190 K206 W208 K241
Binding residue
(residue number reindexed from 1)		Y127 Y165 F173 H176 E178 K194 W196 K229
Annotation score1
Binding affinityMOAD: ic50=0.131uM
PDBbind-CN: -logKd/Ki=6.88,IC50=0.131uM
BindingDB: IC50=131nM
Enzymatic activity
Catalytic site (original residue number in PDB) G170 Y177 H188 E190 H276 S288
Catalytic site (residue number reindexed from 1) G158 Y165 H176 E178 H264 S276
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:6h4x, PDBe:6h4x, PDBj:6h4x
PDBsum6h4x
PubMed31158747
UniProtO75164|KDM4A_HUMAN Lysine-specific demethylase 4A (Gene Name=KDM4A)

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