Structure of PDB 6h4x Chain D Binding Site BS03

Receptor Information
>6h4x Chain D (length=337) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
PSARIMTFYPTMEEFRNFSRYIAYIESQGAHRAGLAKVVPPKEWKPRASY
DDIDDLVIPAPIQQLVTGQSGLFTQYNIQKKAMTVREFRKIANSDKYCTP
RYSEFEELERKYWKNLTFNPPIYGADVNGTLYEKHVDEWNIGRLRTILDL
VEGVNTPYLYFGMWKTSFAWHTEDMDLYSINYLHFGEPKSWYSVPPEHGK
RLERLAKGFFPGSAQSCEAFLRHKMTLISPLMLKKYGIPFDKVTQEAGEF
MITFPYGYHAGFNHGFNCAESTNFATRRWIEYGKQAVLCSCRKDMVKISM
DVFVRKFQPERYKLWKAGKDNTVIDHTLPTPEAAEFL
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 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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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 Y175 Y177 F185 H188 E190 K206 W208 H276
Binding residue
(residue number reindexed from 1)		Y123 Y158 Y160 F168 H171 E173 K189 W191 H259
Annotation score1
Binding affinityMOAD: 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) G153 Y160 H171 E173 H259 S271
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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