Structure of PDB 6h52 Chain A Binding Site BS05

Receptor Information
>6h52 Chain A (length=457) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SMFLPPPECPVFEPSWEEFADPFAFIHKIRPIAEQTGICKVRPPPDWQPP
FACDVDKLHFTPRIQRLNELEAQTRVKRDYTLRTFGEMADAFKSDYFNMP
VHMVPTELVEKEFWRLVSTIEEDVTVEYGADIASKEFGSGFPVRDGIKLS
PEEEEYLDSGWNLNNMPVMEQSVLAHITADICGMKLPWLYVGMCFSSFCW
HIEDHWSYSINYLHWGEPKTWYGVPGYAAEQLENVMKKLAPELFVSQPDL
LHQLVTIMNPNTLMTHEVPVYRTNQCAGEFVITFPRAYHSGFNQGFNFAE
AVNFCTVDWLPLGRQCVEHYRLLHRYCVFSHDEMICKMASKADVLDVVVA
STVQKDMAIMIEDEKALRETVRKLGVIDSERMDFELLPDDERQCVKCKTT
CFMSAISCSCKPGLLVCLHHVKELCSCPPYKYKLRYRYTLDDLYPMMNAL
KLRAESY
Ligand information
Ligand IDFQN
InChIInChI=1S/C20H24N6O/c27-20-17-5-8-21-19(18(17)22-13-23-20)26-12-15(11-24-26)14-6-9-25(10-7-14)16-3-1-2-4-16/h5,8,11-14,16H,1-4,6-7,9-10H2,(H,22,23,27)
InChIKeyXYBBSEAKIBCXQV-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.385O=C1NC=Nc2c1ccnc2n3cc(cn3)C4CCN(CC4)C5CCCC5
OpenEye OEToolkits 2.0.6c1cnc(c2c1C(=O)NC=N2)n3cc(cn3)C4CCN(CC4)C5CCCC5
FormulaC20 H24 N6 O
Name8-[4-(1-cyclopentylpiperidin-4-yl)pyrazol-1-yl]-3~{H}-pyrido[3,4-d]pyrimidin-4-one
ChEMBLCHEMBL4529932
DrugBank
ZINC
PDB chain6h52 Chain A Residue 813 [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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PDB6h52 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.
Resolution2.14 Å
Binding residue
(original residue number in PDB)		Y425 W486 Y488 F496 H499 E501 K517 W519 H587
Binding residue
(residue number reindexed from 1)		Y128 W188 Y190 F198 H201 E203 K219 W221 H289
Annotation score1
Binding affinityMOAD: ic50=0.068uM
PDBbind-CN: -logKd/Ki=7.17,IC50=0.068uM
BindingDB: IC50=68nM
Enzymatic activity
Catalytic site (original residue number in PDB) G481 Y488 H499 E501 H587 A599
Catalytic site (residue number reindexed from 1) G183 Y190 H201 E203 H289 A301
Enzyme Commision number 1.14.11.67: [histone H3]-trimethyl-L-lysine(4) demethylase.
External links
PDB RCSB:6h52, PDBe:6h52, PDBj:6h52
PDBsum6h52
PubMed31158747
UniProtQ9UGL1|KDM5B_HUMAN Lysine-specific demethylase 5B (Gene Name=KDM5B)

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