Structure of PDB 6h4z Chain A Binding Site BS05

Receptor Information
>6h4z Chain A (length=458) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SMFLPPPECPVFEPSWEEFADPFAFIHKIRPIAEQTGICKVRPPPDWQPP
FACDVDKLHFTPRIQRLNELEAQTRVKARDYTLRTFGEMADAFKSDYFNM
PVHMVPTELVEKEFWRLVSTIEEDVTVEYGADIASKEFGSGFPVRDGIKL
SPEEEEYLDSGWNLNNMPVMEQSVLAHITADICGMKLPWLYVGMCFSSFC
WHIEDHWSYSINYLHWGEPKTWYGVPGYAAEQLENVMKKLAPELFVSQPD
LLHQLVTIMNPNTLMTHEVPVYRTNQCAGEFVITFPRAYHSGFNQGFNFA
EAVNFCTVDWLPLGRQCVEHYRLLHRYCVFSHDEMICKMASKADVLDVVV
ASTVQKDMAIMIEDEKALRETVRKLGVIDSERMDFELLPDDERQCVKCKT
TCFMSAISCSCKPGLLVCLHHVKELCSCPPYKYKLRYRYTLDDLYPMMNA
LKLRAESY
Ligand information
Ligand IDFQ5
InChIInChI=1S/C23H23ClN6O/c24-19-3-1-2-18(12-19)17-6-10-29(11-7-17)9-5-16-13-28-30(14-16)22-21-20(4-8-25-22)23(31)27-15-26-21/h1-4,8,12-15,17H,5-7,9-11H2,(H,26,27,31)
InChIKeyLDSDVQOOEYCWQS-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.6c1cc(cc(c1)Cl)C2CCN(CC2)CCc3cnn(c3)c4c5c(ccn4)C(=O)NC=N5
CACTVS 3.385Clc1cccc(c1)C2CCN(CC2)CCc3cnn(c3)c4nccc5C(=O)NC=Nc45
FormulaC23 H23 Cl N6 O
Name8-[4-[2-[4-(3-chlorophenyl)piperidin-1-yl]ethyl]pyrazol-1-yl]-3~{H}-pyrido[3,4-d]pyrimidin-4-one
ChEMBLCHEMBL3774537
DrugBank
ZINCZINC000653728054
PDB chain6h4z Chain A Residue 805 [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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PDB6h4z 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.
Resolution2.3 Å
Binding residue
(original residue number in PDB)		Y425 D428 C480 W486 Y488 F496 H499 E501 K517 W519 H587
Binding residue
(residue number reindexed from 1)		Y129 D132 C183 W189 Y191 F199 H202 E204 K220 W222 H290
Annotation score1
Binding affinityMOAD: Ki=0.002uM
PDBbind-CN: -logKd/Ki=7.64,IC50=0.023uM
BindingDB: EC50=600nM,Ki=2.0nM,IC50=23nM
Enzymatic activity
Catalytic site (original residue number in PDB) G481 Y488 H499 E501 H587 A599
Catalytic site (residue number reindexed from 1) G184 Y191 H202 E204 H290 A302
Enzyme Commision number 1.14.11.67: [histone H3]-trimethyl-L-lysine(4) demethylase.
External links
PDB RCSB:6h4z, PDBe:6h4z, PDBj:6h4z
PDBsum6h4z
PubMed31158747
UniProtQ9UGL1|KDM5B_HUMAN Lysine-specific demethylase 5B (Gene Name=KDM5B)

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