Structure of PDB 5ylt Chain A Binding Site BS02

Receptor Information
>5ylt Chain A (length=247) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
RHGVCWIYYPDGGSLVGEVNEDGEMTGEKIAYVYPDERTALYGKFIDGEM
IEGKLATLMSTEEGRPHFELMPGNSVYHFDKSTSSCISTNALLPDPYESE
RVYVAESLISSAGEGLFSKVAVGPNTVMSFYNGVRITHQEVDSRDWALNG
NTLSLDEETVIDVPEPYNHVSKYCASLGHKANHSFTPNCIYDMFVHPRFG
PIKCIRTLRAVEADEELTVAYGYDHSPPGKSAPEWYQVELKAFQATQ
Ligand information
Ligand IDC7N
InChIInChI=1S/C21H21NO/c1-22-12-10-16(11-13-22)21-19-5-3-2-4-15(19)6-7-17-14-18(23)8-9-20(17)21/h2-9,14,23H,10-13H2,1H3
InChIKeySJMZFTTXPYYBAG-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.385CN1CCC(CC1)=C2c3ccccc3C=Cc4cc(O)ccc24
OpenEye OEToolkits 2.0.6CN1CCC(=C2c3ccccc3C=Cc4c2ccc(c4)O)CC1
FormulaC21 H21 N O
Name2-(1-methylpiperidin-4-ylidene)tricyclo[9.4.0.0^{3,8}]pentadeca-1(11),3(8),4,6,9,12,14-heptaen-6-ol
ChEMBL
DrugBank
ZINC
PDB chain5ylt Chain A Residue 402 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB5ylt Development of Novel Inhibitors for Histone Methyltransferase SET7/9 based on Cyproheptadine.
Resolution1.69 Å
Binding residue
(original residue number in PDB)		N263 G264 T266 Y305 Y335 G336 D338 P341 Y353
Binding residue
(residue number reindexed from 1)		N149 G150 T152 Y191 Y221 G222 D224 P227 Y236
Annotation score1
Binding affinityMOAD: ic50=0.41uM
PDBbind-CN: -logKd/Ki=6.39,IC50=0.41uM
Enzymatic activity
Catalytic site (original residue number in PDB) Y245 H293 H297 Y305 Y335
Catalytic site (residue number reindexed from 1) Y131 H179 H183 Y191 Y221
Enzyme Commision number 2.1.1.364: [histone H3]-lysine(4) N-methyltransferase.
Gene Ontology
Molecular Function
GO:0016279 protein-lysine N-methyltransferase activity
GO:0140945 histone H3K4 monomethyltransferase activity
Biological Process
GO:0006355 regulation of DNA-templated transcription
Cellular Component
GO:0005694 chromosome

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:5ylt, PDBe:5ylt, PDBj:5ylt
PDBsum5ylt
PubMed29882380
UniProtQ8WTS6|SETD7_HUMAN Histone-lysine N-methyltransferase SETD7 (Gene Name=SETD7)

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