Structure of PDB 5ylt Chain A Binding Site BS01

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 IDSFG
InChIInChI=1S/C15H23N7O5/c16-6(1-2-7(17)15(25)26)3-8-10(23)11(24)14(27-8)22-5-21-9-12(18)19-4-20-13(9)22/h4-8,10-11,14,23-24H,1-3,16-17H2,(H,25,26)(H2,18,19,20)/t6-,7-,8+,10+,11+,14+/m0/s1
InChIKeyLMXOHSDXUQEUSF-YECHIGJVSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.0c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)C[C@H](CC[C@@H](C(=O)O)N)N)O)O)N
OpenEye OEToolkits 1.7.0c1nc(c2c(n1)n(cn2)C3C(C(C(O3)CC(CCC(C(=O)O)N)N)O)O)N
CACTVS 3.370N[CH](CC[CH](N)C(O)=O)C[CH]1O[CH]([CH](O)[CH]1O)n2cnc3c(N)ncnc23
CACTVS 3.370N[C@@H](CC[C@H](N)C(O)=O)C[C@H]1O[C@H]([C@H](O)[C@@H]1O)n2cnc3c(N)ncnc23
ACDLabs 12.01O=C(O)C(N)CCC(N)CC3OC(n2cnc1c(ncnc12)N)C(O)C3O
FormulaC15 H23 N7 O5
NameSINEFUNGIN;
ADENOSYL-ORNITHINE
ChEMBLCHEMBL1214186
DrugBankDB01910
ZINCZINC000004217451
PDB chain5ylt Chain A Residue 401 [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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PDB5ylt Development of Novel Inhibitors for Histone Methyltransferase SET7/9 based on Cyproheptadine.
Resolution1.69 Å
Binding residue
(original residue number in PDB)		A226 E228 G264 N265 H293 K294 N296 H297 Y335 W352 E356
Binding residue
(residue number reindexed from 1)		A112 E114 G150 N151 H179 K180 N182 H183 Y221 W235 E239
Annotation score3
Binding affinityBindingDB: IC50=2500nM
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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