Structure of PDB 7rfk Chain A Binding Site BS03

Receptor Information
>7rfk Chain A (length=568) Species: 272563 (Clostridioides difficile 630) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
QDNFLLSKEYENSLDVDTKKASGIYYTPKIIVDYIVKKTLKNHDIIKNPY
PRILDISCGCGNFLLEVYDILYDLFEENIYELKKKYDENYWTVDNIHRHI
LNYCIYGADIDEKAISILKDSLTNKKVVESDIKINLFCCDSLKKKWRYKF
DYIVGNPPYIGHKKLEKKYKKFLLEKYSEVYKDKADLYFCFYKKIIDILK
QGGIGSVITPRYFLESLSGKDLREYIKSNVNVQEIVDFLGANIFKNIGVS
SCILTFDKKKTKETYIDVFKIKNEDICINKFETLEELLKSSKFEHFNINQ
RLLSDEWILVNKDDETFYNKIQEKCKYSLEDIAISFQGIITGCDKAFILS
KDDVKLNLVDDKFLKCWIKSKNINKYIVDKSEYRLIYSNDIDNENTNKRI
LDEIIGLYKTKLENRRECKSGIRKWYELQWGREKLFFERKKIMYPYKSNE
NRFAIDYDNNFSSADVYSFFIKEEYLDKFSYEYLVGILNSSVYDKYFKIT
AKKMSKNIYDYYPNKVMKIRIFRDNNYEEIENLSKQIISILLNKSIDKGK
VEKLQIKMDNLIMDSLGI
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 chain7rfk Chain A Residue 601 [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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PDB7rfk Repurposing epigenetic inhibitors to target the Clostridioides difficile- specific DNA adenine methyltransferase and sporulation regulator CamA.
Resolution2.05 Å
Binding residue
(original residue number in PDB)		S27 G28 Y30 Y31 T32 D60 S62 N67 F68 D114 I115 D149 S150 N165 P167
Binding residue
(residue number reindexed from 1)		S22 G23 Y25 Y26 T27 D55 S57 N62 F63 D109 I110 D140 S141 N156 P158
Annotation score3
Enzymatic activity
Enzyme Commision number 2.1.1.72: site-specific DNA-methyltransferase (adenine-specific).
Gene Ontology
Molecular Function
GO:0003676 nucleic acid binding
GO:0008168 methyltransferase activity
GO:0009007 site-specific DNA-methyltransferase (adenine-specific) activity
Biological Process
GO:0006304 DNA modification
GO:0032259 methylation

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:7rfk, PDBe:7rfk, PDBj:7rfk
PDBsum7rfk
PubMed34523387
UniProtQ183J3

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