Structure of PDB 7rfn Chain B Binding Site BS03

Receptor Information
>7rfn Chain B (length=550) Species: 272563 (Clostridioides difficile 630) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
GIYYTPKIIVDYIVKKTLKNHDIIKNPYPRILDISCGCGNFLLEVYDILY
DLFEENIYELKKKYDENYWTVDNIHRHILNYCIYGADIDEKAISILKDSL
TNKKVVNDLDESDIKINLFCCDSLKKKWRYKFDYIVGNPPYIGHKKLEKK
YKKFLLEKYSEVYKDKADLYFCFYKKIIDILKQGGIGSVITPRYFLESLS
GKDLREYIKSNVNVQEIVDFLGANIFKNIGVSSCILTFDKKKTKETYIDV
FKIKNEDICINKFETLEELLKSSKFEHFNINQRLLSDEWILVNKDDETFY
NKIQEKCKYSLEDIAISFQGIITGCDKAFILSKDDVKLNLVDDKFLKCWI
KSKNINKYIVDKSEYRLIYSNDIDNENTNKRILDEIIGLYKTKLENRREC
KSGIRKWYELQWGREKLFFERKKIMYPYKSNENRFAIDYDNNFSSADVYS
FFIKEEYLDKFSYEYLVGILNSSVYDKYFKITAKKMSKNIYDYYPNKVMK
IRIFRDNNYEEIENLSKQIISILLNKSIDKGKVEKLQIKMDNLIMDSLGI
Ligand information
Ligand IDMJ7
InChIInChI=1S/C27H31ClN6O3S/c28-20-8-6-18(7-9-20)19-5-3-4-17(12-19)13-30-10-1-2-11-38-14-21-23(35)24(36)27(37-21)34-16-33-22-25(29)31-15-32-26(22)34/h3-9,12,15-16,21,23-24,27,30,35-36H,1-2,10-11,13-14H2,(H2,29,31,32)/t21-,23-,24-,27-/m1/s1
InChIKeyUDFJXRJYAZANFF-VBHAUSMQSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.7c1cc(cc(c1)c2ccc(cc2)Cl)CNCCCCSC[C@@H]3[C@H]([C@H]([C@@H](O3)n4cnc5c4ncnc5N)O)O
CACTVS 3.385Nc1ncnc2n(cnc12)[CH]3O[CH](CSCCCCNCc4cccc(c4)c5ccc(Cl)cc5)[CH](O)[CH]3O
ACDLabs 12.01C1(OC(C(C1O)O)n3c2ncnc(c2nc3)N)CSCCCCNCc5cc(c4ccc(cc4)Cl)ccc5
CACTVS 3.385Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CSCCCCNCc4cccc(c4)c5ccc(Cl)cc5)[C@@H](O)[C@H]3O
OpenEye OEToolkits 2.0.7c1cc(cc(c1)c2ccc(cc2)Cl)CNCCCCSCC3C(C(C(O3)n4cnc5c4ncnc5N)O)O
FormulaC27 H31 Cl N6 O3 S
Name5'-S-(4-{[(4'-chloro[1,1'-biphenyl]-3-yl)methyl]amino}butyl)-5'-thioadenosine
ChEMBLCHEMBL5185202
DrugBank
ZINC
PDB chain7rfn Chain B Residue 601 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB7rfn Repurposing epigenetic inhibitors to target the Clostridioides difficile- specific DNA adenine methyltransferase and sporulation regulator CamA.
Resolution2.5 Å
Binding residue
(original residue number in PDB)		G28 Y30 I61 D114 I115 D149 S150 P167
Binding residue
(residue number reindexed from 1)		G1 Y3 I34 D87 I88 D122 S123 P140
Annotation score2
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:7rfn, PDBe:7rfn, PDBj:7rfn
PDBsum7rfn
PubMed34523387
UniProtQ183J3

[Back to BioLiP]