Structure of PDB 8fs1 Chain A Binding Site BS03

Receptor Information
>8fs1 Chain A (length=544) Species: 1496 (Clostridioides difficile) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
YYTPKIIVDYIVKKTLKNHDIIKNPYPRILDISCGCGNFLLEVYDILYDL
FEENIYELKKKYDENYWTVDNIHRHILNYCIYGADIDEKAISILKDSLTN
KKVDESDIKINLFCCDSLKKKWRYKFDYIVGNPPYIGHKKLEKKYKKFLL
EKYSEVYKDKADLYFCFYKKIIDILKQGGIGSVITPRYFLESLSGKDLRE
YIKSNVNVQEIVDFLGANIFKNIGVSSCILTFDKKKTKETYIDVFKIKNE
DICINKFETLEELLKSSKFEHFNINQRLLSDEWILVNKDDETFYNKIQEK
CKYSLEDIAISFQGIITGCDKAFILSKDDVKLNLVDDKFLKCWIKSKNIN
KYIVDKSEYRLIYSNDIDNENTNKRILDEIIGLYKTKLENRRECKSGIRK
WYELQWGREKLFFERKKIMYPYKSNENRFAIDYDNNFSSADVYSFFIKEE
YLDKFSYEYLVGILNSSVYDKYFKITAKKMSKNIYDYYPNKVMKIRIFRD
NNYEEIENLSKQIISILLNKSIDKGKVEKLQIKMDNLIMDSLGI
Ligand information
Ligand IDYB0
InChIInChI=1S/C29H42N8O3S/c30-29(33-16-21-10-5-2-6-11-21)32-14-15-41-17-22-24(38)25(39)28(40-22)37-19-36-23-26(34-18-35-27(23)37)31-13-7-12-20-8-3-1-4-9-20/h1,3-4,8-9,18-19,21-22,24-25,28,38-39H,2,5-7,10-17H2,(H3,30,32,33)(H,31,34,35)/t22-,24-,25-,28-/m1/s1
InChIKeyIJAWJZSCQJWFLW-ZYWWQZICSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.7c1ccc(cc1)CCCNc2c3c(ncn2)n(cn3)C4C(C(C(O4)CSCCNC(=N)NCC5CCCCC5)O)O
CACTVS 3.385O[CH]1[CH](O)[CH](O[CH]1CSCCNC(=N)NCC2CCCCC2)n3cnc4c(NCCCc5ccccc5)ncnc34
ACDLabs 12.01N=C(NCC1CCCCC1)NCCSCC1OC(n2cnc3c(NCCCc4ccccc4)ncnc32)C(O)C1O
CACTVS 3.385O[C@H]1[C@@H](O)[C@@H](O[C@@H]1CSCCNC(=N)NCC2CCCCC2)n3cnc4c(NCCCc5ccccc5)ncnc34
OpenEye OEToolkits 2.0.7[H]/N=C(/NCCSC[C@@H]1[C@H]([C@H]([C@@H](O1)n2cnc3c2ncnc3NCCCc4ccccc4)O)O)\NCC5CCCCC5
FormulaC29 H42 N8 O3 S
Name5'-S-{2-[N'-(cyclohexylmethyl)carbamimidamido]ethyl}-N-(3-phenylpropyl)-5'-thioadenosine
ChEMBL
DrugBank
ZINC
PDB chain8fs1 Chain A Residue 602 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB8fs1 Comparative Study of Adenosine Analogs as Inhibitors of Protein Arginine Methyltransferases and a Clostridioides difficile- Specific DNA Adenine Methyltransferase.
Resolution2.74 Å
Binding residue
(original residue number in PDB)		Y30 S62 D114 I115 D149 S150 P167 Y178 F200
Binding residue
(residue number reindexed from 1)		Y1 S33 D85 I86 D116 S117 P134 Y145 F167
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

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Molecular Function
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Biological Process
External links
PDB RCSB:8fs1, PDBe:8fs1, PDBj:8fs1
PDBsum8fs1
PubMed37082867
UniProtQ183J3

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