Structure of PDB 8fs2 Chain B Binding Site BS03

Receptor Information
>8fs2 Chain B (length=551) Species: 1496 (Clostridioides difficile) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SGIYYTPKIIVDYIVKKTLKNHDIIKNPYPRILDISCGCGNFLLEVYDIL
YDLFEENIYELKKKYDENYWTVDNIHRHILNYCIYGADIDEKAISILKDS
LTNKKVVNDLDESDIKINLFCCDSLKKKWRYKFDYIVGNPPYIGHKKLEK
KYKKFLLEKYSEVYKDKADLYFCFYKKIIDILKQGGIGSVITPRYFLESL
SGKDLREYIKSNVNVQEIVDFLGANIFKNIGVSSCILTFDKKKTKETYID
VFKIKNEDICINKFETLEELLKSSKFEHFNINQRLLSDEWILVNKDDETF
YNKIQEKCKYSLEDIAISFQGIITGCDKAFILSKDDVKLNLVDDKFLKCW
IKSKNINKYIVDKSEYRLIYSNDIDNENTNKRILDEIIGLYKTKLENRRE
CKSGIRKWYELQWGREKLFFERKKIMYPYKSNENRFAIDYDNNFSSADVY
SFFIKEEYLDKFSYEYLVGILNSSVYDKYFKITAKKMSKNIYDYYPNKVM
KIRIFRDNNYEEIENLSKQIISILLNKSIDKGKVEKLQIKMDNLIMDSLG
I
Ligand information
Ligand IDYB5
InChIInChI=1S/C30H44N8O3S/c31-30(34-17-22-11-5-2-6-12-22)33-15-8-16-42-18-23-25(39)26(40)29(41-23)38-20-37-24-27(35-19-36-28(24)38)32-14-7-13-21-9-3-1-4-10-21/h1,3-4,9-10,19-20,22-23,25-26,29,39-40H,2,5-8,11-18H2,(H3,31,33,34)(H,32,35,36)/t23-,25-,26-,29-/m1/s1
InChIKeyIFVSTAFZZAWVFJ-CTDWIVFPSA-N
SMILES
SoftwareSMILES
CACTVS 3.385O[CH]1[CH](O)[CH](O[CH]1CSCCCNC(=N)NCC2CCCCC2)n3cnc4c(NCCCc5ccccc5)ncnc34
CACTVS 3.385O[C@H]1[C@@H](O)[C@@H](O[C@@H]1CSCCCNC(=N)NCC2CCCCC2)n3cnc4c(NCCCc5ccccc5)ncnc34
ACDLabs 12.01N=C(NCC1CCCCC1)NCCCSCC1OC(n2cnc3c(NCCCc4ccccc4)ncnc32)C(O)C1O
OpenEye OEToolkits 2.0.7c1ccc(cc1)CCCNc2c3c(ncn2)n(cn3)C4C(C(C(O4)CSCCCNC(=N)NCC5CCCCC5)O)O
OpenEye OEToolkits 2.0.7[H]/N=C(/NCCCSC[C@@H]1[C@H]([C@H]([C@@H](O1)n2cnc3c2ncnc3NCCCc4ccccc4)O)O)\NCC5CCCCC5
FormulaC30 H44 N8 O3 S
Name5'-S-{3-[N'-(cyclohexylmethyl)carbamimidamido]propyl}-N-(3-phenylpropyl)-5'-thioadenosine
ChEMBL
DrugBank
ZINC
PDB chain8fs2 Chain B Residue 605 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB8fs2 Comparative Study of Adenosine Analogs as Inhibitors of Protein Arginine Methyltransferases and a Clostridioides difficile- Specific DNA Adenine Methyltransferase.
Resolution2.59 Å
Binding residue
(original residue number in PDB)		Y30 S62 D114 I115 D149 S150 P167 Y178 F200
Binding residue
(residue number reindexed from 1)		Y4 S36 D88 I89 D123 S124 P141 Y152 F174
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:8fs2, PDBe:8fs2, PDBj:8fs2
PDBsum8fs2
PubMed37082867
UniProtQ183J3

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