Structure of PDB 8cy1 Chain A Binding Site BS03

Receptor Information
>8cy1 Chain A (length=546) Species: 1496 (Clostridioides difficile) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
GIYYTPKIIVDYIVKKTLKNHDIIKNPYPRILDISCGCGNFLLEVYDILY
DLFEENIYELKKKYDENYWTVDNIHRHILNYCIYGADIDEKAISILKDSL
TNKKVDESDIKINLFCCDSLKKKWRYKFDYIVGNPPYIGHKKLEKKYKKF
LLEKYSEVYKDKADLYFCFYKKIIDILKQGGIGSVITPRYFLESLSGKDL
REYIKSNVNVQEIVDFLGANIFKNIGVSSCILTFDKKKTKETYIDVFKIK
NEDICINKFETLEELLKSSKFEHFNINQRLLSDEWILVNKDDETFYNKIQ
EKCKYSLEDIAISFQGIITGCDKAFILSKDDVKLNLVDDKFLKCWIKSKN
INKYIVDKSEYRLIYSNDIDNENTNKRILDEIIGLYKTKLENRRECKSGI
RKWYELQWGREKLFFERKKIMYPYKSNENRFAIDYDNNFSSADVYSFFIK
EEYLDKFSYEYLVGILNSSVYDKYFKITAKKMSKNIYDYYPNKVMKIRIF
RDNNYEEIENLSKQIISILLNKSIDKGKVEKLQIKMDNLIMDSLGI
Ligand information
Ligand IDQBU
InChIInChI=1S/C21H27N5O4/c27-11-15-17(28)18(29)21(30-15)26-13-25-16-19(23-12-24-20(16)26)22-10-6-2-5-9-14-7-3-1-4-8-14/h1,3-4,7-8,12-13,15,17-18,21,27-29H,2,5-6,9-11H2,(H,22,23,24)/t15-,17-,18-,21-/m1/s1
InChIKeyOWDHJJGXMJRIBB-QTQZEZTPSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.7c1ccc(cc1)CCCCCNc2c3c(ncn2)n(cn3)C4C(C(C(O4)CO)O)O
OpenEye OEToolkits 2.0.7c1ccc(cc1)CCCCCNc2c3c(ncn2)n(cn3)[C@H]4[C@@H]([C@@H]([C@H](O4)CO)O)O
CACTVS 3.385OC[C@H]1O[C@H]([C@H](O)[C@@H]1O)n2cnc3c(NCCCCCc4ccccc4)ncnc23
CACTVS 3.385OC[CH]1O[CH]([CH](O)[CH]1O)n2cnc3c(NCCCCCc4ccccc4)ncnc23
ACDLabs 12.01OCC1OC(n2cnc3c(NCCCCCc4ccccc4)ncnc32)C(O)C1O
FormulaC21 H27 N5 O4
NameN-(5-phenylpentyl)adenosine
ChEMBL
DrugBank
ZINC
PDB chain8cy1 Chain A Residue 605 [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]
PDB8cy1 Systematic Design of Adenosine Analogs as Inhibitors of a Clostridioides difficile- Specific DNA Adenine Methyltransferase Required for Normal Sporulation and Persistence.
Resolution2.38 Å
Binding residue
(original residue number in PDB)		G28 D114 I115 D149 S150 P167 E175 Y178 F200
Binding residue
(residue number reindexed from 1)		G1 D87 I88 D118 S119 P136 E144 Y147 F169
Annotation score1
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:8cy1, PDBe:8cy1, PDBj:8cy1
PDBsum8cy1
PubMed36581322
UniProtQ183J3

[Back to BioLiP]