Structure of PDB 8cxy Chain C Binding Site BS03

Receptor Information
>8cxy Chain C (length=539) Species: 1496 (Clostridioides difficile) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
IYYTPKIIVDYIVKKTLKNHDIIKNPYPRILDISCGCGNFLLEVYDILYD
LFEENIYELKKKYDENYWTVDNIHRHILNYCIYGADIDEKAISILKDSLT
NKIKINLFCCDSLKKKWRYKFDYIVGNPPYIGHKKLEKKYKKFLLEKYSE
VYKDKADLYFCFYKKIIDILKQGGIGSVITPRYFLESLSGKDLREYIKSN
VNVQEIVDFLGANIFKNIGVSSCILTFDKKKTKETYIDVFKIKNEDICIN
KFETLEELLKSSKFEHFNINQRLLSDEWILVNKDDETFYNKIQEKCKYSL
EDIAISFQGIITGCDKAFILSKDDVKLNLVDDKFLKCWIKSKNINKYIVD
KSEYRLIYSNDIDNENTNKRILDEIIGLYKTKLENRRECKSGIRKWYELQ
WGREKLFFERKKIMYPYKSNENRFAIDYDNNFSSADVYSFFIKEEYLDKF
SYEYLVGILNSSVYDKYFKITAKKMSKNIYDYYPNKVMKIRIFRDNNYEE
IENLSKQIISILLNKSIDKGKVEKLQIKMDNLIMDSLGI
Ligand information
Ligand IDQ8R
InChIInChI=1S/C18H21N5O4/c24-8-12-14(25)15(26)18(27-12)23-10-22-13-16(20-9-21-17(13)23)19-7-6-11-4-2-1-3-5-11/h1-5,9-10,12,14-15,18,24-26H,6-8H2,(H,19,20,21)/t12-,14-,15-,18-/m1/s1
InChIKeyLGZYEDZSPHLISU-SCFUHWHPSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.7c1ccc(cc1)CCNc2c3c(ncn2)n(cn3)[C@H]4[C@@H]([C@@H]([C@H](O4)CO)O)O
OpenEye OEToolkits 2.0.7c1ccc(cc1)CCNc2c3c(ncn2)n(cn3)C4C(C(C(O4)CO)O)O
ACDLabs 12.01OCC1OC(n2cnc3c(NCCc4ccccc4)ncnc32)C(O)C1O
CACTVS 3.385OC[CH]1O[CH]([CH](O)[CH]1O)n2cnc3c(NCCc4ccccc4)ncnc23
CACTVS 3.385OC[C@H]1O[C@H]([C@H](O)[C@@H]1O)n2cnc3c(NCCc4ccccc4)ncnc23
FormulaC18 H21 N5 O4
NameN-(2-phenylethyl)adenosine
ChEMBLCHEMBL1257013
DrugBank
ZINC
PDB chain8cxy Chain C Residue 603 [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]
PDB8cxy Systematic Design of Adenosine Analogs as Inhibitors of a Clostridioides difficile- Specific DNA Adenine Methyltransferase Required for Normal Sporulation and Persistence.
Resolution2.19 Å
Binding residue
(original residue number in PDB)		D114 I115 D149 S150 P167 Y178
Binding residue
(residue number reindexed from 1)		D86 I87 D111 S112 P129 Y140
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:8cxy, PDBe:8cxy, PDBj:8cxy
PDBsum8cxy
PubMed36581322
UniProtQ183J3

[Back to BioLiP]