Structure of PDB 8cxz Chain C Binding Site BS03

Receptor Information
>8cxz Chain C (length=540) Species: 1496 (Clostridioides difficile) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
GIYYTPKIIVDYIVKKTLKNHDIIKNPYPRILDISCGCGNFLLEVYDILY
DLFEENIYELKKKYDENYWTVDNIHRHILNYCIYGADIDEKAISILKDSL
TNKIKINLFCCDSLKKKWRYKFDYIVGNPPYIGHKKLEKKYKKFLLEKYS
EVYKDKADLYFCFYKKIIDILKQGGIGSVITPRYFLESLSGKDLREYIKS
NVNVQEIVDFLGANIFKNIGVSSCILTFDKKKTKETYIDVFKIKNEDICI
NKFETLEELLKSSKFEHFNINQRLLSDEWILVNKDDETFYNKIQEKCKYS
LEDIAISFQGIITGCDKAFILSKDDVKLNLVDDKFLKCWIKSKNINKYIV
DKSEYRLIYSNDIDNENTNKRILDEIIGLYKTKLENRRECKSGIRKWYEL
QWGREKLFFERKKIMYPYKSNENRFAIDYDNNFSSADVYSFFIKEEYLDK
FSYEYLVGILNSSVYDKYFKITAKKMSKNIYDYYPNKVMKIRIFRDNNYE
EIENLSKQIISILLNKSIDKGKVEKLQIKMDNLIMDSLGI
Ligand information
Ligand IDQ8Y
InChIInChI=1S/C19H23N5O4/c25-9-13-15(26)16(27)19(28-13)24-11-23-14-17(21-10-22-18(14)24)20-8-4-7-12-5-2-1-3-6-12/h1-3,5-6,10-11,13,15-16,19,25-27H,4,7-9H2,(H,20,21,22)/t13-,15-,16-,19-/m1/s1
InChIKeyUBRRRMDHTZACMR-NVQRDWNXSA-N
SMILES
SoftwareSMILES
ACDLabs 12.01OCC1OC(n2cnc3c(NCCCc4ccccc4)ncnc32)C(O)C1O
OpenEye OEToolkits 2.0.7c1ccc(cc1)CCCNc2c3c(ncn2)n(cn3)C4C(C(C(O4)CO)O)O
OpenEye OEToolkits 2.0.7c1ccc(cc1)CCCNc2c3c(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(NCCCc4ccccc4)ncnc23
CACTVS 3.385OC[CH]1O[CH]([CH](O)[CH]1O)n2cnc3c(NCCCc4ccccc4)ncnc23
FormulaC19 H23 N5 O4
NameN-(3-phenylpropyl)adenosine
ChEMBLCHEMBL2113484
DrugBank
ZINC
PDB chain8cxz 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]
PDB8cxz Systematic Design of Adenosine Analogs as Inhibitors of a Clostridioides difficile- Specific DNA Adenine Methyltransferase Required for Normal Sporulation and Persistence.
Resolution2.35 Å
Binding residue
(original residue number in PDB)		D114 I115 D149 S150 P167 Y178 F200
Binding residue
(residue number reindexed from 1)		D87 I88 D112 S113 P130 Y141 F163
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:8cxz, PDBe:8cxz, PDBj:8cxz
PDBsum8cxz
PubMed36581322
UniProtQ183J3

[Back to BioLiP]