Structure of PDB 8cxu Chain B Binding Site BS03

Receptor Information
>8cxu Chain B (length=550) Species: 272563 (Clostridioides difficile 630) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
GIYYTPKIIVDYIVKKTLKNHDIIKNPYPRILDISCGCGNFLLEVYDILY
DLFEENIYELKKKYDENYWTVDNIHRHILNYCIYGADIDEKAISILKDSL
TNKKVVNDLDESDIKINLFCCDSLKKKWRYKFDYIVGNPPYIGHKKLEKK
YKKFLLEKYSEVYKDKADLYFCFYKKIIDILKQGGIGSVITPRYFLESLS
GKDLREYIKSNVNVQEIVDFLGANIFKNIGVSSCILTFDKKKTKETYIDV
FKIKNEDICINKFETLEELLKSSKFEHFNINQRLLSDEWILVNKDDETFY
NKIQEKCKYSLEDIAISFQGIITGCDKAFILSKDDVKLNLVDDKFLKCWI
KSKNINKYIVDKSEYRLIYSNDIDNENTNKRILDEIIGLYKTKLENRREC
KSGIRKWYELQWGREKLFFERKKIMYPYKSNENRFAIDYDNNFSSADVYS
FFIKEEYLDKFSYEYLVGILNSSVYDKYFKITAKKMSKNIYDYYPNKVMK
IRIFRDNNYEEIENLSKQIISILLNKSIDKGKVEKLQIKMDNLIMDSLGI
Ligand information
Ligand IDT96
InChIInChI=1S/C17H20N6O4/c18-10-3-1-9(2-4-10)5-19-15-12-16(21-7-20-15)23(8-22-12)17-14(26)13(25)11(6-24)27-17/h1-4,7-8,11,13-14,17,24-26H,5-6,18H2,(H,19,20,21)/t11-,13-,14-,17-/m1/s1
InChIKeyPMUVNAUPWLXPSA-LSCFUAHRSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.7c1cc(ccc1CNc2c3c(ncn2)n(cn3)[C@H]4[C@@H]([C@@H]([C@H](O4)CO)O)O)N
CACTVS 3.385Nc1ccc(CNc2ncnc3n(cnc23)[C@@H]4O[C@H](CO)[C@@H](O)[C@H]4O)cc1
ACDLabs 12.01Nc1ccc(cc1)CNc1ncnc2c1ncn2C1OC(CO)C(O)C1O
CACTVS 3.385Nc1ccc(CNc2ncnc3n(cnc23)[CH]4O[CH](CO)[CH](O)[CH]4O)cc1
OpenEye OEToolkits 2.0.7c1cc(ccc1CNc2c3c(ncn2)n(cn3)C4C(C(C(O4)CO)O)O)N
FormulaC17 H20 N6 O4
NameN-[(4-aminophenyl)methyl]adenosine
ChEMBLCHEMBL259188
DrugBank
ZINCZINC000005161863
PDB chain8cxu Chain B Residue 608 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB8cxu Systematic Design of Adenosine Analogs as Inhibitors of a Clostridioides difficile- Specific DNA Adenine Methyltransferase Required for Normal Sporulation and Persistence.
Resolution2.28 Å
Binding residue
(original residue number in PDB)		G28 S62 D114 I115 D149 S150 P167 Y178 F200
Binding residue
(residue number reindexed from 1)		G1 S35 D87 I88 D122 S123 P140 Y151 F173
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:8cxu, PDBe:8cxu, PDBj:8cxu
PDBsum8cxu
PubMed36581322
UniProtQ183J3

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