Structure of PDB 8cy0 Chain B Binding Site BS03

Receptor Information
>8cy0 Chain B (length=550) Species: 1496 (Clostridioides difficile) [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 IDQ9W
InChIInChI=1S/C20H25N5O4/c26-10-14-16(27)17(28)20(29-14)25-12-24-15-18(22-11-23-19(15)25)21-9-5-4-8-13-6-2-1-3-7-13/h1-3,6-7,11-12,14,16-17,20,26-28H,4-5,8-10H2,(H,21,22,23)/t14-,16-,17-,20-/m1/s1
InChIKeyQNQVVNSRYWTXJV-WVSUBDOOSA-N
SMILES
SoftwareSMILES
CACTVS 3.385OC[C@H]1O[C@H]([C@H](O)[C@@H]1O)n2cnc3c(NCCCCc4ccccc4)ncnc23
OpenEye OEToolkits 2.0.7c1ccc(cc1)CCCCNc2c3c(ncn2)n(cn3)C4C(C(C(O4)CO)O)O
OpenEye OEToolkits 2.0.7c1ccc(cc1)CCCCNc2c3c(ncn2)n(cn3)[C@H]4[C@@H]([C@@H]([C@H](O4)CO)O)O
ACDLabs 12.01OCC1OC(n2cnc3c(NCCCCc4ccccc4)ncnc32)C(O)C1O
CACTVS 3.385OC[CH]1O[CH]([CH](O)[CH]1O)n2cnc3c(NCCCCc4ccccc4)ncnc23
FormulaC20 H25 N5 O4
NameN-(4-phenylbutyl)adenosine
ChEMBLCHEMBL2113406
DrugBank
ZINC
PDB chain8cy0 Chain B Residue 609 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB8cy0 Systematic Design of Adenosine Analogs as Inhibitors of a Clostridioides difficile- Specific DNA Adenine Methyltransferase Required for Normal Sporulation and Persistence.
Resolution2.65 Å
Binding residue
(original residue number in PDB)		G28 D114 I115 D149 S150 P167 Y178 F200
Binding residue
(residue number reindexed from 1)		G1 D87 I88 D122 S123 P140 Y151 F173
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

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Molecular Function
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Biological Process
External links
PDB RCSB:8cy0, PDBe:8cy0, PDBj:8cy0
PDBsum8cy0
PubMed36581322
UniProtQ183J3

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