Structure of PDB 8cy5 Chain B Binding Site BS03

Receptor Information
>8cy5 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 IDT8Q
InChIInChI=1S/C23H36N6O6/c1-23(2,3)35-22(33)28-9-6-14(7-10-28)5-4-8-24-19-16-20(26-12-25-19)29(13-27-16)21-18(32)17(31)15(11-30)34-21/h12-15,17-18,21,30-32H,4-11H2,1-3H3,(H,24,25,26)/t15-,17-,18-,21-/m1/s1
InChIKeyNYCVBKCHESHFLR-QTQZEZTPSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.7CC(C)(C)OC(=O)N1CCC(CC1)CCCNc2c3c(ncn2)n(cn3)[C@H]4[C@@H]([C@@H]([C@H](O4)CO)O)O
CACTVS 3.385CC(C)(C)OC(=O)N1CCC(CCCNc2ncnc3n(cnc23)[CH]4O[CH](CO)[CH](O)[CH]4O)CC1
CACTVS 3.385CC(C)(C)OC(=O)N1CCC(CCCNc2ncnc3n(cnc23)[C@@H]4O[C@H](CO)[C@@H](O)[C@H]4O)CC1
OpenEye OEToolkits 2.0.7CC(C)(C)OC(=O)N1CCC(CC1)CCCNc2c3c(ncn2)n(cn3)C4C(C(C(O4)CO)O)O
ACDLabs 12.01CC(C)(C)OC(=O)N1CCC(CC1)CCCNc1ncnc2c1ncn2C1OC(CO)C(O)C1O
FormulaC23 H36 N6 O6
NameN-{3-[1-(tert-butoxycarbonyl)piperidin-4-yl]propyl}adenosine
ChEMBL
DrugBank
ZINC
PDB chain8cy5 Chain B Residue 607 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB8cy5 Systematic Design of Adenosine Analogs as Inhibitors of a Clostridioides difficile- Specific DNA Adenine Methyltransferase Required for Normal Sporulation and Persistence.
Resolution2.5 Å
Binding residue
(original residue number in PDB)		G28 D114 I115 D149 S150 P167 K173 L174 E175 Y178 F200
Binding residue
(residue number reindexed from 1)		G1 D87 I88 D122 S123 P140 K146 L147 E148 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:8cy5, PDBe:8cy5, PDBj:8cy5
PDBsum8cy5
PubMed36581322
UniProtQ183J3

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