Structure of PDB 8cxw Chain B Binding Site BS03

Receptor Information
>8cxw Chain B (length=549) Species: 272563 (Clostridioides difficile 630) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
IYYTPKIIVDYIVKKTLKNHDIIKNPYPRILDISCGCGNFLLEVYDILYD
LFEENIYELKKKYDENYWTVDNIHRHILNYCIYGADIDEKAISILKDSLT
NKKVVNDLDESDIKINLFCCDSLKKKWRYKFDYIVGNPPYIGHKKLEKKY
KKFLLEKYSEVYKDKADLYFCFYKKIIDILKQGGIGSVITPRYFLESLSG
KDLREYIKSNVNVQEIVDFLGANIFKNIGVSSCILTFDKKKTKETYIDVF
KIKNEDICINKFETLEELLKSSKFEHFNINQRLLSDEWILVNKDDETFYN
KIQEKCKYSLEDIAISFQGIITGCDKAFILSKDDVKLNLVDDKFLKCWIK
SKNINKYIVDKSEYRLIYSNDIDNENTNKRILDEIIGLYKTKLENRRECK
SGIRKWYELQWGREKLFFERKKIMYPYKSNENRFAIDYDNNFSSADVYSF
FIKEEYLDKFSYEYLVGILNSSVYDKYFKITAKKMSKNIYDYYPNKVMKI
RIFRDNNYEEIENLSKQIISILLNKSIDKGKVEKLQIKMDNLIMDSLGI
Ligand information
Ligand IDQ8L
InChIInChI=1S/C18H19IN6O4/c1-20-17(28)14-12(26)13(27)18(29-14)25-8-24-11-15(22-7-23-16(11)25)21-6-9-3-2-4-10(19)5-9/h2-5,7-8,12-14,18,26-27H,6H2,1H3,(H,20,28)(H,21,22,23)/t12-,13+,14-,18+/m0/s1
InChIKeyHUJXGQILHAUCCV-MOROJQBDSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.7CNC(=O)C1C(C(C(O1)n2cnc3c2ncnc3NCc4cccc(c4)I)O)O
CACTVS 3.385CNC(=O)[CH]1O[CH]([CH](O)[CH]1O)n2cnc3c(NCc4cccc(I)c4)ncnc23
OpenEye OEToolkits 2.0.7CNC(=O)[C@@H]1[C@H]([C@H]([C@@H](O1)n2cnc3c2ncnc3NCc4cccc(c4)I)O)O
CACTVS 3.385CNC(=O)[C@H]1O[C@H]([C@H](O)[C@@H]1O)n2cnc3c(NCc4cccc(I)c4)ncnc23
ACDLabs 12.01Ic1cccc(c1)CNc1ncnc2c1ncn2C1OC(C(O)C1O)C(=O)NC
FormulaC18 H19 I N6 O4
NamePiclidenoson
ChEMBLCHEMBL119709
DrugBankDB05511
ZINCZINC000003811810
PDB chain8cxw 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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PDB8cxw Systematic Design of Adenosine Analogs as Inhibitors of a Clostridioides difficile- Specific DNA Adenine Methyltransferase Required for Normal Sporulation and Persistence.
Resolution2.78 Å
Binding residue
(original residue number in PDB)		D114 I115 D149 S150 P167 Y178
Binding residue
(residue number reindexed from 1)		D86 I87 D121 S122 P139 Y150
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
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Biological Process
External links
PDB RCSB:8cxw, PDBe:8cxw, PDBj:8cxw
PDBsum8cxw
PubMed36581322
UniProtQ183J3

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