Structure of PDB 8cxx Chain B Binding Site BS03

Receptor Information
>8cxx 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 IDT9I
InChIInChI=1S/C19H21N5O4/c25-7-13-15(26)16(27)19(28-13)24-9-22-14-17(20-8-21-18(14)24)23-12-6-5-10-3-1-2-4-11(10)12/h1-4,8-9,12-13,15-16,19,25-27H,5-7H2,(H,20,21,23)/t12-,13-,15-,16-,19-/m1/s1
InChIKeyFSKMJUWPFLDDRS-BYMDKACISA-N
SMILES
SoftwareSMILES
ACDLabs 12.01OCC1OC(n2cnc3c(NC4CCc5ccccc54)ncnc32)C(O)C1O
OpenEye OEToolkits 2.0.7c1ccc2c(c1)CC[C@H]2Nc3c4c(ncn3)n(cn4)[C@H]5[C@@H]([C@@H]([C@H](O5)CO)O)O
CACTVS 3.385OC[CH]1O[CH]([CH](O)[CH]1O)n2cnc3c(N[CH]4CCc5ccccc45)ncnc23
OpenEye OEToolkits 2.0.7c1ccc2c(c1)CCC2Nc3c4c(ncn3)n(cn4)C5C(C(C(O5)CO)O)O
CACTVS 3.385OC[C@H]1O[C@H]([C@H](O)[C@@H]1O)n2cnc3c(N[C@@H]4CCc5ccccc45)ncnc23
FormulaC19 H21 N5 O4
NameN-[(1R)-2,3-dihydro-1H-inden-1-yl]adenosine
ChEMBLCHEMBL2235600
DrugBank
ZINCZINC000003780890
PDB chain8cxx Chain B Residue 1009 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB8cxx Systematic Design of Adenosine Analogs as Inhibitors of a Clostridioides difficile- Specific DNA Adenine Methyltransferase Required for Normal Sporulation and Persistence.
Resolution2.34 Å
Binding residue
(original residue number in PDB)		G28 I29 D114 I115 D149 S150 P167 Y178 L196
Binding residue
(residue number reindexed from 1)		G1 I2 D87 I88 D122 S123 P140 Y151 L169
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:8cxx, PDBe:8cxx, PDBj:8cxx
PDBsum8cxx
PubMed36581322
UniProtQ183J3

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