Structure of PDB 7rfm Chain C Binding Site BS03

Receptor Information
>7rfm Chain C (length=537) Species: 272563 (Clostridioides difficile 630) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
YYTPKIIVDYIVKKTLKNHDIIKNPYPRILDISCGCGNFLLEVYDILYDL
FEENIYELKKKYDENYWTVDNIHRHILNYCIYGADIDEKAISILKDSLTN
IKINLFCCDSLKKKWRYKFDYIVGNPPYIGHKKLEKKYKKFLLEKYSEVY
KDKADLYFCFYKKIIDILKQGGIGSVITPRYFLESLSGKDLREYIKSNVN
VQEIVDFLGANIFKNIGVSSCILTFDKKKTKETYIDVFKIKNEDICINKF
ETLEELLKSSKFEHFNINQRLLSDEWILVNKDDETFYNKIQEKCKYSLED
IAISFQGIITGCDKAFILSKDDVKLNLVDDKFLKCWIKSKNINKYIVDKS
EYRLIYSNDIDNENTNKRILDEIIGLYKTKLENRRECKSGIRKWYELQWG
REKLFFERKKIMYPYKSNENRFAIDYDNNFSSADVYSFFIKEEYLDKFSY
EYLVGILNSSVYDKYFKITAKKMSKNIYDYYPNKVMKIRIFRDNNYEEIE
NLSKQIISILLNKSIDKGKVEKLQIKMDNLIMDSLGI
Ligand information
Ligand ID0QK
InChIInChI=1S/C28H41N7O4/c1-17(2)34(13-6-12-30-27(38)33-19-9-7-18(8-10-19)28(3,4)5)15-21-22(36)23(37)26(39-21)35-14-11-20-24(29)31-16-32-25(20)35/h7-11,14,16-17,21-23,26,36-37H,6,12-13,15H2,1-5H3,(H2,29,31,32)(H2,30,33,38)/t21-,22-,23-,26-/m1/s1
InChIKeyWXRGFPHDRFQODR-ICLZECGLSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.6CC(C)N(CCCNC(=O)Nc1ccc(cc1)C(C)(C)C)CC2C(C(C(O2)n3ccc4c3ncnc4N)O)O
OpenEye OEToolkits 1.7.6CC(C)N(CCCNC(=O)Nc1ccc(cc1)C(C)(C)C)C[C@@H]2[C@H]([C@H]([C@@H](O2)n3ccc4c3ncnc4N)O)O
CACTVS 3.370CC(C)N(CCCNC(=O)Nc1ccc(cc1)C(C)(C)C)C[CH]2O[CH]([CH](O)[CH]2O)n3ccc4c(N)ncnc34
CACTVS 3.370CC(C)N(CCCNC(=O)Nc1ccc(cc1)C(C)(C)C)C[C@H]2O[C@H]([C@H](O)[C@@H]2O)n3ccc4c(N)ncnc34
ACDLabs 12.01O=C(Nc1ccc(cc1)C(C)(C)C)NCCCN(C(C)C)CC4OC(n3ccc2c(ncnc23)N)C(O)C4O
FormulaC28 H41 N7 O4
Name7-{5-[(3-{[(4-tert-butylphenyl)carbamoyl]amino}propyl)(propan-2-yl)amino]-5-deoxy-beta-D-ribofuranosyl}-7H-pyrrolo[2,3-d]pyrimidin-4-amine
ChEMBLCHEMBL2169919
DrugBank
ZINCZINC000089469833
PDB chain7rfm Chain C Residue 601 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB7rfm Repurposing epigenetic inhibitors to target the Clostridioides difficile- specific DNA adenine methyltransferase and sporulation regulator CamA.
Resolution2.68 Å
Binding residue
(original residue number in PDB)		Y30 S62 G64 C65 D114 I115 D116 D149 S150 P167
Binding residue
(residue number reindexed from 1)		Y1 S33 G35 C36 D85 I86 D87 D109 S110 P127
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:7rfm, PDBe:7rfm, PDBj:7rfm
PDBsum7rfm
PubMed34523387
UniProtQ183J3

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