Structure of PDB 7rfm Chain A Binding Site BS03

Receptor Information
>7rfm Chain A (length=550) Species: 272563 (Clostridioides difficile 630) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
KKASGIYYTPKIIVDYIVKKTLKNHDIIKNPYPRILDISCGCGNFLLEVY
DILYDLFEENIYELKKKYDENYWTVDNIHRHILNYCIYGADIDEKAISIL
KDSLTNKKVDESDIKINLFCCDSLKKKWRYKFDYIVGNPPYIGHKKLEKK
YKKFLLEKYSEVYKDKADLYFCFYKKIIDILKQGGIGSVITPRYFLESLS
GKDLREYIKSNVNVQEIVDFLGANIFKNIGVSSCILTFDKKKTKETYIDV
FKIKNEDICINKFETLEELLKSSKFEHFNINQRLLSDEWILVNKDDETFY
NKIQEKCKYSLEDIAISFQGIITGCDKAFILSKDDVKLNLVDDKFLKCWI
KSKNINKYIVDKSEYRLIYSNDIDNENTNKRILDEIIGLYKTKLENRREC
KSGIRKWYELQWGREKLFFERKKIMYPYKSNENRFAIDYDNNFSSADVYS
FFIKEEYLDKFSYEYLVGILNSSVYDKYFKITAKKMSKNIYDYYPNKVMK
IRIFRDNNYEEIENLSKQIISILLNKSIDKGKVEKLQIKMDNLIMDSLGI
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 A Residue 701 [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)		K25 Y30 S62 G64 C65 D114 I115 A119 D149 S150 N165 P167
Binding residue
(residue number reindexed from 1)		K2 Y7 S39 G41 C42 D91 I92 A96 D122 S123 N138 P140
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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