Structure of PDB 7rfm Chain B Binding Site BS03

Receptor Information
>7rfm Chain B (length=555) Species: 272563 (Clostridioides difficile 630) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
TKKASGIYYTPKIIVDYIVKKTLKNHDIIKNPYPRILDISCGCGNFLLEV
YDILYDLFEENIYELKKKYDENYWTVDNIHRHILNYCIYGADIDEKAISI
LKDSLTNKKVVNDLDESDIKINLFCCDSLKKKWRYKFDYIVGNPPYIGHK
KLEKKYKKFLLEKYSEVYKDKADLYFCFYKKIIDILKQGGIGSVITPRYF
LESLSGKDLREYIKSNVNVQEIVDFLGANIFKNIGVSSCILTFDKKKTKE
TYIDVFKIKNEDICINKFETLEELLKSSKFEHFNINQRLLSDEWILVNKD
DETFYNKIQEKCKYSLEDIAISFQGIITGCDKAFILSKDDVKLNLVDDKF
LKCWIKSKNINKYIVDKSEYRLIYSNDIDNENTNKRILDEIIGLYKTKLE
NRRECKSGIRKWYELQWGREKLFFERKKIMYPYKSNENRFAIDYDNNFSS
ADVYSFFIKEEYLDKFSYEYLVGILNSSVYDKYFKITAKKMSKNIYDYYP
NKVMKIRIFRDNNYEEIENLSKQIISILLNKSIDKGKVEKLQIKMDNLIM
DSLGI
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 B 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)		K25 Y30 G64 C65 N67 D114 I115 D116 A119 D149 S150 P167
Binding residue
(residue number reindexed from 1)		K3 Y8 G42 C43 N45 D92 I93 D94 A97 D127 S128 P145
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
View graph for
Biological Process
External links
PDB RCSB:7rfm, PDBe:7rfm, PDBj:7rfm
PDBsum7rfm
PubMed34523387
UniProtQ183J3

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