Structure of PDB 7rfl Chain B Binding Site BS03

Receptor Information
>7rfl Chain B (length=556) Species: 272563 (Clostridioides difficile 630) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
DTKKASGIYYTPKIIVDYIVKKTLKNHDIIKNPYPRILDISCGCGNFLLE
VYDILYDLFEENIYELKKKYDENYWTVDNIHRHILNYCIYGADIDEKAIS
ILKDSLTNKKVVNDLDESDIKINLFCCDSLKKKWRYKFDYIVGNPPYIGH
KKLEKKYKKFLLEKYSEVYKDKADLYFCFYKKIIDILKQGGIGSVITPRY
FLESLSGKDLREYIKSNVNVQEIVDFLGANIFKNIGVSSCILTFDKKKTK
ETYIDVFKIKNEDICINKFETLEELLKSSKFEHFNINQRLLSDEWILVNK
DDETFYNKIQEKCKYSLEDIAISFQGIITGCDKAFILSKDDVKLNLVDDK
FLKCWIKSKNINKYIVDKSEYRLIYSNDIDNENTNKRILDEIIGLYKTKL
ENRRECKSGIRKWYELQWGREKLFFERKKIMYPYKSNENRFAIDYDNNFS
SADVYSFFIKEEYLDKFSYEYLVGILNSSVYDKYFKITAKKMSKNIYDYY
PNKVMKIRIFRDNNYEEIENLSKQIISILLNKSIDKGKVEKLQIKMDNLI
MDSLGI
Ligand information
Ligand IDAW2
InChIInChI=1S/C28H40BrN7O4/c1-16(2)35(12-6-11-31-27(39)34-18-9-7-17(8-10-18)28(3,4)5)14-20-22(37)23(38)26(40-20)36-13-19(29)21-24(30)32-15-33-25(21)36/h7-10,13,15-16,20,22-23,26,37-38H,6,11-12,14H2,1-5H3,(H2,30,32,33)(H2,31,34,39)/t20-,22-,23-,26-/m1/s1
InChIKeyIQCKJUKAQJINMK-HUBRGWSESA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.6CC(C)N(CCCNC(=O)Nc1ccc(cc1)C(C)(C)C)CC2C(C(C(O2)n3cc(c4c3ncnc4N)Br)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)n3cc(c4c3ncnc4N)Br)O)O
ACDLabs 12.01Brc2c1c(ncnc1n(c2)C3OC(C(O)C3O)CN(C(C)C)CCCNC(=O)Nc4ccc(cc4)C(C)(C)C)N
FormulaC28 H40 Br N7 O4
Name5-bromo-7-{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
ChEMBLCHEMBL3087498
DrugBank
ZINCZINC000097956664
PDB chain7rfl Chain B Residue 701 [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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PDB7rfl Repurposing epigenetic inhibitors to target the Clostridioides difficile- specific DNA adenine methyltransferase and sporulation regulator CamA.
Resolution2.38 Å
Binding residue
(original residue number in PDB)		K25 Y30 I61 G64 C65 D114 I115 A119 D149 S150 P167 F200
Binding residue
(residue number reindexed from 1)		K4 Y9 I40 G43 C44 D93 I94 A98 D128 S129 P146 F179
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:7rfl, PDBe:7rfl, PDBj:7rfl
PDBsum7rfl
PubMed34523387
UniProtQ183J3

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