Structure of PDB 9c3s Chain D Binding Site BS04

Receptor Information

>9c3s Chain D (length=241) Species: 95486 (Burkholderia cenocepacia)

HNRDFLTDAAHLPDASIDLIVADPPYGLGKDYGNDSDKRSGDDFLAWTRE
WLELAIPKLKPSGSMYIFCTWQYAPEIFSFLKTQLTMVNEIIWDRRVPSM
GGTTRRFTSVHDNIGFFAVSRAYYFDLDPVRIPYDADTKKARSRKLFEGS
KWLEMGYNPKDVWSVSRLHRQHAERVDHPTQKPLEIIERMVLASCPPGGR
VLDPFMGSGTTAVACARQGRDFVGYEINESYCAIAHERVNA

Ligand information

• Ligand ID: SFG
• InChI: InChI=1S/C15H23N7O5/c16-6(1-2-7(17)15(25)26)3-8-10(23)11(24)14(27-8)22-5-21-9-12(18)19-4-20-13(9)22/h4-8,10-11,14,23-24H,1-3,16-17H2,(H,25,26)(H2,18,19,20)/t6-,7-,8+,10+,11+,14+/m0/s1
• InChIKey: LMXOHSDXUQEUSF-YECHIGJVSA-N
• SMILES:
  OpenEye OEToolkits 1.7.0: c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)C[C@H](CC[C@@H](C(=O)O)N)N)O)O)N
  OpenEye OEToolkits 1.7.0: c1nc(c2c(n1)n(cn2)C3C(C(C(O3)CC(CCC(C(=O)O)N)N)O)O)N
  CACTVS 3.370: N[CH](CC[CH](N)C(O)=O)C[CH]1O[CH]([CH](O)[CH]1O)n2cnc3c(N)ncnc23
  CACTVS 3.370: N[C@@H](CC[C@H](N)C(O)=O)C[C@H]1O[C@H]([C@H](O)[C@@H]1O)n2cnc3c(N)ncnc23
  ACDLabs 12.01: O=C(O)C(N)CCC(N)CC3OC(n2cnc1c(ncnc12)N)C(O)C3O
• Formula: C15 H23 N7 O5
• Name: SINEFUNGIN;
  ADENOSYL-ORNITHINE
• ChEMBL: CHEMBL1214186
• DrugBank: DB01910
• ZINC: ZINC000004217451
• PDB chain: 9c3s Chain D Residue 301

Receptor-Ligand Complex Structure

Structure summary

• PDB: 9c3s Burkholderia cenocepacia epigenetic regulator M.BceJIV simultaneously engages two DNA recognition sequences for methylation.
• Resolution: 2.16 Å
• Binding residue (original residue number in PDB): D40 D59 S72 H214 T216 K218 F241 M242 S244 E262 I263 Y267
• Binding residue (residue number reindexed from 1): D4 D23 S36 H178 T180 K182 F205 M206 S208 E226 I227 Y231
• Annotation score: 1

External links

• PDB: RCSB:9c3s, PDBe:9c3s, PDBj:9c3s
• PDBsum: 9c3s
• PubMed: 39244607
• UniProt: A0A8I1DKW0