Structure of PDB 3f8f Chain B Binding Site BS01

Receptor Information

>3f8f Chain B (length=111) Species: 416870 (Lactococcus cremoris subsp. cremoris MG1363)

PKEMLRAQTNVILLNVLKQGDNYVYGIIKQVKEASNGEMELNEATLYTIF
KRLEKDGIISSYWGDESQGGRRKYYRLTEIGHENMRLAFESWSRVDKIIE
NLEANKKSEAI

Ligand information

• Ligand ID: DM1
• InChI: InChI=1S/C27H29NO10/c1-10-22(30)14(28)7-17(37-10)38-16-9-27(35,11(2)29)8-13-19(16)26(34)21-20(24(13)32)23(31)12-5-4-6-15(36-3)18(12)25(21)33/h4-6,10,14,16-17,22,30,32,34-35H,7-9,28H2,1-3H3/t10-,14-,16-,17-,22+,27-/m0/s1
• InChIKey: STQGQHZAVUOBTE-VGBVRHCVSA-N
• SMILES:
  ACDLabs 10.04: O=C2c1c(O)c5c(c(O)c1C(=O)c3cccc(OC)c23)CC(O)(C(=O)C)CC5OC4OC(C(O)C(N)C4)C
  OpenEye OEToolkits 1.5.0: CC1C(C(CC(O1)OC2CC(Cc3c2c(c4c(c3O)C(=O)c5cccc(c5C4=O)OC)O)(C(=O)C)O)N)O
  CACTVS 3.341: COc1cccc2C(=O)c3c(O)c4C[C@](O)(C[C@H](O[C@H]5C[C@H](N)[C@H](O)[C@H](C)O5)c4c(O)c3C(=O)c12)C(C)=O
  OpenEye OEToolkits 1.5.0: C[C@H]1[C@H]([C@H](C[C@@H](O1)O[C@H]2C[C@@](Cc3c2c(c4c(c3O)C(=O)c5cccc(c5C4=O)OC)O)(C(=O)C)O)N)O
  CACTVS 3.341: COc1cccc2C(=O)c3c(O)c4C[C](O)(C[CH](O[CH]5C[CH](N)[CH](O)[CH](C)O5)c4c(O)c3C(=O)c12)C(C)=O
• Formula: C27 H29 N O10
• Name: DAUNOMYCIN;
  DAUNORUBICIN
• ChEMBL: CHEMBL178
• DrugBank: DB00694
• ZINC: ZINC000003917708
• PDB chain: 3f8f Chain A Residue 127

Receptor-Ligand Complex Structure

Structure summary

• PDB: 3f8f Structure of the transcriptional regulator LmrR and its mechanism of multidrug recognition.
• Resolution: 2.2 Å
• Binding residue (original residue number in PDB): V15 W96
• Binding residue (residue number reindexed from 1): V11 W92
• Annotation score: 1
• Binding affinity: PDBbind-CN: -logKd/Ki=6.63,Kd=236nM

External links

• PDB: RCSB:3f8f, PDBe:3f8f, PDBj:3f8f
• PDBsum: 3f8f
• PubMed: 19096365
• UniProt: A2RI36