Structure of PDB 5x5m Chain B Binding Site BS01

Receptor Information

>5x5m Chain B (length=205) Species: 272626 (Listeria innocua Clip11262)

KKIDFKKEEKKFYAPKRKPERIFVPEMNFLMVDGKGDPDGEEYQKAVQSL
YAIAYTIKMSKMGETRLDGYSDFVVPPLEGFWWSEGKFDLKDRDAWLWTS
ILRQPDFVTEEVLEWAKEVARKKKPDVDTSRVKLVRFEEGECVQMMHVGP
FSEAVHTVAEMHQFMETEGLRNDTGAIRKHHLIYLSDPRKANPEKMKTIL
RLPVS

Ligand information

• Ligand ID: 7YU
• InChI: InChI=1S/C35H29N5O8S/c1-47-25-10-19-14(7-23(25)41)6-20(36-19)33(45)40-13-15-12-35(15)18-9-21(37-28(18)24(42)11-26(35)40)32(44)39-5-4-16-17-8-22(34(46)49-3)38-27(17)31(48-2)30(43)29(16)39/h6-11,15,36-38,41,43H,4-5,12-13H2,1-3H3/t15-,35-/m1/s1
• InChIKey: CMFSXTISUXTEGX-QXPWRNTLSA-N
• SMILES:
  CACTVS 3.385: COc1cc2[nH]c(cc2cc1O)C(=O)N3C[CH]4C[C]45C3=CC(=O)c6[nH]c(cc56)C(=O)N7CCc8c9cc([nH]c9c(OC)c(O)c78)C(=O)SC
  OpenEye OEToolkits 2.0.6: COc1cc2c(cc1O)cc([nH]2)C(=O)N3C[C@H]4C[C@@]45C3=CC(=O)c6c5cc([nH]6)C(=O)N7CCc8c7c(c(c9c8cc([nH]9)C(=O)SC)OC)O
  CACTVS 3.385: COc1cc2[nH]c(cc2cc1O)C(=O)N3C[C@H]4C[C@@]45C3=CC(=O)c6[nH]c(cc56)C(=O)N7CCc8c9cc([nH]c9c(OC)c(O)c78)C(=O)SC
  OpenEye OEToolkits 2.0.6: COc1cc2c(cc1O)cc([nH]2)C(=O)N3CC4CC45C3=CC(=O)c6c5cc([nH]6)C(=O)N7CCc8c7c(c(c9c8cc([nH]9)C(=O)SC)OC)O
• Formula: C35 H29 N5 O8 S
• Name: (+)-Yatakemycin
• ChEMBL: CHEMBL1241093
• ZINC: ZINC000072170367
• PDB chain: 5x5m Chain B Residue 302

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5x5m GyrI-like proteins catalyze cyclopropanoid hydrolysis to confer cellular protection
• Resolution: 1.211 Å
• Binding residue (original residue number in PDB): P41 Y46 V50 Q51 Y54 Y58 W85 W99 F154 Y187 P191 R192
• Binding residue (residue number reindexed from 1): P38 Y43 V47 Q48 Y51 Y55 W82 W96 F151 Y184 P188 R189
• Annotation score: 1
• Binding affinity: MOAD: ic50=4pM

External links

• PDB: RCSB:5x5m, PDBe:5x5m, PDBj:5x5m
• PDBsum: 5x5m
• PubMed: 29133784
• UniProt: Q929T5