Structure of PDB 5l9i Chain A Binding Site BS01

Receptor Information

>5l9i Chain A (length=326) Species: 1183423 (Agrobacterium tumefaciens str. B6)

HMDVVIASSGGGWQEAQDKALWAPAAKALNITYTQDTFQNWAEARAQVES
GSVTWDIIQIGIADEPQAKAAGVLEKLDPDIVNKADFPPGSVTDSFVANS
NYSTLIAWNKKTYGDNGPKSMADFFDVKKFPGKRALWNQPIGMIEAAALA
LGTPRDKVYEFLSTEEGRKAAIAKLTELAPSVSVWWESGAQAAQLIKDGE
VDMIITWGGRVQGAINDGANFAYTFNDAQLGTDGYAIVKGAPHRDAAMRF
LKEMSKAEYQKDLPNSFATAPANMKAYDLAKYTPEKMATMASAPENVAVQ
YSVDPNFWAKHAKWASEAYDNVRLSR

Ligand information

• Ligand ID: SNW
• InChI: InChI=1S/C11H20N2O8/c12-7(15)2-1-5(10(18)19)13-4-11(20)9(17)8(16)6(14)3-21-11/h5-6,8-9,13-14,16-17,20H,1-4H2,(H2,12,15)(H,18,19)/t5-,6+,8+,9-,11+/m0/s1
• InChIKey: SNIATPDKUZZXAT-VISRLPHGSA-N
• SMILES:
  CACTVS 3.385: NC(=O)CC[C@H](NC[C@@]1(O)OC[C@@H](O)[C@@H](O)[C@@H]1O)C(O)=O
  CACTVS 3.385: NC(=O)CC[CH](NC[C]1(O)OC[CH](O)[CH](O)[CH]1O)C(O)=O
  OpenEye OEToolkits 2.0.5: C1[C@H]([C@H]([C@@H]([C@](O1)(CN[C@@H](CCC(=O)N)C(=O)O)O)O)O)O
  OpenEye OEToolkits 2.0.5: C1C(C(C(C(O1)(CNC(CCC(=O)N)C(=O)O)O)O)O)O
• Formula: C11 H20 N2 O8
• Name: Deoxyfructosylglutamine;
  santhopine
• ZINC: ZINC000584905675
• PDB chain: 5l9i Chain A Residue 401

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5l9i Structural Basis for High Specificity of Amadori Compound and Mannopine Opine Binding in Bacterial Pathogens.
• Resolution: 1.9 Å
• Binding residue (original residue number in PDB): S37 W41 Q67 Q87 Y130 W235 R238 D261 T297
• Binding residue (residue number reindexed from 1): S9 W13 Q39 Q59 Y102 W207 R210 D233 T269
• Annotation score: 1
• Binding affinity: MOAD: Kd=99nM
  PDBbind-CN: -logKd/Ki=7.00,Kd=99nM

External links

• PDB: RCSB:5l9i, PDBe:5l9i, PDBj:5l9i
• PDBsum: 5l9i
• PubMed: 27609514