Structure of PDB 5l9o Chain A Binding Site BS01

Receptor Information

>5l9o Chain A (length=241) Species: 176299 (Agrobacterium fabrum str. C58)

DNPLGLIDPTTISVGTMGDAKPYAFTTADGNFTGFDIELFLNVAGRLGFK
KEQVVFTGQEFSALMPSVANGRFDVAAAAIGTTAKRKETVDFSDGYLAGF
LSVLTSEAGITDAAGLKGKRLGVVQGTLQEIYAEKNFAGTDLVKFPDNNS
AVSALNNGTVDAHFLDFEAAKDYSARYPALKIAVNIPSFDAPAGFVIRKG
NDALRNALDKGLKEAMQDGTWKKLHEKWFPGTPMPAAYLPK

Ligand information

• Ligand ID: GOP
• InChI: InChI=1S/C11H22N2O8/c12-8(17)2-1-5(11(20)21)13-3-6(15)9(18)10(19)7(16)4-14/h5-7,9-10,13-16,18-19H,1-4H2,(H2,12,17)(H,20,21)/t5-,6-,7+,9+,10+/m0/s1
• InChIKey: VPRLICVDSGMIKO-ZSAGQLGGSA-N
• SMILES:
  CACTVS 3.385: NC(=O)CC[CH](NC[CH](O)[CH](O)[CH](O)[CH](O)CO)C(O)=O
  OpenEye OEToolkits 2.0.5: C(CC(=O)N)[C@@H](C(=O)O)NC[C@@H]([C@H]([C@@H]([C@@H](CO)O)O)O)O
  CACTVS 3.385: NC(=O)CC[C@H](NC[C@H](O)[C@@H](O)[C@H](O)[C@H](O)CO)C(O)=O
  OpenEye OEToolkits 2.0.5: C(CC(=O)N)C(C(=O)O)NCC(C(C(C(CO)O)O)O)O
• Formula: C11 H22 N2 O8
• Name: Glucopine
• ZINC: ZINC000071758446
• PDB chain: 5l9o Chain A Residue 301

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5l9o Structural Basis for High Specificity of Amadori Compound and Mannopine Opine Binding in Bacterial Pathogens.
• Resolution: 1.84 Å
• Binding residue (original residue number in PDB): F96 A113 A114 G116 R121 A133 G134 T162 L163 Q164 D201 S223 A226
• Binding residue (residue number reindexed from 1): F61 A78 A79 G81 R86 A98 G99 T127 L128 Q129 D166 S188 A191
• Annotation score: 1
• Binding affinity: MOAD: Kd=4uM
  PDBbind-CN: -logKd/Ki=5.40,Kd=4uM

Gene Ontology

Molecular Function

• GO:0015276 ligand-gated monoatomic ion channel activity

Biological Process

• GO:0034220 monoatomic ion transmembrane transport

Cellular Component

• GO:0016020 membrane
• GO:0042597 periplasmic space

External links

• PDB: RCSB:5l9o, PDBe:5l9o, PDBj:5l9o
• PDBsum: 5l9o
• PubMed: 27609514
• UniProt: Q7D447