Structure of PDB 5gx7 Chain A Binding Site BS01

Receptor Information

>5gx7 Chain A (length=474) Species: 519441 (Streptobacillus moniliformis DSM 12112)

PKETTIFAMHLGKALDPNLPVFVKAEKDTNIKLVNVASQNQTDQIQAYNL
MLTEGKLPDIVSYELSADLENLGIEGGLIPLEDLINQHAPNLKKFFEENP
RYKKDAVAVDGHIYMIPNYYDYFNIKVSQGYFIRQDWLEKLGLKEPRTVD
ELYTTLKAFREKDPNGNGKKDEVPFFVRANNVRKVLTSLVDLFKASPIWY
EENGMVKYGPAQKEFKHAIKELSKWYKEGLIDEEIFTRGLESRDYLLSNN
LGGATDDWIASTSSYNRNLADKIPGFNLKLVLPYELNGNAKTRHARTTYL
GGWGISKDAKDPVSLIKYFDYWYSVEGRRLWNFGIEGSEYTLVDGKPVFT
DKVLKNPDGKTPLAVLREVGAQYRLGAFQDAQYELGWASESAKAGYKYYM
DNDVVLDELPILKYTKEKSKEFVSIDTAMRAVVEEKAQQWILGSGDIDKE
WDAYIKRLENLGLSKAEQIQNEAF

Ligand information

• Ligand ID: NG6
• InChI: InChI=1S/C8H15NO9S/c1-3(10)9-5-7(12)6(11)4(18-8(5)13)2-17-19(14,15)16/h4-8,11-13H,2H2,1H3,(H,9,10)(H,14,15,16)/t4-,5-,6+,7-,8-/m1/s1
• InChIKey: WJFVEEAIYIOATH-JAJWTYFOSA-N
• SMILES:
  ACDLabs 10.04: O=S(=O)(O)OCC1OC(O)C(NC(=O)C)C(O)C1O
  OpenEye OEToolkits 1.5.0: CC(=O)NC1C(C(C(OC1O)COS(=O)(=O)O)O)O
  OpenEye OEToolkits 1.5.0: CC(=O)N[C@@H]1[C@H]([C@H]([C@H](O[C@H]1O)COS(=O)(=O)O)O)O
  CACTVS 3.341: CC(=O)N[CH]1[CH](O)O[CH](CO[S](O)(=O)=O)[CH](O)[CH]1O
  CACTVS 3.341: CC(=O)N[C@H]1[C@H](O)O[C@H](CO[S](O)(=O)=O)[C@H](O)[C@@H]1O
• Formula: C8 H15 N O9 S
• Name: 2-acetamido-2-deoxy-6-O-sulfo-beta-D-galactopyranose;
  N-ACETYL-D-GALACTOSAMINE 6-SULFATE;
  N-acetyl-6-O-sulfo-beta-D-galactosamine;
  2-acetamido-2-deoxy-6-O-sulfo-beta-D-galactose;
  2-acetamido-2-deoxy-6-O-sulfo-D-galactose;
  2-acetamido-2-deoxy-6-O-sulfo-galactose
• DrugBank: DB02186
• ZINC: ZINC000004096360
• PDB chain: 5gx7 Chain D Residue 1

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5gx7 A bacterial ABC transporter enables import of mammalian host glycosaminoglycans
• Resolution: 1.991 Å
• Binding residue (original residue number in PDB): H36 Y146 R204 K210 W284 R393
• Binding residue (residue number reindexed from 1): H10 Y120 R178 K184 W258 R367
• Annotation score: 1
• Binding affinity: PDBbind-CN: -logKd/Ki=5.56,IC50=2.76uM

Gene Ontology

Molecular Function

• GO:0046872 metal ion binding

External links

• PDB: RCSB:5gx7, PDBe:5gx7, PDBj:5gx7
• PDBsum: 5gx7
• PubMed: 28432302
• UniProt: D1AWE0