Structure of PDB 6h9v Chain B Binding Site BS01

Receptor Information

>6h9v Chain B (length=303) Species: 546981 (Norovirus Hu/GII-4/Saga4/2006/JP)

SKPFTVPILTVEEMTNSRFPIPLEKLFTGPSGAFVVQPQNGRCTTDGVLL
GTTQLSPVNICTFRGDVTHIAGSRNYTMNLASLNWNNYDPTEEIPAPLGT
PDFVGKIQGLLTQTTKGDGSTRGHKATVYTGSAPFTPKLGSVQFSTDTDF
ETHQNTKFTPVGVIQDTTHRNEPQQWVLPSYSGRNVHNVHLAPAVAPTFP
GEQLLFFRSTMPGCSGYPNMDLDCLLPQEWVQHFYQEAAPAQSDVALLRF
VNPDTGRVLFECKLHKSGYVTVAHTGQHDLVIPPNGYFRFDSWVNQFYTL
APM

Ligand information

• Ligand ID: MFU
• InChI: InChI=1S/C7H14O5/c1-3-4(8)5(9)6(10)7(11-2)12-3/h3-10H,1-2H3/t3-,4+,5+,6-,7+/m0/s1
• InChIKey: OHWCAVRRXKJCRB-CXNFULCWSA-N
• SMILES:
  OpenEye OEToolkits 1.5.0: CC1C(C(C(C(O1)OC)O)O)O
  OpenEye OEToolkits 1.5.0: C[C@H]1[C@H]([C@H]([C@@H]([C@@H](O1)OC)O)O)O
  ACDLabs 10.04: OC1C(O)C(O)C(OC1OC)C
  CACTVS 3.341: CO[CH]1O[CH](C)[CH](O)[CH](O)[CH]1O
  CACTVS 3.341: CO[C@@H]1O[C@@H](C)[C@@H](O)[C@@H](O)[C@@H]1O
• Formula: C7 H14 O5
• Name: methyl alpha-L-fucopyranoside;
  ALPHA-L-METHYL-FUCOSE;
  methyl 6-deoxy-alpha-L-galactopyranoside;
  methyl alpha-L-fucoside;
  methyl L-fucoside;
  methyl fucoside
• ChEMBL: CHEMBL1234282
• DrugBank: DB03879
• ZINC: ZINC000002509839
• PDB chain: 6h9v Chain B Residue 601

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6h9v A post-translational modification of human Norovirus capsid protein attenuates glycan binding.
• Resolution: 1.52 Å
• Binding residue (original residue number in PDB): T344 R345 D374
• Binding residue (residue number reindexed from 1): T121 R122 D149
• Annotation score: 1
• Binding affinity: PDBbind-CN: -logKd/Ki=0.66,Kd=220mM

External links

• PDB: RCSB:6h9v, PDBe:6h9v, PDBj:6h9v
• PDBsum: 6h9v
• PubMed: 30899001
• UniProt: B5BTR7