Structure of PDB 7yck Chain A Binding Site BS01

Receptor Information

>7yck Chain A (length=198) Species: 2697049 (Severe acute respiratory syndrome coronavirus 2)

TNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGV
SPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGC
VIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNG
VEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCGPKKS

Ligand information

• Ligand ID: FUC
• InChI: InChI=1S/C6H12O5/c1-2-3(7)4(8)5(9)6(10)11-2/h2-10H,1H3/t2-,3+,4+,5-,6+/m0/s1
• InChIKey: SHZGCJCMOBCMKK-SXUWKVJYSA-N
• SMILES:
  CACTVS 3.341: C[C@@H]1O[C@@H](O)[C@@H](O)[C@H](O)[C@@H]1O
  ACDLabs 10.04: OC1C(O)C(OC(O)C1O)C
  OpenEye OEToolkits 1.5.0: CC1C(C(C(C(O1)O)O)O)O
  OpenEye OEToolkits 1.5.0: C[C@H]1[C@H]([C@H]([C@@H]([C@@H](O1)O)O)O)O
  CACTVS 3.341: C[CH]1O[CH](O)[CH](O)[CH](O)[CH]1O
• Formula: C6 H12 O5
• Name: alpha-L-fucopyranose;
  alpha-L-fucose;
  6-deoxy-alpha-L-galactopyranose;
  L-fucose;
  fucose
• ChEMBL: CHEMBL1232862
• DrugBank: DB04473
• ZINC: ZINC000001532814
• PDB chain: 7yck Chain G Residue 4

Receptor-Ligand Complex Structure

Structure summary

• PDB: 7yck Structural basis for a conserved neutralization epitope on the receptor-binding domain of SARS-CoV-2.
• Resolution: 2.6 Å
• Binding residue (original residue number in PDB): S366 V367
• Binding residue (residue number reindexed from 1): S34 V35
• Annotation score: 4

External links

• PDB: RCSB:7yck, PDBe:7yck, PDBj:7yck
• PDBsum: 7yck
• PubMed: 36658148
• UniProt: P0DTC2|SPIKE_SARS2 Spike glycoprotein (Gene Name=S)