SMTL ID : 8h3e.1

Complex structure of a small molecule (SPC-14) bound SARS-CoV-2 spike protein, closed state

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-trimer

Ligands

3 x Q83: 7-(6-nitro-2,3-dihydroindol-1-yl)-7-oxidanylidene-heptanoic acid(Non-covalent)

Q83.1: 15 residues within 4Å: Chain A: C.336, F.338, I.358, A.363, Y.365, L.368, F.374, F.377, L.387, F.392, V.395, I.434, L.513, F.515, V.524 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:I.358, A:Y.365, A:F.377, A:F.392, A:V.395, A:L.513 Q83.7: 15 residues within 4Å: Chain B: C.336, F.338, I.358, A.363, Y.365, L.368, F.374, F.377, L.387, F.392, V.395, I.434, L.513, F.515, V.524 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:I.358, B:Y.365, B:F.377, B:F.392, B:V.395 Q83.13: 15 residues within 4Å: Chain C: C.336, F.338, I.358, A.363, Y.365, L.368, F.374, F.377, L.387, F.392, V.395, I.434, L.513, F.515, V.524 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:Y.365, C:F.377, C:F.392, C:V.395, C:L.513

15 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.2: 2 residues within 4Å: Chain A: Y.28, N.61 No protein-ligand interaction detected (PLIP) NAG.3: 2 residues within 4Å: Chain A: N.343, S.371 No protein-ligand interaction detected (PLIP) NAG.4: 1 residues within 4Å: Chain A: N.603 No protein-ligand interaction detected (PLIP) NAG.5: 1 residues within 4Å: Chain A: N.657 No protein-ligand interaction detected (PLIP) NAG.6: 2 residues within 4Å: Chain A: N.331, Q.580 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.580 NAG.8: 2 residues within 4Å: Chain B: Y.28, N.61 No protein-ligand interaction detected (PLIP) NAG.9: 2 residues within 4Å: Chain B: N.343, S.371 No protein-ligand interaction detected (PLIP) NAG.10: 1 residues within 4Å: Chain B: N.603 No protein-ligand interaction detected (PLIP) NAG.11: 1 residues within 4Å: Chain B: N.657 No protein-ligand interaction detected (PLIP) NAG.12: 2 residues within 4Å: Chain B: N.331, Q.580 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Q.580 NAG.14: 2 residues within 4Å: Chain C: Y.28, N.61 No protein-ligand interaction detected (PLIP) NAG.15: 2 residues within 4Å: Chain C: N.343, S.371 No protein-ligand interaction detected (PLIP) NAG.16: 1 residues within 4Å: Chain C: N.603 No protein-ligand interaction detected (PLIP) NAG.17: 1 residues within 4Å: Chain C: N.657 No protein-ligand interaction detected (PLIP) NAG.18: 2 residues within 4Å: Chain C: N.331, Q.580 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.331

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wang, Q. et al., In Silico Discovery of Small Molecule Modulators Targeting the Achilles' Heel of SARS-CoV-2 Spike Protein. Acs Cent.Sci. (2023)

Release Date

2023-03-22

Peptides

Spike glycoprotein,Fibritin: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Spike glycoprotein,Fibritin

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