SMTL ID : 8p9y.1

SARS-CoV-2 S protein S:D614G mutant in 3-down with binding site of an entry inhibitor

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 4.30 Å

Oligo State

homo-trimer

Ligands

10 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.1: 2 residues within 4Å: Chain A: N.720, L.925 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 7 residues within 4Å: Chain A: F.344, G.345, F.348, N.349, L.374, S.377 Ligands: XIO.37 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.377 NAG-NAG.3: 3 residues within 4Å: Chain A: E.138, N.170, N.171 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 3 residues within 4Å: Chain B: N.720, L.925, Q.929 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 2 residues within 4Å: Chain B: N.337, Q.586 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 2 residues within 4Å: Chain B: I.1135, N.1137 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 1 residues within 4Å: Chain B: N.349 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 3 residues within 4Å: Chain C: N.720, L.925, Q.929 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 2 residues within 4Å: Chain C: E.287, N.288 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 3 residues within 4Å: Chain C: G.345, N.349, S.377 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:S.377

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

NAG.11: 3 residues within 4Å: Chain A: T.114, N.240, T.242 Ligand excluded by PLIP NAG.12: 1 residues within 4Å: Chain A: N.1137 Ligand excluded by PLIP NAG.13: 2 residues within 4Å: Chain A: N.712 Chain B: D.799 Ligand excluded by PLIP NAG.14: 2 residues within 4Å: Chain A: N.804, S.806 Ligand excluded by PLIP NAG.15: 2 residues within 4Å: Chain A: Y.34, N.67 Ligand excluded by PLIP NAG.16: 3 residues within 4Å: Chain A: A.709, N.1077 Chain B: Q.898 Ligand excluded by PLIP NAG.17: 3 residues within 4Å: Chain A: N.1101, T.1103, F.1106 Ligand excluded by PLIP NAG.18: 2 residues within 4Å: Chain A: N.288 Chain C: K.564 Ligand excluded by PLIP NAG.19: 1 residues within 4Å: Chain A: N.622 Ligand excluded by PLIP NAG.22: 3 residues within 4Å: Chain A: E.471 Chain B: T.114, N.240 Ligand excluded by PLIP NAG.23: 2 residues within 4Å: Chain B: N.622, T.624 Ligand excluded by PLIP NAG.24: 3 residues within 4Å: Chain B: N.712, I.1133, G.1134 Ligand excluded by PLIP NAG.25: 3 residues within 4Å: Chain B: N.1101, H.1104, F.1106 Ligand excluded by PLIP NAG.26: 2 residues within 4Å: Chain B: N.170, N.171 Ligand excluded by PLIP NAG.27: 1 residues within 4Å: Chain B: N.288 Ligand excluded by PLIP NAG.28: 2 residues within 4Å: Chain B: H.661, N.663 Ligand excluded by PLIP NAG.29: 2 residues within 4Å: Chain B: N.804, S.806 Ligand excluded by PLIP NAG.30: 1 residues within 4Å: Chain B: N.1077 Ligand excluded by PLIP NAG.31: 1 residues within 4Å: Chain C: N.1137 Ligand excluded by PLIP NAG.32: 3 residues within 4Å: Chain C: N.1101, T.1103, H.1104 Ligand excluded by PLIP NAG.33: 2 residues within 4Å: Chain C: E.1075, N.1077 Ligand excluded by PLIP NAG.34: 2 residues within 4Å: Chain C: N.712, I.1133 Ligand excluded by PLIP NAG.35: 2 residues within 4Å: Chain C: N.804, S.806 Ligand excluded by PLIP NAG.36: 2 residues within 4Å: Chain C: N.622, T.624 Ligand excluded by PLIP

3 x NA: SODIUM ION(Non-functional Binders)

NA.20: 1 residues within 4Å: Ligands: XIO.37 No protein-ligand interaction detected (PLIP) NA.21: 1 residues within 4Å: Ligands: XIO.37 No protein-ligand interaction detected (PLIP) NA.38: 1 residues within 4Å: Ligands: XIO.37 No protein-ligand interaction detected (PLIP)

1 x XIO: [(2~{S})-2-[[4-(2-azanylethanoylamino)-7-[[(2~{S})-3-[2-(4-nitrophenyl)sulfanyl-1~{H}-indol-3-yl]-1-oxidanylidene-1-sodiooxy-propan-2-yl]amino]-4-[3-[[(2~{S})-3-[2-(4-nitrophenyl)sulfanyl-1~{H}-indol-3-yl]-1-oxidanylidene-1-sodiooxy-propan-2-yl]amino]-3-oxidanylidene-propyl]-7-oxidanylidene-heptanoyl]amino]-3-[2-(4-nitrophenyl)sulfanyl-1~{H}-indol-3-yl]propanoyl]oxysodium(Non-covalent)

XIO.37: 8 residues within 4Å: Chain A: N.349 Chain C: T.484, F.492, N.493 Ligands: NAG-NAG.2, NA.20, NA.21, NA.38 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:T.484, C:F.492, C:N.493

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gargantilla, M. et al., C-2 Thiophenyl Tryptophan Trimers Inhibit Cellular Entry of SARS-CoV-2 through Interaction with the Viral Spike (S) Protein. J.Med.Chem. (2023)

Release Date

2023-09-27

Peptides

Spike protein S1,Spike glycoprotein: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Spike protein S1,Spike glycoprotein

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