- Coordinates
- PDB Format
- 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)
- 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 PLIPNAG.12: 1 residues within 4Å:- Chain A: N.1137
Ligand excluded by PLIPNAG.13: 2 residues within 4Å:- Chain A: N.712
- Chain B: D.799
Ligand excluded by PLIPNAG.14: 2 residues within 4Å:- Chain A: N.804, S.806
Ligand excluded by PLIPNAG.15: 2 residues within 4Å:- Chain A: Y.34, N.67
Ligand excluded by PLIPNAG.16: 3 residues within 4Å:- Chain A: A.709, N.1077
- Chain B: Q.898
Ligand excluded by PLIPNAG.17: 3 residues within 4Å:- Chain A: N.1101, T.1103, F.1106
Ligand excluded by PLIPNAG.18: 2 residues within 4Å:- Chain A: N.288
- Chain C: K.564
Ligand excluded by PLIPNAG.19: 1 residues within 4Å:- Chain A: N.622
Ligand excluded by PLIPNAG.22: 3 residues within 4Å:- Chain A: E.471
- Chain B: T.114, N.240
Ligand excluded by PLIPNAG.23: 2 residues within 4Å:- Chain B: N.622, T.624
Ligand excluded by PLIPNAG.24: 3 residues within 4Å:- Chain B: N.712, I.1133, G.1134
Ligand excluded by PLIPNAG.25: 3 residues within 4Å:- Chain B: N.1101, H.1104, F.1106
Ligand excluded by PLIPNAG.26: 2 residues within 4Å:- Chain B: N.170, N.171
Ligand excluded by PLIPNAG.27: 1 residues within 4Å:- Chain B: N.288
Ligand excluded by PLIPNAG.28: 2 residues within 4Å:- Chain B: H.661, N.663
Ligand excluded by PLIPNAG.29: 2 residues within 4Å:- Chain B: N.804, S.806
Ligand excluded by PLIPNAG.30: 1 residues within 4Å:- Chain B: N.1077
Ligand excluded by PLIPNAG.31: 1 residues within 4Å:- Chain C: N.1137
Ligand excluded by PLIPNAG.32: 3 residues within 4Å:- Chain C: N.1101, T.1103, H.1104
Ligand excluded by PLIPNAG.33: 2 residues within 4Å:- Chain C: E.1075, N.1077
Ligand excluded by PLIPNAG.34: 2 residues within 4Å:- Chain C: N.712, I.1133
Ligand excluded by PLIPNAG.35: 2 residues within 4Å:- Chain C: N.804, S.806
Ligand excluded by PLIPNAG.36: 2 residues within 4Å:- Chain C: N.622, T.624
Ligand excluded by PLIP- 3 x NA: SODIUM ION(Non-functional Binders)
- 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)
- 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
AB
BC
C
- Coordinates
- PDB Format
- 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)
- 24 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)
- 3 x NA: SODIUM ION(Non-functional Binders)
- 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)
- 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
AB
BC
C