SMTL ID : 7tgr.1

Structure of SARS-CoV-2 main protease in complex with GC376

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.68 Å

Oligo State

homo-dimer

Ligands

2 x K36: (1S,2S)-2-({N-[(benzyloxy)carbonyl]-L-leucyl}amino)-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propane-1-sulfonic acid(Covalent)

K36.1: 19 residues within 4Å: Chain A: H.41, M.49, Y.54, F.140, L.141, N.142, G.143, S.144, C.145, H.163, H.164, M.165, E.166, H.172, D.187, R.188, Q.189 Chain B: S.1 Ligands: B1S.2 10 PLIP interactions: 9 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:H.41, A:M.49, A:M.165 Hydrogen bonds: A:G.143, A:S.144, A:C.145, A:H.164, A:E.166, A:E.166, B:S.1 K36.8: 19 residues within 4Å: Chain A: S.1 Chain B: H.41, M.49, Y.54, F.140, L.141, N.142, G.143, S.144, C.145, H.163, H.164, M.165, E.166, H.172, D.187, R.188, Q.189 Ligands: B1S.9 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:H.41, B:M.49, B:M.165 Hydrogen bonds: B:G.143, B:S.144, B:C.145, B:H.164, B:E.166

2 x B1S: (1R,2S)-2-({N-[(benzyloxy)carbonyl]-L-leucyl}amino)-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propane-1-sulfonic acid(Covalent)

B1S.2: 14 residues within 4Å: Chain A: H.41, Y.54, F.140, L.141, N.142, C.145, H.163, H.164, M.165, E.166, H.172, D.187, Q.189 Ligands: K36.1 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:H.41, A:M.165 Hydrogen bonds: A:H.164, A:E.166, A:E.166 Water bridges: A:H.41, A:N.142, A:G.143 B1S.9: 14 residues within 4Å: Chain B: H.41, Y.54, F.140, L.141, N.142, C.145, H.163, H.164, M.165, E.166, H.172, D.187, Q.189 Ligands: K36.8 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:H.41, B:M.165 Hydrogen bonds: B:H.164, B:E.166 Water bridges: B:H.41, B:N.142, B:G.143

2 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.3: 2 residues within 4Å: Chain A: L.227, N.228 2 PLIP interactions: 2 interactions with chain A Water bridges: A:L.227, A:N.231 EDO.10: 2 residues within 4Å: Chain B: L.227, N.228 2 PLIP interactions: 2 interactions with chain B Water bridges: B:L.227, B:N.231

4 x CL: CHLORIDE ION(Non-functional Binders)

CL.4: 3 residues within 4Å: Chain A: K.5 Chain B: K.5 Ligands: CL.11 Ligand excluded by PLIP CL.5: 1 residues within 4Å: Chain A: C.85 Ligand excluded by PLIP CL.11: 3 residues within 4Å: Chain A: K.5 Chain B: K.5 Ligands: CL.4 Ligand excluded by PLIP CL.12: 1 residues within 4Å: Chain B: C.85 Ligand excluded by PLIP

2 x K: POTASSIUM ION(Non-covalent)

K.6: 4 residues within 4Å: Chain A: N.221, F.223, D.263, S.267 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:N.221, A:F.223, A:D.263, H2O.4 K.13: 4 residues within 4Å: Chain B: N.221, F.223, D.263, S.267 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:N.221, B:F.223, B:D.263, H2O.10

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

NA.7: 4 residues within 4Å: Chain A: R.105, D.176, E.178, N.180 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.176 NA.14: 4 residues within 4Å: Chain B: R.105, D.176, E.178, N.180 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.178, B:N.180

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Moghadasi, S.A. et al., Gain-of-Signal Assays for Probing Inhibition of SARS-CoV-2 M pro /3CL pro in Living Cells. Mbio (2022)

Release Date

2022-05-04

Peptides

3C-like proteinase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

3C-like proteinase

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