SMTL ID : 6wtt.1 (1 other biounit)

Crystals Structure of the SARS-CoV-2 (COVID-19) main protease with inhibitor GC-376

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.15 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, F.140, L.141, N.142, G.143, S.144, C.145, H.163, H.164, M.165, E.166, P.168, H.172, D.187, Q.189, T.190, A.191, Q.192 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:H.41, A:M.165 Hydrogen bonds: A:F.140, A:G.143, A:S.144, A:S.144, A:C.145, A:H.164, A:E.166, A:Q.189 Water bridges: A:Q.189 K36.8: 19 residues within 4Å: Chain B: H.41, M.49, F.140, L.141, N.142, G.143, S.144, C.145, H.163, H.164, M.165, E.166, P.168, H.172, D.187, Q.189, T.190, A.191, Q.192 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:H.41, B:M.165 Hydrogen bonds: B:F.140, B:G.143, B:S.144, B:S.144, B:C.145, B:H.164, B:E.166, B:E.166, B:Q.189 Water bridges: B:Q.189

2 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.2: 4 residues within 4Å: Chain A: L.227, T.243, Q.244, D.245 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.244, A:D.245 PEG.9: 4 residues within 4Å: Chain B: L.227, T.243, Q.244, D.245 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Q.244, B:D.245

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 4 residues within 4Å: Chain A: F.223, K.269, E.270, Q.273 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.273 Water bridges: A:N.221 GOL.10: 4 residues within 4Å: Chain B: F.223, K.269, E.270, Q.273 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Q.273 Water bridges: B:N.221

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

CL.4: 1 residues within 4Å: Chain B: P.122 Ligand excluded by PLIP CL.5: 5 residues within 4Å: Chain A: K.5, Y.126, Q.127 Chain B: K.5 Ligands: CL.12 Ligand excluded by PLIP CL.6: 1 residues within 4Å: Chain A: F.103 Ligand excluded by PLIP CL.11: 1 residues within 4Å: Chain A: P.122 Ligand excluded by PLIP CL.12: 5 residues within 4Å: Chain A: K.5 Chain B: K.5, Y.126, Q.127 Ligands: CL.5 Ligand excluded by PLIP CL.13: 1 residues within 4Å: Chain B: F.103 Ligand excluded by PLIP

2 x MG: MAGNESIUM ION(Non-covalent)

MG.7: 2 residues within 4Å: Chain A: L.58, M.82 No protein-ligand interaction detected (PLIP) MG.14: 2 residues within 4Å: Chain B: L.58, M.82 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ma, C. et al., Boceprevir, GC-376, and calpain inhibitors II, XII inhibit SARS-CoV-2 viral replication by targeting the viral main protease. Cell Res. (2020)

Release Date

2020-05-20

Peptides

3C-like proteinase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

3C-like proteinase

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