SMTL ID : 7cb7.1

1.7A resolution structure of SARS-CoV-2 main protease (Mpro) in complex with broad-spectrum coronavirus protease inhibitor GC376

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.69 Å

Oligo State

homo-dimer

Ligands

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

NA.1: 5 residues within 4Å: Chain A: G.3, G.4, G.5, S.6 Chain B: V.176 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.4, A:S.6 Water bridges: A:S.6

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)

K36.2: 18 residues within 4Å: Chain A: H.46, M.54, Y.59, F.145, L.146, N.147, G.148, S.149, C.150, H.168, H.169, M.170, E.171, H.177, D.192, R.193, Q.194 Ligands: B1S.3 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:H.46, A:M.54, A:M.170 Hydrogen bonds: A:F.145, A:G.148, A:S.149, A:S.149, A:C.150, A:H.169, A:E.171, A:E.171, A:Q.194 Water bridges: A:N.147, A:Q.194 K36.5: 19 residues within 4Å: Chain A: G.1 Chain B: H.46, M.54, Y.59, F.145, L.146, N.147, G.148, S.149, C.150, H.168, H.169, M.170, E.171, H.177, D.192, R.193, Q.194 Ligands: B1S.4 12 PLIP interactions: 11 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:M.170, B:Q.194 Hydrogen bonds: B:G.148, B:S.149, B:C.150, B:H.169, B:E.171, B:E.171, B:E.171, B:Q.194 Water bridges: B:G.148, A:G.1

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.3: 19 residues within 4Å: Chain A: L.32, H.46, M.54, Y.59, F.145, L.146, N.147, G.148, S.149, C.150, H.168, H.169, M.170, E.171, H.177, D.192, R.193, Q.194 Ligands: K36.2 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:H.46, A:M.54, A:M.170 Hydrogen bonds: A:F.145, A:H.169, A:E.171, A:E.171, A:Q.194 Water bridges: A:G.148, A:G.148 B1S.4: 17 residues within 4Å: Chain A: G.1 Chain B: H.46, M.54, F.145, L.146, N.147, S.149, C.150, H.168, H.169, M.170, E.171, H.177, D.192, R.193, Q.194 Ligands: K36.5 12 PLIP interactions: 11 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:M.54, B:Q.194 Hydrogen bonds: B:H.169, B:E.171, B:E.171, B:E.171, B:Q.194 Water bridges: B:H.46, B:N.147, B:G.148, B:G.148, A:G.1

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wang, Y.C. et al., Structural basis of SARS-CoV-2 main protease inhibition by a broad-spectrum anti-coronaviral drug. Am J Cancer Res (2020)

Release Date

2021-05-05

Peptides

3C-like proteinase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

3C-like proteinase