SMTL ID : 7t46.1

Structure of SARS-CoV-2 3CL protease in complex with inhibitor 8c

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.45 Å

Oligo State

homo-dimer

Ligands

2 x F8C: (1S,2S)-1-hydroxy-2-{[N-({[7-(2-methylpropanoyl)-7-azaspiro[3.5]nonan-2-yl]oxy}carbonyl)-L-leucyl]amino}-3-[(3S)-2-oxopyrrolidin-3-yl]propane-1-sulfonic acid(Covalent)

F8C.1: 18 residues within 4Å: Chain A: H.45, F.144, L.145, N.146, G.147, S.148, C.149, H.167, H.168, M.169, E.170, L.171, P.172, H.176, D.191, R.192, Q.193 Ligands: F5L.2 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:H.45, A:E.170 Hydrogen bonds: A:F.144, A:G.147, A:S.148, A:C.149, A:H.168, A:E.170, A:E.170, A:Q.193, A:Q.193 F8C.3: 19 residues within 4Å: Chain B: H.45, M.53, Y.58, F.144, N.146, G.147, S.148, C.149, H.167, H.168, M.169, E.170, L.171, P.172, H.176, D.191, R.192, Q.193 Ligands: F5L.4 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:H.45, B:M.53, B:Q.193 Hydrogen bonds: B:G.147, B:C.149, B:H.168, B:E.170, B:E.170, B:Q.193

2 x F5L: (1R,2S)-1-hydroxy-2-{[N-({[7-(2-methylpropanoyl)-7-azaspiro[3.5]nonan-2-yl]oxy}carbonyl)-L-leucyl]amino}-3-[(3S)-2-oxopyrrolidin-3-yl]propane-1-sulfonic acid(Covalent)

F5L.2: 16 residues within 4Å: Chain A: H.45, F.144, N.146, S.148, C.149, H.167, H.168, M.169, E.170, L.171, P.172, H.176, D.191, R.192, Q.193 Ligands: F8C.1 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:H.45 Hydrogen bonds: A:S.148, A:H.168, A:E.170, A:E.170, A:E.170, A:Q.193, A:Q.193 Water bridges: A:H.45, A:G.147, A:G.147 F5L.4: 18 residues within 4Å: Chain B: H.45, M.53, Y.58, F.144, N.146, S.148, C.149, H.167, H.168, M.169, E.170, L.171, P.172, H.176, D.191, R.192, Q.193 Ligands: F8C.3 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:H.45, B:M.53, B:M.169, B:Q.193 Hydrogen bonds: B:S.148, B:H.168, B:E.170, B:Q.193 Water bridges: B:G.147, B:G.147

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Dampalla, C.S. et al., Structure-Guided Design of Potent Spirocyclic Inhibitors of Severe Acute Respiratory Syndrome Coronavirus-2 3C-like Protease. J.Med.Chem. (2022)

Release Date

2021-12-22

Peptides

3C-like proteinase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

3C-like proteinase

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