SMTL ID : 7t44.1

Structure of SARS-CoV-2 3CL protease in complex with inhibitor 4c

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.45 Å

Oligo State

homo-dimer

Ligands

2 x ESS: (1R,2S)-2-[(N-{[(2-azaspiro[3.3]heptan-6-yl)oxy]carbonyl}-L-leucyl)amino]-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propane-1-sulfonic acid(Covalent)

ESS.1: 19 residues within 4Å: Chain A: H.45, M.53, F.144, L.145, 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, T.194 Ligands: ET6.2 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:H.45 Hydrogen bonds: A:F.144, A:H.168, A:E.170, A:E.170, A:Q.193, A:Q.193 Water bridges: A:G.147, A:G.147 ESS.3: 17 residues within 4Å: Chain B: H.45, M.53, F.144, L.145, N.146, C.149, H.167, H.168, M.169, E.170, L.171, P.172, H.176, D.191, R.192, Q.193 Ligands: ET6.4 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:H.45, B:M.53, B:E.170, B:D.191 Hydrogen bonds: B:F.144, B:H.168, B:E.170, B:E.170, B:Q.193 Water bridges: B:G.147, B:Q.193, B:Q.193

2 x ET6: (1S,2S)-1-hydroxy-2-{[N-({[2-(methanesulfonyl)-2-azaspiro[3.3]heptan-6-yl]oxy}carbonyl)-L-leucyl]amino}-3-[(3S)-2-oxopyrrolidin-3-yl]propane-1-sulfonic acid(Covalent)

ET6.2: 19 residues within 4Å: Chain A: H.45, M.53, 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, Q.193, T.194 Ligands: ESS.1 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:M.53, A:D.191 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 ET6.4: 19 residues within 4Å: Chain B: H.45, M.53, 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: ESS.3 14 PLIP interactions: 14 interactions with chain B Hydrophobic interactions: B:H.45, B:M.53, B:E.170, B:D.191 Hydrogen bonds: B:F.144, B:G.147, B:S.148, B:C.149, B:H.168, B:E.170, B:E.170, B:Q.193 Water bridges: B:Q.193, B:Q.193

1 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.5: 4 residues within 4Å: Chain B: A.259, Q.260, T.261, G.262 No protein-ligand interaction detected (PLIP)

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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