SMTL ID : 7lzx.1

Structure of SARS-CoV-2 3CL protease in complex with inhibitor 1c

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.65 Å

Oligo State

homo-dimer

Ligands

2 x YMG: (1S,2S)-2-((S)-2-((((4,4-dimethylcyclohexyl)oxy)carbonyl)amino)-4-methylpentanamido)-1-hydroxy-3-((S)-2-oxopyrrolidin-3-yl)propane-1-sulfonic acid(Covalent)

YMG.1: 16 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, P.172, H.176, D.191, Q.193 Ligands: YMD.2 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:H.45 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 YMG.3: 18 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, Q.193 Ligands: YMD.4 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:H.45, B:M.169, 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, B:Q.193

2 x YMD: (1R,2S)-2-((S)-2-((((4,4-dimethylcyclohexyl)oxy)carbonyl)amino)-4-methylpentanamido)-1-hydroxy-3-((S)-2-oxopyrrolidin-3-yl)propane-1-sulfonic acid(Covalent)

YMD.2: 15 residues within 4Å: Chain A: H.45, F.144, L.145, N.146, S.148, C.149, H.167, H.168, M.169, E.170, P.172, H.176, D.191, Q.193 Ligands: YMG.1 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:H.45 Hydrogen bonds: A:F.144, A:S.148, A:H.168, A:E.170, A:E.170, A:Q.193, A:Q.193 Water bridges: A:G.147, A:G.147 YMD.4: 16 residues within 4Å: Chain B: H.45, M.53, F.144, N.146, S.148, C.149, H.167, H.168, M.169, E.170, L.171, P.172, H.176, D.191, Q.193 Ligands: YMG.3 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:H.45, B:M.169, B:D.191 Hydrogen bonds: B:F.144, B:H.168, B:E.170, B:E.170, 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 Inhibitors of SARS-CoV-2 3CL Protease: Structural, Biochemical, and Cell-Based Studies. J.Med.Chem. (2021)

Release Date

2021-03-24

Peptides

3C-like proteinase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

3C-like proteinase

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