SMTL ID : 7tq5.1

Structure of SARS-CoV-2 3CL protease in complex with the cyclopropane based inhibitor 10d

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.65 Å

Oligo State

homo-dimer

Ligands

2 x IRW: (1S,2S)-1-hydroxy-2-{[N-({[(1R,2R)-2-(4-methoxyphenyl)cyclopropyl]methoxy}carbonyl)-L-leucyl]amino}-3-[(3S)-2-oxopyrrolidin-3-yl]propane-1-sulfonic acid(Covalent)

IRW.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, P.172, H.176, D.191, Q.193, T.194, A.195 Ligands: ITX.2 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:H.45, A:P.172, A:D.191, A:A.195 Hydrogen bonds: A:G.147, A:S.148, A:S.148, A:C.149, A:H.168, A:E.170, A:E.170, A:E.170, A:Q.193, A:Q.193 Water bridges: A:A.195 IRW.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: ITX.5 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:H.45 Hydrogen bonds: B:G.147, B:C.149, B:H.168, B:E.170, B:E.170, B:Q.193, B:Q.193

2 x ITX: (1R,2S)-1-hydroxy-2-{[N-({[(1R,2R)-2-(4-methoxyphenyl)cyclopropyl]methoxy}carbonyl)-L-leucyl]amino}-3-[(3S)-2-oxopyrrolidin-3-yl]propane-1-sulfonic acid(Covalent)

ITX.2: 17 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, T.194, A.195 Ligands: IRW.1 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:D.191, A:A.195 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:G.147, A:G.147, A:A.195 ITX.5: 18 residues within 4Å: Chain B: 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 Ligands: IRW.4 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:H.45 Hydrogen bonds: B:S.148, B:H.168, B:E.170, B:E.170, B:Q.193, B:Q.193 Water bridges: B:G.147, B:G.147

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

CL.3: 2 residues within 4Å: Chain B: L.231, N.232 Ligand excluded by PLIP

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

PG4.6: 9 residues within 4Å: Chain B: E.18, G.19, M.21, W.35, A.74, G.75, V.77, L.79, N.99 2 PLIP interactions: 2 interactions with chain B Water bridges: B:G.75, B:Q.78

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Dampalla, C.S. et al., Broad-Spectrum Cyclopropane-Based Inhibitors of Coronavirus 3C-like Proteases: Biochemical, Structural, and Virological Studies. Acs Pharmacol Transl Sci (2023)

Release Date

2022-02-09

Peptides

3C-like proteinase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

3C-like proteinase

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