SMTL ID : 9asy.1

Crystal structure of SARS-CoV-2 3CL protease in complex with a m-chlorobenzyl 2-pyrrolidone inhibitor

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-dimer

Ligands

2 x 01: (1R,2S)-2-({N-[({(2S)-1-[(3-chlorophenyl)methyl]-5-oxopyrrolidin-2-yl}methoxy)carbonyl]-L-leucyl}amino)-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propane-1-sulfonic acid

01.1: 18 residues within 4Å: Chain A: H.45, F.144, N.146, C.149, H.167, H.168, M.169, E.170, L.171, P.172, H.176, D.191, R.192, Q.193, T.194, A.195, Q.196 Ligands: 02.2 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:H.45 Hydrogen bonds: A:E.170, A:Q.196 Water bridges: A:G.147 01.5: 19 residues within 4Å: Chain B: H.45, 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, T.194, A.195, Q.196 Ligands: 02.6 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:H.45 Hydrogen bonds: B:E.170, B:E.170, B:Q.193, B:Q.196 Water bridges: B:G.147

2 x 02: (1S,2S)-2-({N-[({(2S)-1-[(3-chlorophenyl)methyl]-5-oxopyrrolidin-2-yl}methoxy)carbonyl]-L-leucyl}amino)-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propane-1-sulfonic acid

02.2: 21 residues within 4Å: Chain A: H.45, 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, T.194, A.195, Q.196 Ligands: 01.1 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:H.45, A:E.170 Hydrogen bonds: A:G.147, A:S.148, A:C.149, A:E.170, A:Q.196 02.6: 21 residues within 4Å: Chain B: 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, T.194, A.195, Q.196 Ligands: 01.5 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:H.45 Hydrogen bonds: B:G.147, B:S.148, B:C.149, B:E.170, B:E.170, B:Q.193, B:Q.196

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

PG4.3: 4 residues within 4Å: Chain A: A.259, Q.260, T.261, G.262 No protein-ligand interaction detected (PLIP)

1 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.4: 3 residues within 4Å: Chain B: Q.87, N.88, N.184 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:Q.87, B:N.88, B:N.184 Water bridges: B:N.88, B:E.182, B:E.182

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Dampalla, C.S. et al., Structure-Guided Design of Potent Coronavirus Inhibitors with a 2-Pyrrolidone Scaffold: Biochemical, Crystallographic, and Virological Studies. J.Med.Chem. (2024)

Release Date

2024-07-10

Peptides

3C-like proteinase nsp5: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

3C-like proteinase nsp5

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