SMTL ID : 9kgs.1

Discovery of an orally bioavailable reversible covalent SARS-CoV-2 Mpro inhibitor with pan-coronavirus activity

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-dimer

Ligands

2 x PIV- 01- 02- 03: (S)-2-((R)-2-cyclopentyl-N-methyl-2-pivalamidoacetamido)-N-((S)-1-imino-3-((S)-2-oxopiperidin-3-yl)propan-2-yl)pentanamide(Non-covalent)

PIV-01-02-03.1: 20 residues within 4Å: Chain B: H.46, M.54, F.145, L.146, N.147, S.149, C.150, H.168, H.169, M.170, E.171, L.172, P.173, D.192, R.193, Q.194, T.195, A.196, Q.197 Ligands: 04.3 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:L.172, B:D.192 Hydrogen bonds: B:H.46, B:F.145, B:H.169, B:E.171, B:E.171, B:Q.194 PIV-01-02-03.2: 20 residues within 4Å: Chain A: H.46, M.54, F.145, L.146, N.147, S.149, C.150, H.168, H.169, M.170, E.171, L.172, P.173, H.177, D.192, R.193, Q.194, T.195, Q.197 Ligands: 04.4 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:N.147, A:D.192 Hydrogen bonds: A:F.145, A:H.169, A:E.171, A:E.171, A:Q.194 Water bridges: A:N.147

2 x 04: cyclopropylcarbamic acid

04.3: 5 residues within 4Å: Chain B: T.31, G.148, S.149, C.150 Ligands: PIV-01-02-03.1 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:G.148, B:C.150 Water bridges: B:H.46 04.4: 7 residues within 4Å: Chain A: T.30, T.31, N.147, G.148, S.149, C.150 Ligands: PIV-01-02-03.2 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:T.30 Hydrogen bonds: A:G.148, A:C.150 Water bridges: A:N.147

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tan, Q.W. et al., Discovery of an Orally Bioavailable Reversible Covalent SARS-CoV-2 M pro Inhibitor with Pan-Coronavirus Activity. J.Med.Chem. (2025)

Release Date

2025-08-20

Peptides

3C-like proteinase nsp5: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
A

3C-like proteinase nsp5

Related Entries With Identical Sequence