SMTL ID : 9kgr.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 1.47 Å

Oligo State

homo-dimer

Ligands

2 x PIV- 01- NVA- 02: (S)-2-((R)-2-cyclopentyl-2-pivalamidoacetamido)-N-((2S,3R)-4-(cyclopropylamino)-3-hydroxy-4-oxo-1-((S)-2-oxopiperidin-3-yl)butan-2-yl)pentanamide(Non-covalent)

PIV-01-NVA-02.1: 18 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, P.173, D.192, R.193, Q.194, T.195, Q.197 Ligands: 03.3 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:F.145, B:S.149, B:H.169, B:E.171, B:E.171, B:Q.194, B:Q.194 PIV-01-NVA-02.2: 17 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, P.173, D.192, R.193, T.195, Q.197 Ligands: 03.4 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:E.171, A:Q.197 Hydrogen bonds: A:F.145, A:S.149, A:H.169, A:E.171, A:E.171

2 x 03: cyclopropylcarbamic acid

03.3: 7 residues within 4Å: Chain B: T.30, T.31, N.147, G.148, S.149, C.150 Ligands: PIV-01-NVA-02.1 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:T.30 Hydrogen bonds: B:G.148, B:C.150 03.4: 8 residues within 4Å: Chain A: T.30, T.31, L.32, N.147, G.148, S.149, C.150 Ligands: PIV-01-NVA-02.2 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:T.30 Hydrogen bonds: A:G.148, A:C.150

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
A

B
B

3C-like proteinase nsp5

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