SMTL ID : 7uup.1

SARS-CoV-2 Main Protease S144A (Mpro S144A) in Complex with Nirmatrelvir (PF-07321332)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-dimer

Ligands

2 x 4WI: (1R,2S,5S)-N-{(1E,2S)-1-imino-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}-6,6-dimethyl-3-[3-methyl-N-(trifluoroacetyl)-L-valyl]-3-azabicyclo[3.1.0]hexane-2-carboxamide(Covalent)

4WI.1: 19 residues within 4Å: Chain A: H.41, M.49, Y.54, F.140, N.142, G.143, A.144, C.145, H.163, H.164, M.165, E.166, L.167, H.172, D.187, R.188, Q.189, T.190, Q.192 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:H.41, A:M.165, A:E.166 Hydrogen bonds: A:F.140, A:G.143, A:A.144, A:C.145, A:H.164, A:E.166, A:E.166, A:T.190 pi-Stacking: A:H.41 Halogen bonds: A:Q.192 4WI.3: 19 residues within 4Å: Chain B: H.41, M.49, Y.54, F.140, N.142, G.143, A.144, C.145, H.163, H.164, M.165, E.166, L.167, H.172, D.187, R.188, Q.189, T.190, Q.192 13 PLIP interactions: 13 interactions with chain B Hydrophobic interactions: B:H.41, B:M.165, B:E.166 Hydrogen bonds: B:F.140, B:G.143, B:A.144, B:C.145, B:H.164, B:E.166, B:E.166, B:T.190 pi-Stacking: B:H.41 Halogen bonds: B:Q.192

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

CL.2: 5 residues within 4Å: Chain A: S.284, A.285 Chain B: S.284, A.285 Ligands: CL.4 Ligand excluded by PLIP CL.4: 5 residues within 4Å: Chain A: S.284, A.285 Chain B: S.284, A.285 Ligands: CL.2 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Westberg, M. et al., An orally bioavailable SARS-CoV-2 main protease inhibitor exhibits improved affinity and reduced sensitivity to mutations. Sci Transl Med (2024)

Release Date

2023-10-11

Peptides

3C-like proteinase nsp5: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

3C-like proteinase nsp5

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