SMTL ID : 9bo4.1

Crystal Structure of T21I SARS-CoV-2 Main Protease in Complex with Nirmatrelvir

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.28 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: 22 residues within 4Å: Chain A: H.41, M.49, Y.54, F.140, L.141, N.142, G.143, S.144, C.145, H.163, H.164, M.165, E.166, L.167, P.168, H.172, D.187, R.188, Q.189, T.190, Q.192 Chain B: S.1 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:H.41, A:M.49, A:M.165, A:E.166 Hydrogen bonds: A:F.140, A:N.142, A:G.143, A:C.145, A:H.163, A:H.164, A:E.166, A:E.166, A:T.190 Halogen bonds: A:Q.192 4WI.2: 24 residues within 4Å: Chain A: S.1 Chain B: H.41, C.44, M.49, Y.54, F.140, L.141, N.142, G.143, S.144, C.145, H.163, H.164, M.165, E.166, L.167, P.168, H.172, D.187, R.188, Q.189, T.190, A.191, Q.192 16 PLIP interactions: 15 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:H.41, B:M.165, B:E.166 Hydrogen bonds: B:F.140, B:N.142, B:G.143, B:S.144, B:C.145, B:H.163, B:H.164, B:E.166, B:E.166, B:E.166, B:T.190, A:S.1 Halogen bonds: B:Q.192

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kenneson, J.R. et al., Exploring Possible Drug-Resistant Variants of SARS-CoV-2 Main Protease (Mpro) with Noncovalent Preclinical Candidate, Mpro61. Acs Bio Med Chem Au (2025)

Release Date

2025-02-12

Peptides

3C-like proteinase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

3C-like proteinase

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