SMTL ID : 8e5c.1

Crystal Structure of SARS CoV-2 Mpro mutant L50F with Nirmatrelvir captured in two conformational states

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-dimer

Ligands

2 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.1: 6 residues within 4Å: Chain A: R.4, K.5, W.207, L.282, E.288, F.291 No protein-ligand interaction detected (PLIP) DMS.13: 6 residues within 4Å: Chain B: R.4, K.5, W.207, L.282, E.288, F.291 No protein-ligand interaction detected (PLIP)

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(Non-covalent)

4WI.2: 22 residues within 4Å: Chain A: L.27, 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 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:H.41, A:M.49, A:M.165, A:E.166 Hydrogen bonds: A:G.143, A:S.144, A:C.145, A:H.164, A:E.166, A:E.166, A:T.190 Halogen bonds: A:Q.192 4WI.14: 22 residues within 4Å: Chain B: L.27, 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 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:H.41, B:M.49, B:M.165, B:E.166 Hydrogen bonds: B:G.143, B:S.144, B:C.145, B:H.164, B:E.166, B:E.166, B:T.190 Halogen bonds: B:Q.192

12 x NA: SODIUM ION(Non-functional Binders)

NA.3: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) NA.4: 1 residues within 4Å: Chain A: Y.101 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.101 Water bridges: A:Y.101 NA.5: 1 residues within 4Å: Chain A: T.257 No protein-ligand interaction detected (PLIP) NA.6: 2 residues within 4Å: Chain B: G.2, N.214 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:G.2, B:N.214 Water bridges: B:S.1, B:F.3 NA.7: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) NA.8: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) NA.15: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) NA.16: 1 residues within 4Å: Chain B: Y.101 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Y.101 Water bridges: B:Y.101 NA.17: 1 residues within 4Å: Chain B: T.257 No protein-ligand interaction detected (PLIP) NA.18: 2 residues within 4Å: Chain A: G.2, N.214 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.2, A:N.214 Water bridges: A:S.1, A:F.3 NA.19: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) NA.20: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

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

CL.9: 3 residues within 4Å: Chain A: R.4, K.5 Chain B: K.5 Ligand excluded by PLIP CL.10: 2 residues within 4Å: Chain A: N.142, G.143 Ligand excluded by PLIP CL.11: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.12: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.21: 3 residues within 4Å: Chain A: K.5 Chain B: R.4, K.5 Ligand excluded by PLIP CL.22: 2 residues within 4Å: Chain B: N.142, G.143 Ligand excluded by PLIP CL.23: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.24: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Flynn, J.M. et al., Contributions of Hyperactive Mutations in M pro from SARS-CoV-2 to Drug Resistance. Acs Infect Dis. (2024)

Release Date

2024-02-07

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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