SMTL ID : 8dt9.1

Crystal Structure of SARS CoV-2 Mpro mutant L141R with Pfizer Intravenous Inhibitor PF-00835231

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-dimer

Ligands

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

DMS.1: 3 residues within 4Å: Chain A: L.50, N.51, R.188 No protein-ligand interaction detected (PLIP) DMS.5: 3 residues within 4Å: Chain B: N.142, Q.189 Ligands: V2M.6 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Q.189

2 x V2M: N-[(2S)-1-({(2S,3S)-3,4-dihydroxy-1-[(3S)-2-oxopyrrolidin-3-yl]butan-2-yl}amino)-4-methyl-1-oxopentan-2-yl]-4-methoxy-1H-indole-2-carboxamide(Covalent)

V2M.2: 20 residues within 4Å: Chain A: L.27, H.41, M.49, F.140, R.141, N.142, G.143, S.144, C.145, H.163, H.164, M.165, E.166, P.168, H.172, D.187, Q.189, T.190, A.191 Chain B: S.1 16 PLIP interactions: 14 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:H.41, A:P.168, A:A.191 Hydrogen bonds: A:G.143, A:S.144, A:S.144, A:C.145, A:H.164, A:E.166, A:E.166, A:E.166, A:Q.189, B:S.1 Water bridges: A:Q.189, A:Q.189, B:S.1 V2M.6: 21 residues within 4Å: Chain B: L.27, H.41, M.49, F.140, R.141, N.142, G.143, S.144, C.145, H.163, H.164, M.165, E.166, P.168, H.172, D.187, R.188, Q.189, T.190, A.191 Ligands: DMS.5 15 PLIP interactions: 15 interactions with chain B Hydrophobic interactions: B:M.49, B:M.165, B:P.168, B:A.191 Hydrogen bonds: B:F.140, B:G.143, B:S.144, B:S.144, B:C.145, B:H.164, B:E.166, B:E.166, B:E.166, B:Q.189, B:Q.189

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

NA.3: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) NA.4: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) 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.9: 2 residues within 4Å: Chain B: K.236, Y.237 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.236 NA.10: 3 residues within 4Å: Chain B: A.255, Q.256, G.258 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Q.256 NA.11: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) NA.12: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) NA.13: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (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
B

3C-like proteinase nsp5