SMTL ID : 7aeg.1

SARS-CoV-2 main protease in a covalent complex with SDZ 224015 derivative, compound 5

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

monomer

Ligands

1 x PHQ- VAL- ALA- ASP- CF0: N-[(benzyloxy)carbonyl]-L-valyl-N-[(1S)-1-(carboxymethyl)-3-fluoro-2-oxopropyl]-L-alaninamide(Non-covalent)

PHQ-VAL-ALA-ASP-CF0.1: 19 residues within 4Å: Chain A: H.41, M.49, 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, R.188, Q.189, T.190, Q.192 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:P.168 Hydrogen bonds: A:N.142, A:G.143, A:S.144, A:H.164, A:E.166, A:E.166 Salt bridges: A:H.163

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

DMS.2: 3 residues within 4Å: Chain A: Q.74, L.75, R.76 No protein-ligand interaction detected (PLIP) DMS.3: 2 residues within 4Å: Chain A: H.64, N.65 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.65 DMS.4: 5 residues within 4Å: Chain A: M.6, A.7, F.8, Q.127, R.298 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.298 Salt bridges: A:D.295 pi-Cation interactions: A:F.8 DMS.5: 7 residues within 4Å: Chain A: E.14, G.15, M.17, W.31, A.70, G.71, K.97 No protein-ligand interaction detected (PLIP) DMS.6: 2 residues within 4Å: Chain A: K.100, Y.101 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.101 pi-Cation interactions: A:Y.101

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Redhead, M.A. et al., Bispecific repurposed medicines targeting the viral and immunological arms of COVID-19. Sci Rep (2021)

Release Date

2021-07-07

Peptides

3C-like proteinase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

3C-like proteinase

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