SMTL ID : 7aeh.1

SARS-CoV-2 main protease in a covalent complex with a pyridine derivative of ABT-957, compound 1

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.30 Å

Oligo State

homo-dimer

Ligands

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

DMS.1: 3 residues within 4Å: Chain A: Q.74, L.75, R.76 No protein-ligand interaction detected (PLIP) DMS.2: 7 residues within 4Å: Chain A: M.6, A.7, F.8, Q.127, D.295, R.298 Chain B: S.123 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.3: 4 residues within 4Å: Chain A: E.14, G.15, M.17, K.97 No protein-ligand interaction detected (PLIP) DMS.4: 3 residues within 4Å: Chain A: Y.37, Y.101, F.103 1 PLIP interactions: 1 interactions with chain A pi-Cation interactions: A:F.103 DMS.6: 3 residues within 4Å: Chain B: Q.74, L.75, R.76 No protein-ligand interaction detected (PLIP) DMS.7: 7 residues within 4Å: Chain A: S.123 Chain B: M.6, A.7, F.8, Q.127, D.295, R.298 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:D.295, B:R.298 Salt bridges: B:D.295 pi-Cation interactions: B:F.8 DMS.8: 4 residues within 4Å: Chain B: E.14, G.15, M.17, K.97 No protein-ligand interaction detected (PLIP) DMS.9: 3 residues within 4Å: Chain B: Y.37, Y.101, F.103 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Y.37, B:Y.101 pi-Cation interactions: B:F.103

2 x R8H: (2~{R})-5-oxidanylidene-~{N}-[(2~{R},3~{S})-3-oxidanyl-4-oxidanylidene-1-phenyl-4-(pyridin-2-ylmethylamino)butan-2-yl]-1-(phenylmethyl)pyrrolidine-2-carboxamide(Covalent)

R8H.5: 12 residues within 4Å: Chain A: T.25, T.26, H.41, F.140, L.141, N.142, G.143, S.144, C.145, H.163, H.164, E.166 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:T.25, A:E.166 Hydrogen bonds: A:N.142, A:G.143, A:S.144, A:C.145, A:H.164 Water bridges: A:H.41, A:H.164, A:E.166 R8H.10: 12 residues within 4Å: Chain B: T.25, T.26, H.41, F.140, L.141, N.142, G.143, S.144, C.145, H.163, H.164, E.166 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:T.25, B:E.166 Hydrogen bonds: B:N.142, B:G.143, B:S.144, B:C.145, B:H.164 Water bridges: B:H.41, B:H.164, B:E.166

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 nsp5: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

3C-like proteinase nsp5

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