SMTL ID : 7b83.1

Structure of SARS-CoV-2 Main Protease bound to pyrithione zinc

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-dimer

Ligands

2 x PK8: 9-oxa-7-thia-1-azonia-8$l^{2}-zincabicyclo[4.3.0]nona-1,3,5-triene(Non-covalent)

PK8.1: 9 residues within 4Å: Chain A: T.25, T.26, L.27, H.41, N.142, G.143, C.145, H.164 Ligands: DMS.3 5 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions, 1 Ligand-Ligand interactions Metal complexes: A:H.41, A:C.145, H2O.1, H2O.6, PK8.1 PK8.5: 9 residues within 4Å: Chain B: T.25, T.26, L.27, H.41, N.142, G.143, C.145, H.164 Ligands: DMS.7 5 PLIP interactions: 2 interactions with chain B, 1 Ligand-Ligand interactions, 2 Ligand-Water interactions Metal complexes: B:H.41, B:C.145, PK8.5, H2O.12, H2O.17

2 x IMD: IMIDAZOLE(Non-covalent)

IMD.2: 3 residues within 4Å: Chain A: R.222, T.224, D.263 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.263 Water bridges: A:T.224 IMD.6: 3 residues within 4Å: Chain B: R.222, T.224, D.263 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.263 Water bridges: B:T.224

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

DMS.3: 12 residues within 4Å: Chain A: F.140, L.141, N.142, S.144, C.145, H.163, H.164, M.165, E.166, H.172 Chain B: S.1 Ligands: PK8.1 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:H.163 Water bridges: A:E.166 Salt bridges: A:E.166 DMS.7: 12 residues within 4Å: Chain A: S.1 Chain B: F.140, L.141, N.142, S.144, C.145, H.163, H.164, M.165, E.166, H.172 Ligands: PK8.5 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:H.163 Water bridges: B:E.166 Salt bridges: B:E.166

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

CL.4: 6 residues within 4Å: Chain A: T.111, Q.127, E.290, F.291, T.292, D.295 Ligand excluded by PLIP CL.8: 6 residues within 4Å: Chain B: T.111, Q.127, E.290, F.291, T.292, D.295 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gunther, S. et al., X-ray screening identifies active site and allosteric inhibitors of SARS-CoV-2 main protease. Science (2021)

Release Date

2021-01-13

Peptides

3C-like proteinase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

3C-like proteinase

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