SMTL ID : 6xbi.1

Crystal structure of the SARS-CoV-2 (COVID-19) main protease in complex with inhibitor UAW248

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

homo-dimer

Ligands

2 x UZ7- LEU- LEU- UZ4- UZ1: inhibitor UAW248(Non-covalent)

UZ7-LEU-LEU-UZ4-UZ1.1: 20 residues within 4Å: Chain A: T.27, T.28, H.43, M.51, F.142, N.144, G.145, S.146, C.147, H.165, H.166, M.167, E.168, P.170, H.174, D.189, Q.191, T.192, A.193, Q.194 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:T.27, A:P.170, A:A.193 Hydrogen bonds: A:G.145, A:S.146, A:S.146, A:C.147, A:H.166, A:E.168, A:E.168, A:E.168, A:E.168, A:Q.191 Water bridges: A:Q.191 UZ7-LEU-LEU-UZ4-UZ1.2: 20 residues within 4Å: Chain B: T.27, T.28, H.43, M.51, F.142, N.144, G.145, S.146, C.147, H.165, H.166, M.167, E.168, P.170, H.174, D.189, Q.191, T.192, A.193, Q.194 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:T.27, B:P.170, B:D.189 Hydrogen bonds: B:G.145, B:S.146, B:S.146, B:C.147, B:H.166, B:E.168, B:E.168, B:E.168, B:Q.191

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 4 residues within 4Å: Chain A: L.229, N.230, N.233, L.234 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.233, A:L.234 GOL.4: 3 residues within 4Å: Chain A: Q.85, F.105, E.180 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:Q.85 Water bridges: A:Q.85, A:F.105, A:F.105, A:D.178, A:E.180

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

NA.5: 3 residues within 4Å: Chain A: T.228, L.229, L.264 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:L.229 Water bridges: A:N.230

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

DMS.6: 7 residues within 4Å: Chain A: S.125, G.126 Chain B: M.8, A.9, F.10, Q.129, R.300 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Q.129, B:R.300 pi-Cation interactions: B:F.10

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sacco, M.D. et al., Structure and inhibition of the SARS-CoV-2 main protease reveal strategy for developing dual inhibitors against M pro and cathepsin L. Sci Adv (2020)

Release Date

2020-06-17

Peptides

3C-like proteinase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

3C-like proteinase

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