SMTL ID : 6xbh.1

Crystal structure of the SARS-CoV-2 (COVID-19) main protease in complex with inhibitor UAW247

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

homo-dimer

Ligands

2 x P6S- PHE- ELL: inhibitor UAW247(Non-covalent)

P6S-PHE-ELL.1: 17 residues within 4Å: Chain A: H.43, M.51, Y.56, F.142, L.143, N.144, G.145, S.146, C.147, H.165, H.166, M.167, E.168, H.174, D.189, R.190, Q.191 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:H.43, A:E.168 Hydrogen bonds: A:F.142, A:G.145, A:S.146, A:C.147, A:H.166, A:E.168, A:Q.191 P6S-PHE-ELL.4: 17 residues within 4Å: Chain B: H.43, M.51, Y.56, F.142, L.143, N.144, G.145, S.146, C.147, H.165, H.166, M.167, E.168, H.174, D.189, R.190, Q.191 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:H.43, B:E.168 Hydrogen bonds: B:F.142, B:G.145, B:S.146, B:C.147, B:H.166, B:E.168, B:E.168, B:Q.191

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 3 residues within 4Å: Chain A: S.64, N.65, H.66 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.65, A:H.66 GOL.5: 3 residues within 4Å: Chain B: S.64, N.65, H.66 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.65, B:H.66, B:H.66

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

NA.3: 3 residues within 4Å: Chain A: N.65, R.78, V.79 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.65, A:V.79 Water bridges: A:N.65 NA.6: 3 residues within 4Å: Chain B: N.65, R.78, V.79 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.65, B:V.79 Water bridges: B:N.65

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
A

3C-like proteinase

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