SMTL ID : 7lyi.1

Crystal structure of the SARS-CoV-2 (COVID-19) main protease in complex with inhibitor UAWJ9-36-3

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-dimer

Ligands

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 3 residues within 4Å: Chain A: S.64, N.65, H.66 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.65, A:H.66, A:H.66 GOL.4: 3 residues within 4Å: Chain B: S.64, N.65, H.66 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.65, B:H.66

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

NA.2: 3 residues within 4Å: Chain A: N.65, H.66, V.79 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.65, A:V.79 NA.5: 3 residues within 4Å: Chain B: N.65, H.66, V.79 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:V.79, B:V.79

2 x YHI: benzyl (1R,2S,5S)-2-({(2S)-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}carbamoyl)-6,6-dimethyl-3-azabicyclo[3.1.0]hexane-3-carboxylate(Covalent)

YHI.3: 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 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:H.43 Hydrogen bonds: A:F.142, A:G.145, A:C.147, A:H.166, A:E.168, A:E.168 Water bridges: A:F.142 YHI.6: 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 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:H.43 Hydrogen bonds: B:F.142, B:G.145, B:C.147, B:H.166, B:E.168 Water bridges: B:F.142

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Xia, Z. et al., Rational Design of Hybrid SARS-CoV-2 Main Protease Inhibitors Guided by the Superimposed Cocrystal Structures with the Peptidomimetic Inhibitors GC-376, Telaprevir, and Boceprevir. Acs Pharmacol Transl Sci (2021)

Release Date

2021-03-17

Peptides

3C-like proteinase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

3C-like proteinase

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