SMTL ID : 7rc1.1

X-ray Structure of SARS-CoV main protease covalently modified by compound GRL-0686

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.63 Å

Oligo State

homo-dimer

Ligands

2 x 4IO: 5-chloropyridin-3-yl 1-(3-nitrobenzene-1-sulfonyl)-1H-indole-5-carboxylate(Covalent)

4IO.1: 14 residues within 4Å: Chain A: L.27, P.39, H.41, M.49, C.145, H.164, M.165, E.166, L.167, D.187, R.188, Q.189, T.190, Q.192 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:H.41, A:H.164, A:M.165, A:D.187 pi-Stacking: A:H.41 4IO.7: 14 residues within 4Å: Chain B: L.27, P.39, H.41, M.49, C.145, H.164, M.165, E.166, L.167, D.187, R.188, Q.189, T.190, Q.192 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:H.41, B:H.164, B:M.165, B:D.187 pi-Stacking: B:H.41

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

DMS.2: 1 residues within 4Å: Chain A: N.84 No protein-ligand interaction detected (PLIP) DMS.3: 8 residues within 4Å: Chain A: G.15, C.16, M.17, V.18, W.31, A.70, G.71, K.97 No protein-ligand interaction detected (PLIP) DMS.4: 5 residues within 4Å: Chain A: Q.19, Q.69, A.70, G.71, N.119 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.71 DMS.5: 2 residues within 4Å: Chain A: K.100, Y.101 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.101 pi-Cation interactions: A:Y.101 DMS.6: 4 residues within 4Å: Chain A: S.1, N.214, F.305 Chain B: T.169 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.1 DMS.8: 1 residues within 4Å: Chain B: N.84 No protein-ligand interaction detected (PLIP) DMS.9: 8 residues within 4Å: Chain B: G.15, C.16, M.17, V.18, W.31, A.70, G.71, K.97 No protein-ligand interaction detected (PLIP) DMS.10: 5 residues within 4Å: Chain B: Q.19, Q.69, A.70, G.71, N.119 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:G.71 DMS.11: 2 residues within 4Å: Chain B: K.100, Y.101 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Y.101 pi-Cation interactions: B:Y.101 DMS.12: 4 residues within 4Å: Chain A: T.169 Chain B: S.1, N.214, F.305 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.1

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ghosh, A.K. et al., Indole Chloropyridinyl Ester-Derived SARS-CoV-2 3CLpro Inhibitors: Enzyme Inhibition, Antiviral Efficacy, Structure-Activity Relationship, and X-ray Structural Studies. J.Med.Chem. (2021)

Release Date

2021-09-29

Peptides

3C-like proteinase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

3C-like proteinase

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