SMTL ID : 6w79.1

Structure of SARS-CoV main protease bound to potent broad-spectrum non-covalent inhibitor X77

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.46 Å

Oligo State

homo-dimer

Ligands

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

DMS.1: 4 residues within 4Å: Chain A: R.40, N.84, C.85 Ligands: MES.3 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.40 DMS.5: 4 residues within 4Å: Chain B: R.40, N.84, C.85 Ligands: MES.7 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.40

2 x X77: N-(4-tert-butylphenyl)-N-[(1R)-2-(cyclohexylamino)-2-oxo-1-(pyridin-3-yl)ethyl]-1H-imidazole-4-carboxamide(Non-covalent)

X77.2: 22 residues within 4Å: Chain A: T.25, T.26, L.27, H.41, C.44, M.49, Y.54, F.140, L.141, N.142, G.143, S.144, C.145, H.163, H.164, M.165, E.166, H.172, D.187, R.188, Q.189 Chain B: S.1 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:M.49, A:Q.189 Hydrogen bonds: A:H.41, A:G.143, A:E.166 X77.6: 22 residues within 4Å: Chain A: S.1 Chain B: T.25, T.26, L.27, H.41, C.44, M.49, Y.54, F.140, L.141, N.142, G.143, S.144, C.145, H.163, H.164, M.165, E.166, H.172, D.187, R.188, Q.189 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:M.49, B:Q.189 Hydrogen bonds: B:H.41, B:G.143, B:E.166

4 x MES: 2-(N-MORPHOLINO)-ETHANESULFONIC ACID(Non-covalent)

MES.3: 8 residues within 4Å: Chain A: R.105, H.134, K.180, F.181, Y.182, G.183, P.184 Ligands: DMS.1 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:F.181, A:G.183 Water bridges: A:R.105, A:F.181 Salt bridges: A:R.105, A:H.134 MES.4: 3 residues within 4Å: Chain A: N.53, D.56, R.60 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.53 Water bridges: A:N.53, A:R.60, A:R.60 Salt bridges: A:D.56 MES.7: 8 residues within 4Å: Chain B: R.105, H.134, K.180, F.181, Y.182, G.183, P.184 Ligands: DMS.5 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:F.181, B:G.183 Water bridges: B:R.105, B:F.181 Salt bridges: B:R.105, B:H.134 MES.8: 3 residues within 4Å: Chain B: N.53, D.56, R.60 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:N.53 Water bridges: B:N.53, B:R.60, B:R.60 Salt bridges: B:D.56

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mesecar, A.D., A taxonomically-driven approach to development of potent, broad-spectrum inhibitors of coronavirus main protease including SARS-CoV-2 (COVID-19). To Be Published

Release Date

2020-08-26

Peptides

Main protease: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Main protease

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