SMTL ID : 6wco.1

Structure of SARS main protease bound to inhibitor X47

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.48 Å

Oligo State

homo-dimer

Ligands

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

MES.1: 8 residues within 4Å: Chain A: R.105, H.134, K.180, F.181, Y.182, G.183, P.184 Ligands: DMS.4 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.105, A:G.183 Water bridges: A:F.181 Salt bridges: A:R.105, A:H.134 MES.2: 3 residues within 4Å: Chain A: N.53, D.56, R.60 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.53 Water bridges: A:R.60, A:R.60 Salt bridges: A:D.56 MES.5: 8 residues within 4Å: Chain B: R.105, H.134, K.180, F.181, Y.182, G.183, P.184 Ligands: DMS.8 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:R.105, B:G.183 Water bridges: B:F.181 Salt bridges: B:R.105, B:H.134 MES.6: 3 residues within 4Å: Chain B: N.53, D.56, R.60 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:N.53 Water bridges: B:R.60, B:R.60 Salt bridges: B:D.56

2 x X47: N-(4-tert-butylphenyl)-N-[(1R)-2-(cyclopentylamino)-2-oxo-1-(pyridin-3-yl)ethyl]-1H-imidazole-4-carboxamide(Non-covalent)

X47.3: 21 residues within 4Å: Chain A: T.25, T.26, L.27, H.41, 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:H.41, A:E.166 Hydrogen bonds: A:G.143, A:E.166 Water bridges: A:H.41 X47.7: 21 residues within 4Å: Chain A: S.1 Chain B: T.25, T.26, L.27, H.41, 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:H.41, B:E.166 Hydrogen bonds: B:G.143, B:E.166 Water bridges: B:H.41

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

DMS.4: 5 residues within 4Å: Chain A: R.40, N.84, C.85, G.179 Ligands: MES.1 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.40, A:R.40 DMS.8: 5 residues within 4Å: Chain B: R.40, N.84, C.85, G.179 Ligands: MES.5 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.40, B:R.40

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

2020-08-05

Peptides

Main protease: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Main protease

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