SMTL ID : 5n19.1

Structure of SARS coronavirus main protease in complex with the alpha-ketoamide (S)-N-benzyl-3-((S)-2-cinnamamido-3-phenylpropanamido)-2-oxo-4-((S)-2-oxopyrrolidin-3-yl)butanamide

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.62 Å

Oligo State

homo-dimer

Ligands

2 x D03: (S)-N-benzyl-3-((S)-2-cinnamamido-3-phenylpropanamido)-2-oxo-4-((S)-2-oxopyrrolidin-3-yl)butanamide(Covalent)

D03.1: 21 residues within 4Å: Chain A: T.25, H.41, C.44, T.45, A.46, M.49, F.140, L.141, N.142, G.143, S.144, C.145, H.163, H.164, M.165, E.166, H.172, V.186, D.187, R.188, Q.189 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:T.25, A:M.165, A:E.166 Hydrogen bonds: A:G.143, A:S.144, A:C.145, A:H.164, A:E.166, A:E.166, A:E.166 Water bridges: A:T.26 pi-Stacking: A:H.41 D03.3: 21 residues within 4Å: Chain B: T.25, H.41, C.44, T.45, A.46, M.49, F.140, L.141, N.142, G.143, S.144, C.145, H.163, H.164, M.165, E.166, H.172, V.186, D.187, R.188, Q.189 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:T.25, B:M.165, B:E.166 Hydrogen bonds: B:G.143, B:S.144, B:C.145, B:H.164, B:E.166, B:E.166 Water bridges: B:T.26 pi-Stacking: B:H.41

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

DMS.2: 3 residues within 4Å: Chain A: R.40, N.84, C.85 1 PLIP interactions: 1 interactions with chain A Water bridges: A:R.40 DMS.4: 3 residues within 4Å: Chain B: R.40, N.84, C.85 1 PLIP interactions: 1 interactions with chain B Water bridges: B:R.40

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lin, D. et al., Alpha-ketoamides as broad-spectrum inhibitors of coronavirus and enterovirus replication. To Be Published

Release Date

2018-02-28

Peptides

SARS coronavirus main protease: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

SARS coronavirus main protease

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