SMTL ID : 6xhn.1

Covalent complex of SARS-CoV main protease with 4-methoxy-N-[(2S)-4-methyl-1-oxo-1-({(2S)-3-oxo-1-[(3S)-2-oxopyrrolidin-3-yl]butan-2-yl}amino)pentan-2-yl]-1H-indole-2-carboxamide

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.38 Å

Oligo State

homo-dimer

Ligands

2 x V3D: (3S)-3-{[N-(4-methoxy-1H-indole-2-carbonyl)-L-leucyl]amino}-2-oxo-4-[(3S)-2-oxopyrrolidin-3-yl]butyl 2-cyanobenzoate(Covalent)

V3D.1: 17 residues within 4Å: Chain A: H.42, F.141, L.142, N.143, G.144, S.145, C.146, H.164, H.165, M.166, E.167, P.169, H.173, D.188, Q.190, T.191, A.192 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:P.169, A:D.188, A:A.192 Hydrogen bonds: A:F.141, A:G.144, A:S.145, A:S.145, A:C.146, A:H.165, A:E.167, A:E.167, A:E.167, A:Q.190 Water bridges: A:Q.190, A:Q.190 V3D.3: 18 residues within 4Å: Chain B: H.42, M.50, F.141, L.142, N.143, G.144, S.145, C.146, H.164, H.165, M.166, E.167, P.169, H.173, R.189, Q.190, T.191, A.192 14 PLIP interactions: 14 interactions with chain B Hydrophobic interactions: B:P.169, B:A.192 Hydrogen bonds: B:F.141, B:G.144, B:S.145, B:S.145, B:C.146, B:H.165, B:E.167, B:E.167, B:E.167, B:Q.190 Water bridges: B:Q.190, B:Q.190

1 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.2: 11 residues within 4Å: Chain A: K.6, M.7, A.8, V.126, Y.127, Q.128 Chain B: R.5, K.6, M.7, A.8, V.126 6 PLIP interactions: 2 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:V.126, A:Q.128, B:R.5, B:A.8, B:Q.128 Water bridges: B:K.6

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hoffman, R.L. et al., Discovery of Ketone-Based Covalent Inhibitors of Coronavirus 3CL Proteases for the Potential Therapeutic Treatment of COVID-19. J.Med.Chem. (2020)

Release Date

2020-07-08

Peptides

3C-like proteinase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

3C-like proteinase

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