SMTL ID : 6xho.1

Covalent complex of SARS-CoV main protease with ethyl (4R)-4-({N-[(4-methoxy-1H-indol-2-yl)carbonyl]-L-leucyl}amino)-5-[(3S)-2-oxopyrrolidin-3-yl]pentanoate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.45 Å

Oligo State

homo-dimer

Ligands

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

EDO.1: 10 residues within 4Å: Chain A: K.6, M.7, A.8, V.126, Y.127, Q.128 Chain B: K.6, M.7, A.8, V.126 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:A.8, B:Q.128, A:V.126, A:Q.128 Water bridges: B:R.5

2 x V34: ethyl (2E,4S)-4-{[N-(4-methoxy-1H-indole-2-carbonyl)-L-leucyl]amino}-5-[(3S)-2-oxopyrrolidin-3-yl]pent-2-enoate(Covalent)

V34.2: 19 residues within 4Å: Chain A: T.26, T.27, 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:T.26, A:H.42, A:P.169, A:D.188, A:A.192 Hydrogen bonds: A:F.141, A:G.144, A:C.146, A:H.165, A:E.167, A:E.167, A:E.167, A:Q.190 Water bridges: A:Q.190 Salt bridges: A:H.42 V34.3: 18 residues within 4Å: Chain B: T.26, T.27, H.42, F.141, L.142, N.143, G.144, S.145, C.146, H.164, H.165, M.166, E.167, H.173, D.188, Q.190, T.191, A.192 15 PLIP interactions: 15 interactions with chain B Hydrophobic interactions: B:T.26, B:D.188, B:Q.190, B:A.192 Hydrogen bonds: B:F.141, B:G.144, 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 Salt bridges: B:H.42

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

Related Entries With Identical Sequence