SMTL ID : 6fv1.2 (2 other biounits)

Structure of human coronavirus NL63 main protease in complex with the alpha-ketoamide (S)-N-((S)-4-(benzylamino)-3,4-dioxo-1-((S)-2-oxopyrrolidin-3-yl)butan-2-yl)-2-cinnamamido-4-methylpentanamide (cinnamoyl-leucine-GlnLactam-CO-CO-NH-benzyl)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

monomer

Ligands

1 x E8E: (2~{S})-4-methyl-~{N}-[(2~{S},3~{R})-3-oxidanyl-4-oxidanylidene-1-[(3~{S})-2-oxidanylidenepyrrolidin-3-yl]-4-[(phenylmethyl)amino]butan-2-yl]-2-[[(~{E})-3-phenylprop-2-enoyl]amino]pentanamide(Covalent)

E8E.1: 20 residues within 4Å: Chain A: V.26, H.41, I.51, F.139, I.140, N.141, G.142, A.143, C.144, H.163, Q.164, I.165, E.166, G.168, D.187, Q.188, P.189, S.190, L.191 Ligands: GOL.3 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:H.41, A:I.51, A:N.141, A:I.165, A:P.189, A:L.191 Hydrogen bonds: A:F.139, A:G.142, A:C.144, A:Q.164, A:E.166 Water bridges: A:T.47, A:T.47

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 9 residues within 4Å: Chain A: K.5, M.6, Q.8, S.110, F.111, N.112, G.126, N.150, E.292 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:K.5, A:Q.8, A:N.112, A:N.112, A:N.150 Water bridges: A:M.6, A:S.110, A:S.110 GOL.3: 2 residues within 4Å: Chain A: E.166 Ligands: E8E.1 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.166 Water bridges: A:N.141 GOL.4: 2 residues within 4Å: Chain A: R.40, Y.53 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.40, A:R.40 Water bridges: A:Q.188

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhang, L. et al., Alpha-ketoamides as broad-spectrum inhibitors of coronavirus and enterovirus replication Structure-based design, synthesis, and activity assessment. J.Med.Chem. (2020)

Release Date

2019-03-20

Peptides

3C-like proteinase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

3C-like proteinase

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