SMTL ID : 9dtz.1

SARS-CoV-2 Mpro in complex with compound 5

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-dimer

Ligands

2 x 01: N-[(2S)-3-cyclopropyl-1-({(2R)-1-imino-3-[(3R)-2-oxopyrrolidin-3-yl]propan-2-yl}amino)-1-oxopropan-2-yl]-4-methoxy-1H-indole-2-carboxamide

01.1: 19 residues within 4Å: Chain A: 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, D.188, R.189, Q.190, T.191, A.192 12 PLIP interactions: 12 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:C.146, A:H.165, A:E.167, A:E.167, A:Q.190 Water bridges: A:N.143 01.3: 17 residues within 4Å: Chain B: 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 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:P.169, B:A.192 Hydrogen bonds: B:F.141, B:G.144, B:S.145, B:C.146, B:H.165, B:E.167, B:E.167, B:Q.190 Water bridges: B:N.143

1 x NA: SODIUM ION(Non-functional Binders)

NA.2: 5 residues within 4Å: Chain A: N.222, F.224, D.264, A.267, S.268 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.222, A:F.224, A:D.264

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Padmanabha Das, K.M. et al., Inhibition of Dimeric SARS-CoV-2 Mpro by Aldehyde and NitrilebasedInhibitors Displays Positive Cooperativity and a Mixture of Covalent and Non-covalent Binding. To Be Published

Release Date

2025-04-30

Peptides

3C-like proteinase nsp5: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

3C-like proteinase nsp5

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