SMTL ID : 7k0f.1

1.65 A resolution structure of SARS-CoV-2 3CL protease in complex with a deuterated GC376 alpha-ketoamide analog (compound 5)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.65 Å

Oligo State

homo-dimer

Ligands

2 x VR4: N-{(2S,3R)-4-(benzylamino)-3-hydroxy-4-oxo-1-[(3S)-2-oxopyrrolidin-3-yl]butan-2-yl}-N~2~-[(benzyloxy)carbonyl]-L-leucinamide(Covalent)

VR4.1: 17 residues within 4Å: Chain A: T.30, H.45, F.144, L.145, N.146, G.147, S.148, C.149, H.167, H.168, M.169, E.170, H.176, D.191, Q.193, T.194, A.195 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:N.146, A:D.191, A:A.195 Hydrogen bonds: A:F.144, A:G.147, A:S.148, A:S.148, A:C.149, A:H.168, A:E.170, A:Q.193, A:Q.193 VR4.2: 16 residues within 4Å: Chain B: T.30, H.45, M.53, F.144, L.145, N.146, G.147, S.148, C.149, H.167, H.168, M.169, E.170, H.176, D.191, Q.193 13 PLIP interactions: 13 interactions with chain B Hydrophobic interactions: B:H.45, B:N.146, B:M.169 Hydrogen bonds: B:F.144, B:G.147, B:S.148, B:C.149, B:H.168, B:E.170, B:E.170, B:Q.193, B:Q.193 Water bridges: B:H.45

1 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.3: 9 residues within 4Å: Chain B: E.18, G.19, M.21, W.35, A.74, V.77, L.79, N.99, K.101 3 PLIP interactions: 3 interactions with chain B Water bridges: B:G.75, B:Q.78, B:G.124

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Dampalla, C.S. et al., Postinfection treatment with a protease inhibitor increases survival of mice with a fatal SARS-CoV-2 infection. Proc.Natl.Acad.Sci.USA (2021)

Release Date

2021-01-13

Peptides

3C-like proteinase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

3C-like proteinase

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