SMTL ID : 7k0h.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

homo-dimer

Ligands

2 x CL: CHLORIDE ION(Non-functional Binders)

CL.1: 3 residues within 4Å: Chain A: K.243, Y.244, Q.280 Ligand excluded by PLIP CL.2: 1 residues within 4Å: Chain A: T.197 Ligand excluded by PLIP

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)

VR4.3: 18 residues within 4Å: Chain A: T.33, H.48, F.147, L.148, N.149, G.150, S.151, C.152, H.170, H.171, M.172, E.173, P.175, H.179, D.194, Q.196, T.197, A.198 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:N.149, A:P.175, A:D.194, A:A.198 Hydrogen bonds: A:F.147, A:G.150, A:S.151, A:S.151, A:C.152, A:H.171, A:E.173, A:Q.196, A:Q.196 VR4.4: 16 residues within 4Å: Chain B: T.33, H.48, M.56, F.147, L.148, N.149, G.150, S.151, C.152, H.170, H.171, M.172, E.173, H.179, D.194, Q.196 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:N.149, B:M.172 Hydrogen bonds: B:G.150, B:S.151, B:S.151, B:C.152, B:H.171, B:E.173, B:E.173, B:Q.196, B:Q.196

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

PG4.5: 10 residues within 4Å: Chain B: E.21, G.22, M.24, W.38, A.77, V.80, Q.81, L.82, N.102, K.104 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:M.24, B:T.100, B:T.100, B:N.102 Water bridges: B:G.78

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

2021-07-07

Peptides

Replicase polyprotein 1a: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Replicase polyprotein 1a

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