SMTL ID : 7lcp.1

N-terminal finger stabilizes feline drug GC376 in coronavirus 3CL protease

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-dimer

Ligands

2 x UED: N~2~-[(benzyloxy)carbonyl]-N-{(2S)-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}-L-leucinamide(Covalent)

UED.1: 14 residues within 4Å: Chain A: H.41, M.49, F.140, L.141, N.142, G.143, S.144, C.145, H.163, H.164, M.165, E.166, H.172, Q.189 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:H.41, A:M.165 Hydrogen bonds: A:F.140, A:N.142, A:G.143, A:S.144, A:C.145, A:H.164, A:E.166, A:E.166, A:Q.189 UED.6: 14 residues within 4Å: Chain B: H.41, M.49, F.140, L.141, N.142, G.143, S.144, C.145, H.163, H.164, M.165, E.166, H.172, Q.189 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:H.41, B:M.165 Hydrogen bonds: B:F.140, B:N.142, B:G.143, B:S.144, B:C.145, B:H.164, B:E.166, B:Q.189

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

EDO.2: 7 residues within 4Å: Chain A: M.6, A.7, F.8, Q.127, R.298 Chain B: S.123, G.124 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.123 EDO.7: 7 residues within 4Å: Chain A: S.123, G.124 Chain B: M.6, A.7, F.8, Q.127, R.298 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:S.123, B:Q.127

6 x CA: CALCIUM ION(Non-covalent)(Non-functional Binders)

CA.3: 3 residues within 4Å: Chain A: T.226, L.227, N.228 No protein-ligand interaction detected (PLIP) CA.4: 3 residues within 4Å: Chain A: R.105, H.134, G.183 No protein-ligand interaction detected (PLIP) CA.5: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) CA.8: 3 residues within 4Å: Chain B: T.226, L.227, N.228 No protein-ligand interaction detected (PLIP) CA.9: 3 residues within 4Å: Chain B: R.105, H.134, G.183 No protein-ligand interaction detected (PLIP) CA.10: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Arutyunova, E. et al., N-Terminal Finger Stabilizes the S1 Pocket for the Reversible Feline Drug GC376 in the SARS-CoV-2 M pro Dimer. J.Mol.Biol. (2021)

Release Date

2021-05-12

Peptides

3C-like proteinase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

3C-like proteinase

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