SMTL ID : 8okk.1

Crystal structure of F2F-2020184-00X bound to the main protease (3CLpro/Mpro) of SARS-CoV-2.

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.63 Å

Oligo State

homo-dimer

Ligands

2 x 83F: tert-butyl-N-[(2S)-3-methyl-1-[(2S,4S)-4-methyl-2-[[(2S)-1-oxidanyl-3-[(3S)-2-oxidanylidenepyrrolidin-3-yl]propan-2-yl]carbamoyl]pyrrolidin-1-yl]-1-oxidanylidene-butan-2-yl]carbamate(Covalent)

83F.1: 22 residues within 4Å: Chain A: L.27, H.41, M.49, F.140, L.141, N.142, G.143, S.144, C.145, H.163, H.164, M.165, E.166, L.167, P.168, H.172, R.188, Q.189, T.190, A.191, Q.192 Chain B: S.1 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:Q.189 Hydrogen bonds: A:F.140, A:N.142, A:G.143, A:C.145, A:H.164, A:E.166, A:E.166, A:E.166, A:H.172, A:Q.189 83F.13: 22 residues within 4Å: Chain A: S.1 Chain B: L.27, H.41, M.49, F.140, L.141, N.142, G.143, S.144, C.145, H.163, H.164, M.165, E.166, L.167, P.168, H.172, R.188, Q.189, T.190, A.191, Q.192 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:Q.192 Hydrogen bonds: B:F.140, B:G.143, B:S.144, B:C.145, B:H.164, B:E.166, B:E.166, B:E.166, B:H.172, B:Q.189

4 x ACT: ACETATE ION(Non-functional Binders)

ACT.2: 10 residues within 4Å: Chain A: G.15, C.16, M.17, V.18, W.31, A.70, G.71, N.95, K.97 Ligands: EDO.3 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:V.18, A:W.31 Hydrogen bonds: A:G.15, A:G.71 Water bridges: A:N.95 Salt bridges: A:K.97 ACT.14: 6 residues within 4Å: Chain B: I.213, L.253, Q.256, V.297, C.300, S.301 No protein-ligand interaction detected (PLIP) ACT.15: 6 residues within 4Å: Chain B: L.271, G.275, M.276, A.285, L.286, L.287 No protein-ligand interaction detected (PLIP) ACT.18: 7 residues within 4Å: Chain B: G.15, M.17, V.18, W.31, A.70, G.71, K.97 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:G.15, B:G.71 Salt bridges: B:K.97

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

EDO.3: 10 residues within 4Å: Chain A: M.17, V.18, Q.19, Q.69, A.70, G.71, N.119, G.120, S.121 Ligands: ACT.2 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:M.17, A:G.71, A:N.119 EDO.4: 5 residues within 4Å: Chain A: Y.118, L.141, N.142 Chain B: S.301, G.302 No protein-ligand interaction detected (PLIP) EDO.6: 5 residues within 4Å: Chain A: S.254, A.255, G.258, I.259, A.260 No protein-ligand interaction detected (PLIP) EDO.9: 5 residues within 4Å: Chain A: R.298, S.301 Chain B: Y.118, S.123, L.141 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.301 EDO.20: 3 residues within 4Å: Chain B: K.100, Y.101, C.156 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.100, B:Y.101

5 x FMT: FORMIC ACID(Non-functional Binders)

FMT.5: 4 residues within 4Å: Chain A: L.272, G.275, M.276, L.287 2 PLIP interactions: 2 interactions with chain A Water bridges: A:M.276, A:L.287 FMT.7: 7 residues within 4Å: Chain A: M.6, A.7, F.8, P.9, R.298 Chain B: S.123, G.124 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:R.298, B:S.123 FMT.8: 3 residues within 4Å: Chain A: R.40, N.84, C.85 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.40, A:R.40 Water bridges: A:N.84 FMT.19: 4 residues within 4Å: Chain A: K.5, Q.127 Chain B: R.4, K.5 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.4, B:K.5 FMT.21: 7 residues within 4Å: Chain B: Q.110, V.202, H.246, I.249, T.292, P.293, F.294 2 PLIP interactions: 2 interactions with chain B Water bridges: B:H.246, B:T.292

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

NA.10: 4 residues within 4Å: Chain A: N.221, F.223, D.263, A.266 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.221, A:N.221, A:F.223 NA.11: 3 residues within 4Å: Chain A: R.105, D.176, E.178 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.178 NA.22: 5 residues within 4Å: Chain B: N.221, F.223, D.263, A.266, S.267 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.221, B:F.223, B:D.263

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

CL.12: 6 residues within 4Å: Chain A: S.284, A.285, L.286 Chain B: S.284, A.285, L.286 Ligand excluded by PLIP CL.23: 2 residues within 4Å: Chain B: F.223, T.224 Ligand excluded by PLIP

1 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.16: 11 residues within 4Å: Chain A: S.123, G.124 Chain B: M.6, A.7, F.8, P.9, Q.127, D.295, R.298, Q.299, F.305 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.298 Salt bridges: B:D.295 pi-Cation interactions: B:F.8

1 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.17: 6 residues within 4Å: Chain B: P.132, N.133, T.196, D.197, T.198, E.240 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:P.132, B:T.198 Water bridges: B:T.196, B:E.240, B:E.240

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Stefanelli, I. et al., Broad-spectrum coronavirus 3C-like protease peptidomimetic inhibitors effectively block SARS-CoV-2 replication in cells: Design, synthesis, biological evaluation, and X-ray structure determination. Eur.J.Med.Chem. (2023)

Release Date

2023-05-03

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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