SMTL ID : 9whe.1

A novel, covalent and highly synthetically accessible SARS-CoV-2 Mpro chloroacetamide inhibitor

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.82 Å

Oligo State

homo-dimer

Ligands

2 x 01: (2~{R})-~{N}-[4,4-bis(fluoranyl)cyclohexyl]-2-[ethanoyl-[4-(1,2-thiazol-5-yl)phenyl]amino]-2-pyrazin-2-yl-ethanamide

01.1: 17 residues within 4Å: Chain A: H.41, C.44, M.49, Y.54, F.140, L.141, N.142, G.143, S.144, C.145, H.163, H.164, M.165, E.166, D.187, R.188 Ligands: EDO.15 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:N.142, A:G.143, A:S.144, A:C.145 Water bridges: A:E.166 pi-Stacking: A:H.41 01.16: 17 residues within 4Å: Chain B: H.41, C.44, M.49, Y.54, F.140, L.141, N.142, G.143, S.144, C.145, H.163, H.164, M.165, E.166, D.187, R.188 Ligands: EDO.30 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:N.142, B:G.143, B:S.144, B:C.145 Water bridges: B:E.166 pi-Stacking: B:H.41

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

ACT.2: 3 residues within 4Å: Chain A: R.40, N.84, C.85 5 PLIP interactions: 5 interactions with chain A Water bridges: A:R.40, A:N.84, A:G.179, A:G.179 Salt bridges: A:R.40 ACT.17: 3 residues within 4Å: Chain B: R.40, N.84, C.85 5 PLIP interactions: 5 interactions with chain B Water bridges: B:R.40, B:N.84, B:G.179, B:G.179 Salt bridges: B:R.40

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

EDO.3: 5 residues within 4Å: Chain A: V.35, H.80, S.81, K.88, K.90 Ligand excluded by PLIP EDO.4: 5 residues within 4Å: Chain A: E.166, L.167, P.168, Q.189 Ligands: EDO.15 Ligand excluded by PLIP EDO.5: 5 residues within 4Å: Chain A: G.215, D.216, R.217, W.218, R.279 Ligand excluded by PLIP EDO.6: 3 residues within 4Å: Chain A: Y.101, K.102, F.103 Ligand excluded by PLIP EDO.7: 3 residues within 4Å: Chain A: G.283 Chain B: L.286 Ligands: EDO.28 Ligand excluded by PLIP EDO.8: 6 residues within 4Å: Chain A: E.14, G.15, M.17, A.70, G.71, K.97 Ligand excluded by PLIP EDO.9: 4 residues within 4Å: Chain A: T.199, Y.239, L.287 Ligands: EDO.13 Ligand excluded by PLIP EDO.10: 6 residues within 4Å: Chain A: M.6, A.7, F.8, Q.127, R.298 Chain B: S.123 Ligand excluded by PLIP EDO.11: 3 residues within 4Å: Chain A: T.243, Q.244, D.245 Ligand excluded by PLIP EDO.12: 6 residues within 4Å: Chain A: Y.37, Q.83, K.88, F.103, L.177, E.178 Ligand excluded by PLIP EDO.13: 7 residues within 4Å: Chain A: R.131, L.287, E.288, D.289 Ligands: EDO.9, EDO.14, EDO.22 Ligand excluded by PLIP EDO.14: 7 residues within 4Å: Chain A: R.131, D.197, T.198, T.199, N.238, D.289 Ligands: EDO.13 Ligand excluded by PLIP EDO.15: 6 residues within 4Å: Chain A: M.49, M.165, E.166, Q.189 Ligands: 01.1, EDO.4 Ligand excluded by PLIP EDO.18: 5 residues within 4Å: Chain B: V.35, H.80, S.81, K.88, K.90 Ligand excluded by PLIP EDO.19: 5 residues within 4Å: Chain B: E.166, L.167, P.168, Q.189 Ligands: EDO.30 Ligand excluded by PLIP EDO.20: 5 residues within 4Å: Chain B: G.215, D.216, R.217, W.218, R.279 Ligand excluded by PLIP EDO.21: 3 residues within 4Å: Chain B: Y.101, K.102, F.103 Ligand excluded by PLIP EDO.22: 3 residues within 4Å: Chain A: L.286 Chain B: G.283 Ligands: EDO.13 Ligand excluded by PLIP EDO.23: 6 residues within 4Å: Chain B: E.14, G.15, M.17, A.70, G.71, K.97 Ligand excluded by PLIP EDO.24: 4 residues within 4Å: Chain B: T.199, Y.239, L.287 Ligands: EDO.28 Ligand excluded by PLIP EDO.25: 6 residues within 4Å: Chain A: S.123 Chain B: M.6, A.7, F.8, Q.127, R.298 Ligand excluded by PLIP EDO.26: 3 residues within 4Å: Chain B: T.243, Q.244, D.245 Ligand excluded by PLIP EDO.27: 6 residues within 4Å: Chain B: Y.37, Q.83, K.88, F.103, L.177, E.178 Ligand excluded by PLIP EDO.28: 7 residues within 4Å: Chain B: R.131, L.287, E.288, D.289 Ligands: EDO.7, EDO.24, EDO.29 Ligand excluded by PLIP EDO.29: 7 residues within 4Å: Chain B: R.131, D.197, T.198, T.199, N.238, D.289 Ligands: EDO.28 Ligand excluded by PLIP EDO.30: 6 residues within 4Å: Chain B: M.49, M.165, E.166, Q.189 Ligands: 01.16, EDO.19 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zagribelnyy, B. et al., A novel, covalent and highly synthetically accessible SARS-CoV-2 Mpro chloroacetamide inhibitor. To Be Published

Release Date

2025-09-17

Peptides

3C-like proteinase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

3C-like proteinase

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