SMTL ID : 7lmj.1

SARS-CoV-1 3CLPro in complex with 2-(1H-benzo[d][1,2,3]triazol-1-yl)-N-(3-chlorobenzyl)-N-(4-(2-oxo-1,2-dihydropyridin-3-yl)phenyl)acetamide

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.69 Å

Oligo State

homo-dimer

Ligands

4 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.1: 5 residues within 4Å: Chain A: L.141, N.142 Chain B: S.1, S.301 Ligands: Y67.4 7 PLIP interactions: 6 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:S.1, B:S.1, A:N.142 Water bridges: B:S.301, B:S.301, B:S.301, B:S.301 PEG.6: 3 residues within 4Å: Chain A: P.252, P.293, V.297 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.256 Water bridges: A:I.249 PEG.7: 5 residues within 4Å: Chain A: S.1, S.301 Chain B: L.141, N.142 Ligands: Y67.10 7 PLIP interactions: 1 interactions with chain B, 6 interactions with chain A Hydrogen bonds: B:N.142, A:S.1, A:S.1 Water bridges: A:S.301, A:S.301, A:S.301, A:S.301 PEG.12: 3 residues within 4Å: Chain B: P.252, P.293, V.297 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Q.256 Water bridges: B:I.249

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 9 residues within 4Å: Chain A: M.165, E.166, L.167, P.168, R.188, Q.189, T.190, Q.192 Ligands: Y67.4 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:E.166, A:R.188, A:Q.189, A:T.190, A:Q.192 GOL.3: 6 residues within 4Å: Chain A: R.105, I.106, Q.107, P.108, H.134, Y.182 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.105, A:I.106 Water bridges: A:Q.107 GOL.5: 2 residues within 4Å: Chain A: E.166 Ligands: Y67.4 No protein-ligand interaction detected (PLIP) GOL.8: 9 residues within 4Å: Chain B: M.165, E.166, L.167, P.168, R.188, Q.189, T.190, Q.192 Ligands: Y67.10 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:E.166, B:R.188, B:Q.189, B:T.190, B:Q.192 GOL.9: 6 residues within 4Å: Chain B: R.105, I.106, Q.107, P.108, H.134, Y.182 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.105, B:I.106 Water bridges: B:Q.107 GOL.11: 2 residues within 4Å: Chain B: E.166 Ligands: Y67.10 No protein-ligand interaction detected (PLIP)

2 x Y67: 2-(benzotriazol-1-yl)-~{N}-[(3-chlorophenyl)methyl]-~{N}-[4-(2-oxidanylidene-1~{H}-pyridin-3-yl)phenyl]ethanamide(Non-covalent)

Y67.4: 21 residues within 4Å: Chain A: T.25, H.41, C.44, T.45, A.46, M.49, F.140, L.141, N.142, S.144, C.145, H.163, H.164, M.165, E.166, D.187, R.188, Q.189 Ligands: PEG.1, GOL.2, GOL.5 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:T.25, A:M.165, A:E.166 Hydrogen bonds: A:E.166 Y67.10: 21 residues within 4Å: Chain B: T.25, H.41, C.44, T.45, A.46, M.49, F.140, L.141, N.142, S.144, C.145, H.163, H.164, M.165, E.166, D.187, R.188, Q.189 Ligands: PEG.7, GOL.8, GOL.11 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:T.25, B:M.165, B:E.166 Hydrogen bonds: B:E.166

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Han, S.H. et al., Structure-Based Optimization of ML300-Derived, Noncovalent Inhibitors Targeting the Severe Acute Respiratory Syndrome Coronavirus 3CL Protease (SARS-CoV-2 3CL pro ). J.Med.Chem. (2022)

Release Date

2021-08-11

Peptides

3C-like proteinase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
AAA

B
AAA

3C-like proteinase

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