SMTL ID : 7lmi.1

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.71 Å

Oligo State

homo-dimer

Ligands

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 8 residues within 4Å: Chain A: E.166, L.167, P.168, R.188, Q.189, T.190, Q.192 Ligands: Y6A.2 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:E.166, A:R.188, A:Q.189, A:T.190, 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 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.105, A:I.106 GOL.4: 8 residues within 4Å: Chain B: E.166, L.167, P.168, R.188, Q.189, T.190, Q.192 Ligands: Y6A.5 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:E.166, B:R.188, B:Q.189, B:T.190, B:T.190, B:Q.192 GOL.6: 6 residues within 4Å: Chain B: R.105, I.106, Q.107, P.108, H.134, Y.182 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.105, B:I.106

2 x Y6A: 2-(benzotriazol-1-yl)-~{N}-[4-(1~{H}-pyrazol-4-yl)phenyl]-~{N}-(thiophen-3-ylmethyl)ethanamide(Non-covalent)

Y6A.2: 17 residues within 4Å: Chain A: 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, R.188, Q.189 Ligands: GOL.1 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:E.166 Hydrogen bonds: A:E.166 Water bridges: A:C.44 pi-Stacking: A:H.41 Y6A.5: 17 residues within 4Å: Chain B: 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, R.188, Q.189 Ligands: GOL.4 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:E.166 Hydrogen bonds: B:T.25, B:E.166 Water bridges: B:C.44 pi-Stacking: B:H.41

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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