SMTL ID : 7t3y.1

Structure of MERS 3CL protease in complex with inhibitor 8c

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-dimer

Ligands

2 x F5L: (1R,2S)-1-hydroxy-2-{[N-({[7-(2-methylpropanoyl)-7-azaspiro[3.5]nonan-2-yl]oxy}carbonyl)-L-leucyl]amino}-3-[(3S)-2-oxopyrrolidin-3-yl]propane-1-sulfonic acid(Covalent)

F5L.1: 17 residues within 4Å: Chain A: H.48, L.56, F.150, L.151, C.152, S.154, C.155, H.173, Q.174, M.175, E.176, L.177, H.182, D.197, K.198, Q.199 Ligands: F8C.2 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.176, A:E.176, A:Q.199 Water bridges: A:G.153 F5L.3: 13 residues within 4Å: Chain B: H.48, L.56, F.150, S.154, C.155, H.173, Q.174, M.175, E.176, H.182, D.197, Q.199 Ligands: F8C.4 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:H.48, B:L.56, B:D.197 Hydrogen bonds: B:Q.174, B:E.176, B:Q.199

2 x F8C: (1S,2S)-1-hydroxy-2-{[N-({[7-(2-methylpropanoyl)-7-azaspiro[3.5]nonan-2-yl]oxy}carbonyl)-L-leucyl]amino}-3-[(3S)-2-oxopyrrolidin-3-yl]propane-1-sulfonic acid(Covalent)

F8C.2: 16 residues within 4Å: Chain A: H.48, F.150, C.152, G.153, S.154, C.155, H.173, Q.174, M.175, E.176, L.177, H.182, D.197, K.198, Q.199 Ligands: F5L.1 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:H.48, A:Q.199 Hydrogen bonds: A:G.153, A:S.154, A:C.155, A:E.176, A:E.176, A:Q.199 F8C.4: 17 residues within 4Å: Chain B: H.48, L.56, F.150, L.151, C.152, G.153, S.154, C.155, H.173, Q.174, M.175, E.176, H.182, D.197, K.198, Q.199 Ligands: F5L.3 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:H.48, B:L.56 Hydrogen bonds: B:G.153, B:S.154, B:C.155, B:Q.174, B:E.176, B:Q.199

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Dampalla, C.S. et al., Structure-Guided Design of Potent Spirocyclic Inhibitors of Severe Acute Respiratory Syndrome Coronavirus-2 3C-like Protease. J.Med.Chem. (2022)

Release Date

2021-12-22

Peptides

3C-like proteinase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

3C-like proteinase

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