SMTL ID : 7t40.1

Structure of MERS 3CL protease in complex with inhibitor 10c

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

homo-dimer

Ligands

2 x FV5: (1R,2S)-1-hydroxy-2-{[N-({[7-(methanesulfonyl)-7-azaspiro[3.5]nonan-2-yl]oxy}carbonyl)-L-leucyl]amino}-3-[(3S)-2-oxopyrrolidin-3-yl]propane-1-sulfonic acid(Covalent)

FV5.1: 17 residues within 4Å: Chain A: H.48, F.150, L.151, C.152, S.154, C.155, H.173, Q.174, M.175, E.176, A.178, H.182, D.197, Q.199, V.200, H.201 Ligands: FVE.2 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:H.48 Hydrogen bonds: A:F.150, A:S.154, A:Q.174, A:E.176, A:E.176, A:Q.199 Water bridges: A:G.153, A:Q.199 FV5.4: 17 residues within 4Å: Chain B: H.48, F.150, L.151, C.152, S.154, C.155, H.173, Q.174, M.175, E.176, A.178, H.182, D.197, Q.199, V.200, H.201 Ligands: FVE.5 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:H.48 Hydrogen bonds: B:F.150, B:S.154, B:Q.174, B:E.176, B:Q.199 Water bridges: B:G.153, B:Q.199

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

FVE.2: 18 residues within 4Å: Chain A: H.48, F.150, L.151, C.152, G.153, S.154, C.155, H.173, Q.174, M.175, E.176, A.178, H.182, D.197, Q.199, V.200, H.201 Ligands: FV5.1 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:H.48 Hydrogen bonds: A:F.150, A:G.153, A:S.154, A:S.154, A:C.155, A:Q.174, A:E.176, A:E.176, A:Q.199 Water bridges: A:Q.199 FVE.5: 18 residues within 4Å: Chain B: H.48, F.150, L.151, C.152, G.153, S.154, C.155, H.173, Q.174, M.175, E.176, A.178, H.182, D.197, Q.199, V.200, H.201 Ligands: FV5.4 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:H.48 Hydrogen bonds: B:F.150, B:G.153, B:S.154, B:S.154, B:C.155, B:Q.174, B:E.176, B:Q.199 Water bridges: B:Q.199

2 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.3: 5 residues within 4Å: Chain A: M.13, H.15, M.305, Q.306 Chain B: T.133 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Water bridges: B:Y.128, B:T.133, A:H.15, A:D.302 PG4.6: 5 residues within 4Å: Chain A: T.133 Chain B: M.13, H.15, M.305, Q.306 3 PLIP interactions: 3 interactions with chain B Water bridges: B:H.15, B:T.137, B:D.302

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
A

3C-like proteinase

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