SMTL ID : 5wkl.1

1.85 A resolution structure of MERS 3CL protease in complex with piperidine-based peptidomimetic inhibitor 17

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.85 Å

Oligo State

homo-dimer

Ligands

2 x AVY: (1R,2S)-2-{[N-({[4-benzyl-1-(tert-butoxycarbonyl)piperidin-4-yl]oxy}carbonyl)-L-leucyl]amino}-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propane-1-sulfonic acid(Covalent)

AVY.1: 16 residues within 4Å: Chain A: H.48, L.56, Y.61, F.150, L.151, C.152, S.154, C.155, H.173, Q.174, M.175, E.176, H.182, D.197, Q.199 Ligands: B3J.2 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:H.48, A:E.176 Hydrogen bonds: A:F.150, A:Q.174, A:E.176, A:Q.199 AVY.3: 16 residues within 4Å: Chain B: H.48, L.56, Y.61, F.150, L.151, C.152, S.154, C.155, H.173, Q.174, M.175, E.176, H.182, D.197, Q.199 Ligands: B3J.4 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:H.48, B:E.176 Hydrogen bonds: B:F.150, B:Q.174, B:E.176, B:Q.199

2 x B3J: (1S,2S)-2-{[N-({[4-benzyl-1-(tert-butoxycarbonyl)piperidin-4-yl]oxy}carbonyl)-L-leucyl]amino}-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propane-1-sulfonic acid(Covalent)

B3J.2: 17 residues within 4Å: Chain A: H.48, L.56, Y.61, F.150, L.151, C.152, G.153, S.154, C.155, H.173, Q.174, M.175, E.176, H.182, D.197, Q.199 Ligands: AVY.1 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:H.48, A:E.176 Hydrogen bonds: A:F.150, A:G.153, A:S.154, A:C.155, A:Q.174, A:E.176, A:Q.199 B3J.4: 17 residues within 4Å: Chain B: H.48, L.56, Y.61, F.150, L.151, C.152, G.153, S.154, C.155, H.173, Q.174, M.175, E.176, H.182, D.197, Q.199 Ligands: AVY.3 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:H.48, B:E.176 Hydrogen bonds: B:F.150, 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

Galasiti Kankanamalage, A.C. et al., Structure-guided design of potent and permeable inhibitors of MERS coronavirus 3CL protease that utilize a piperidine moiety as a novel design element. Eur J Med Chem (2018)

Release Date

2018-04-04

Peptides

Orf1a protein: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Orf1a protein

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