SMTL ID : 9atg.1

Crystal structure of MERS 3CL protease in complex with a 2,2-difluoro-5-methylbenzo[1,3]dioxole 2-pyrrolidone inhibitor

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.75 Å

Oligo State

homo-dimer

Ligands

2 x 01: (1S,2S)-2-({N-[({(2S)-1-[(2,2-difluoro-2H-1,3-benzodioxol-5-yl)methyl]-5-oxopyrrolidin-2-yl}methoxy)carbonyl]-L-leucyl}amino)-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propane-1-sulfonic acid

01.1: 22 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, L.177, A.178, G.180, H.182, D.197, K.198, Q.199, V.200, H.201, Q.202 Ligands: 02.2 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:H.48, A:A.178 Hydrogen bonds: A:G.153, A:S.154, A:S.154, A:C.155, A:E.176, A:E.176, A:A.178, A:Q.202 01.3: 22 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, L.177, A.178, G.180, H.182, D.197, K.198, Q.199, V.200, H.201, Q.202 Ligands: 02.4 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:H.48, B:A.178 Hydrogen bonds: B:G.153, B:S.154, B:S.154, B:C.155, B:E.176, B:E.176, B:A.178, B:H.201, B:Q.202

2 x 02: (1R,2S)-2-({N-[({(2S)-1-[(2,2-difluoro-2H-1,3-benzodioxol-5-yl)methyl]-5-oxopyrrolidin-2-yl}methoxy)carbonyl]-L-leucyl}amino)-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propane-1-sulfonic acid

02.2: 22 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, A.178, G.180, H.182, D.197, K.198, Q.199, V.200, H.201, Q.202 Ligands: 01.1 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:L.56, A:A.178 Hydrogen bonds: A:S.154, A:E.176, A:E.176, A:A.178, A:Q.202 Water bridges: A:G.153 02.4: 22 residues within 4Å: Chain B: H.48, L.56, F.150, L.151, C.152, S.154, C.155, H.173, Q.174, M.175, E.176, L.177, A.178, G.180, H.182, D.197, K.198, Q.199, V.200, H.201, Q.202 Ligands: 01.3 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:L.56, B:A.178 Hydrogen bonds: B:S.154, B:E.176, B:A.178, B:H.201, B:Q.202 Water bridges: B:G.153

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Dampalla, C.S. et al., Structure-Guided Design of Potent Coronavirus Inhibitors with a 2-Pyrrolidone Scaffold: Biochemical, Crystallographic, and Virological Studies. J.Med.Chem. (2024)

Release Date

2024-07-10

Peptides

3C-like proteinase nsp5: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

3C-like proteinase nsp5

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