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Structure paper

TitleBroad-Spectrum Cyclopropane-Based Inhibitors of Coronavirus 3C-like Proteases: Biochemical, Structural, and Virological Studies.
Journal, issue, pagesAcs Pharmacol Transl Sci, Vol. 6, Page 181-194, Year 2023
Publish dateJan 26, 2022 (structure data deposition date)
AuthorsDampalla, C.S. / Nguyen, H.N. / Rathnayake, A.D. / Kim, Y. / Perera, K.D. / Madden, T.K. / Thurman, H.A. / Machen, A.J. / Kashipathy, M.M. / Liu, L. ...Dampalla, C.S. / Nguyen, H.N. / Rathnayake, A.D. / Kim, Y. / Perera, K.D. / Madden, T.K. / Thurman, H.A. / Machen, A.J. / Kashipathy, M.M. / Liu, L. / Battaile, K.P. / Lovell, S. / Chang, K.O. / Groutas, W.C.
External linksAcs Pharmacol Transl Sci / PubMed:36654747
MethodsX-ray diffraction
Resolution1.55 - 2.7 Å
Structure data

PDB-7tq2:
Structure of SARS-CoV-2 3CL protease in complex with the cyclopropane based inhibitor 1c
Method: X-RAY DIFFRACTION / Resolution: 2.3 Å

PDB-7tq3:
Structure of SARS-CoV-2 3CL protease in complex with the cyclopropane based inhibitor 5c
Method: X-RAY DIFFRACTION / Resolution: 2.0 Å

PDB-7tq4:
Structure of SARS-CoV-2 3CL protease in complex with the cyclopropane based inhibitor 6c
Method: X-RAY DIFFRACTION / Resolution: 2.45 Å

PDB-7tq5:
Structure of SARS-CoV-2 3CL protease in complex with the cyclopropane based inhibitor 10d
Method: X-RAY DIFFRACTION / Resolution: 1.65 Å

PDB-7tq6:
Structure of SARS-CoV-2 3CL protease in complex with the cyclopropane based inhibitor 13d
Method: X-RAY DIFFRACTION / Resolution: 1.55 Å

PDB-7tq7:
Structure of MERS 3CL protease in complex with the cyclopropane based inhibitor 13c
Method: X-RAY DIFFRACTION / Resolution: 1.7 Å

PDB-7tq8:
Structure of MERS 3CL protease in complex with the cyclopropane based inhibitor 14d
Method: X-RAY DIFFRACTION / Resolution: 1.65 Å

PDB-8czt:
Structure of MERS 3CL protease in complex with the cyclopropane based inhibitor 15d
Method: X-RAY DIFFRACTION / Resolution: 2.1 Å

PDB-8czu:
Structure of MERS 3CL protease in complex with the cyclopropane based inhibitor 16d
Method: X-RAY DIFFRACTION / Resolution: 2.7 Å

PDB-8czv:
Structure of MERS 3CL protease in complex with the cyclopropane based inhibitor 17d
Method: X-RAY DIFFRACTION / Resolution: 1.95 Å

PDB-8czw:
Structure of SARS-CoV-2 3CL protease in complex with the cyclopropane based inhibitor 15d
Method: X-RAY DIFFRACTION / Resolution: 1.7 Å

PDB-8czx:
Structure of SARS-CoV-2 3CL protease in complex with the cyclopropane based inhibitor 17d
Method: X-RAY DIFFRACTION / Resolution: 1.65 Å

PDB-8dgy:
Structure of MERS 3CL protease in complex with the cyclopropane based inhibitor 16d (high resolution)
Method: X-RAY DIFFRACTION / Resolution: 1.65 Å

Chemicals

ChemComp-ISG:
N-{(2S)-1-oxo-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}-N~2~-({[(1R,2R)-2-phenylcyclopropyl]methoxy}carbonyl)-L-leucinamide

ChemComp-HOH:
WATER

ChemComp-IS5:
N~2~-({[(1R,2R)-2-(3-fluorophenyl)cyclopropyl]methoxy}carbonyl)-N-{(2S)-1-oxo-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}-L-leucinamide

ChemComp-IRZ:
N~2~-({[(1R,2R)-2-(3-chlorophenyl)cyclopropyl]methoxy}carbonyl)-N-{(2S)-1-oxo-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}-L-leucinamide

ChemComp-IRW:
(1S,2S)-1-hydroxy-2-{[N-({[(1R,2R)-2-(4-methoxyphenyl)cyclopropyl]methoxy}carbonyl)-L-leucyl]amino}-3-[(3S)-2-oxopyrrolidin-3-yl]propane-1-sulfonic acid

ChemComp-ITX:
(1R,2S)-1-hydroxy-2-{[N-({[(1R,2R)-2-(4-methoxyphenyl)cyclopropyl]methoxy}carbonyl)-L-leucyl]amino}-3-[(3S)-2-oxopyrrolidin-3-yl]propane-1-sulfonic acid

ChemComp-CL:
Unknown entry

ChemComp-PG4:
TETRAETHYLENE GLYCOL / precipitant*YM

ChemComp-IT3:
(1S,2S)-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]-2-{[N-({[(1R,2R)-2-propylcyclopropyl]methoxy}carbonyl)-L-leucyl]amino}propane-1-sulfonic acid

ChemComp-ITG:
(1R,2S)-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]-2-{[N-({[(1R,2R)-2-propylcyclopropyl]methoxy}carbonyl)-L-leucyl]amino}propane-1-sulfonic acid

ChemComp-IRR:
N-{(2S)-1-oxo-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}-N~2~-({[(1R,2R)-2-propylcyclopropyl]methoxy}carbonyl)-L-leucinamide

ChemComp-IRK:
(1R,2S)-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]-2-{[N-({[(1R,2S)-2-propylcyclopropyl]methoxy}carbonyl)-L-leucyl]amino}propane-1-sulfonic acid

ChemComp-IUB:
(1S,2S)-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]-2-{[N-({[(1R,2S)-2-propylcyclopropyl]methoxy}carbonyl)-L-leucyl]amino}propane-1-sulfonic acid

ChemComp-P8L:
[(1~{S},2~{R})-2-cyclohexylcyclopropyl]methyl ~{N}-[(2~{S})-1-[[(1~{R},2~{S})-1-[bis(oxidanyl)-oxidanylidene-$l^{5}-sulfanyl]-1-oxidanyl-3-[(3~{S})-2-oxidanylidenepyrrolidin-3-yl]propan-2-yl]amino]-4-methyl-1-oxidanylidene-pentan-2-yl]carbamate

ChemComp-P9R:
[(1~{S},2~{S})-2-(cyclohexylmethyl)cyclopropyl]methyl ~{N}-[(2~{S})-1-[[(2~{S})-1-[bis(oxidanyl)-oxidanylidene-$l^{5}-sulfanyl]-1-oxidanyl-3-[(3~{R})-2-oxidanylidene-3,4-dihydropyrrol-3-yl]propan-2-yl]amino]-4-methyl-1-oxidanylidene-pentan-2-yl]carbamate

ChemComp-P8C:
[(1~{S},2~{R})-2-[4,4-bis(fluoranyl)cyclohexyl]cyclopropyl]methyl ~{N}-[(2~{S})-1-[[(1~{R},2~{S})-1-[bis(oxidanyl)-oxidanylidene-$l^{5}-sulfanyl]-1-oxidanyl-3-[(3~{S})-2-oxidanylidenepyrrolidin-3-yl]propan-2-yl]amino]-4-methyl-1-oxidanylidene-pentan-2-yl]carbamate

ChemComp-PJR:
[(1~{S},2~{R})-2-[4,4-bis(fluoranyl)cyclohexyl]cyclopropyl]methyl ~{N}-[(2~{S})-1-[[(1~{S},2~{S})-1-[bis(oxidanyl)-oxidanylidene-$l^{5}-sulfanyl]-1-oxidanyl-3-[(3~{S})-2-oxidanylidenepyrrolidin-3-yl]propan-2-yl]amino]-4-methyl-1-oxidanylidene-pentan-2-yl]carbamate

ChemComp-P8U:
[(1~{S},2~{R})-2-cyclohexylcyclopropyl]methyl ~{N}-[(2~{S})-1-[[(1~{S},2~{S})-1-[bis(oxidanyl)-oxidanylidene-$l^{5}-sulfanyl]-1-oxidanyl-3-[(3~{S})-2-oxidanylidenepyrrolidin-3-yl]propan-2-yl]amino]-4-methyl-1-oxidanylidene-pentan-2-yl]carbamate

ChemComp-S9U:
[(1~{R},2~{R})-2-(cyclohexylmethyl)cyclopropyl]methyl ~{N}-[(2~{S})-1-[[(1~{S},2~{S})-1-[bis(oxidanyl)-oxidanylidene-$l^{5}-sulfanyl]-1-oxidanyl-3-[(3~{S})-2-oxidanylidenepyrrolidin-3-yl]propan-2-yl]amino]-4-methyl-1-oxidanylidene-pentan-2-yl]carbamate

ChemComp-SD6:
[(1~{R},2~{R})-2-(cyclohexylmethyl)cyclopropyl]methyl ~{N}-[(2~{S})-1-[[(1~{R},2~{S})-1-[bis(oxidanyl)-oxidanylidene-$l^{5}-sulfanyl]-1-oxidanyl-3-[(3~{S})-2-oxidanylidenepyrrolidin-3-yl]propan-2-yl]amino]-4-methyl-1-oxidanylidene-pentan-2-yl]carbamate

Source
  • severe acute respiratory syndrome coronavirus 2
  • middle east respiratory syndrome-related coronavirus
KeywordsHYDROLASE/HYDROLASE INHIBITOR / COVID-19 / PROTEASE / severe acute respiratory syndrome coronavirus 2 / SARS-CoV-2 3CL protease Inhhibitors / hydrolase / HYDROLASE-HYDROLASE INHIBITOR complex / MERS 3CL protease Inhhibitors

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