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Structure paper

TitleTargeting prolyl-tRNA synthetase via a series of ATP-mimetics to accelerate drug discovery against toxoplasmosis.
Journal, issue, pagesPlos Pathog., Vol. 19, Page e1011124-e1011124, Year 2023
Publish dateJul 4, 2021 (structure data deposition date)
AuthorsYogavel, M. / Bougdour, A. / Mishra, S. / Malhotra, N. / Chhibber-Goel, J. / Bellini, V. / Harlos, K. / Laleu, B. / Hakimi, M.A. / Sharma, A.
External linksPlos Pathog. / PubMed:36854028
MethodsX-ray diffraction
Resolution1.769 - 3.219 Å
Structure data

PDB-7f98:
Homo sapiens Prolyl-tRNA Synthetase (HsPRS) in Complex with L-proline and compound L95
Method: X-RAY DIFFRACTION / Resolution: 1.999 Å

PDB-7f99:
Homo sapiens Prolyl-tRNA Synthetase (HsPRS) in Complex with L-proline and compound L96
Method: X-RAY DIFFRACTION / Resolution: 1.979 Å

PDB-7f9a:
Homo sapiens Prolyl-tRNA Synthetase (HsPRS) in Complex with L-proline and compound L97
Method: X-RAY DIFFRACTION / Resolution: 1.999 Å

PDB-7f9b:
Homo sapiens Prolyl-tRNA Synthetase (HsPRS) in Complex with L-proline and compound L95
Method: X-RAY DIFFRACTION / Resolution: 1.995 Å

PDB-7f9c:
Homo sapiens Prolyl-tRNA Synthetase (HsPRS) in Complex with L-proline and compound L96
Method: X-RAY DIFFRACTION / Resolution: 2.196 Å

PDB-7f9d:
Homo sapiens Prolyl-tRNA Synthetase (HsPRS) in Complex with L-proline and compound L96
Method: X-RAY DIFFRACTION / Resolution: 2.497 Å

PDB-7fak:
Co-crystal Structure of Toxoplasma gondii Prolyl tRNA Synthetase (TgPRS) in complex with L96 and L-pro
Method: X-RAY DIFFRACTION / Resolution: 1.899 Å

PDB-7fal:
Co-crystal Structure of Toxoplasma gondii Prolyl tRNA Synthetase (TgPRS) in complex with T36 and L-pro
Method: X-RAY DIFFRACTION / Resolution: 3.219 Å

PDB-7fam:
Co-crystal Structure of Toxoplasma gondii Prolyl tRNA Synthetase (TgPRS) in complex with L97 and L-pro
Method: X-RAY DIFFRACTION / Resolution: 2.42 Å

PDB-7fan:
Co-crystal Structure of Toxoplasma gondii Prolyl tRNA Synthetase (TgPRS) in complex with T35 and L-pro
Method: X-RAY DIFFRACTION / Resolution: 1.769 Å

PDB-7vc1:
Toxoplasma gondii Prolyl-tRNA Synthetase (TgPRS) in Complex with inhibitor L95 and L-proline in space group P21
Method: X-RAY DIFFRACTION / Resolution: 1.892 Å

PDB-7vc2:
Toxoplasma gondii Prolyl-tRNA Synthetase (TgPRS) in Complex with inhibitor L96 and L-proline in space group P21
Method: X-RAY DIFFRACTION / Resolution: 2.096 Å

PDB-7vc3:
Toxoplasma gondii Prolyl-tRNA Synthetase (TgPRS) in Complex with inhibitor L97 and L-proline at 1.97 A resolution
Method: X-RAY DIFFRACTION / Resolution: 1.973 Å

Chemicals

ChemComp-JE6:
~{N}-[4-[(3~{S})-3-cyano-3-cyclopropyl-2-oxidanylidene-pyrrolidin-1-yl]-6-methyl-pyridin-2-yl]-2-phenyl-ethanamide

ChemComp-ZN:
Unknown entry

ChemComp-CA:
Unknown entry

ChemComp-PRO:
PROLINE

ChemComp-CL:
Unknown entry

ChemComp-HOH:
WATER

ChemComp-1UI:
4-[(3S)-3-cyano-3-cyclopropyl-2-oxidanylidene-pyrrolidin-1-yl]-N-[[3-fluoranyl-5-(5-methoxypyridin-3-yl)phenyl]methyl]-6-methyl-pyridine-2-carboxamide

ChemComp-1XK:
4-[(3S)-3-cyclopropyl-3-(hydroxymethyl)-2-oxidanylidene-pyrrolidin-1-yl]-N-[[3-fluoranyl-5-(1-methylpyrazol-4-yl)phenyl]methyl]-6-methyl-pyridine-2-carboxamide

ChemComp-MES:
2-(N-MORPHOLINO)-ETHANESULFONIC ACID / pH buffer*YM

ChemComp-FMT:
FORMIC ACID

ChemComp-ACT:
ACETATE ION

ChemComp-1T0:
4-[(3R)-3-cyano-3-(1-methylcyclopropyl)-2-oxidanylidene-pyrrolidin-1-yl]-N-[[3-fluoranyl-5-(1-methylpyrazol-4-yl)phenyl]methyl]-6-methyl-pyridine-2-carboxamide

ChemComp-1TI:
4-[(3S)-3-cyano-3-(1-methylcyclopropyl)-2-oxidanylidene-pyrrolidin-1-yl]-N-[[3-fluoranyl-5-(1-methylpyrazol-4-yl)phenyl]methyl]-6-methyl-pyridine-2-carboxamide

ChemComp-EDO:
1,2-ETHANEDIOL

ChemComp-GOL:
GLYCEROL

ChemComp-NA:
Unknown entry

ChemComp-SO3:
SULFITE ION

ChemComp-ETA:
ETHANOLAMINE

Source
  • homo sapiens (human)
  • toxoplasma gondii (eukaryote)
KeywordsLIGASE / PROTEIN TRANSLATION / MALARIA / INHIBITOR / PRS / LIGASE/LIGASE INHIBITOR / LIGASE-LIGASE INHIBITOR complex / ATP POCKET / TRANSLATION/INHIBITOR / Inhibitor-Bound Structural Comparison / Multi-drug / TRANSLATION-INHIBITOR COMPLEX / TRANSLATION / DOUBLE DRUG

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