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Structure paper

TitleFragment-based drug discovery using cryo-EM.
Journal, issue, pagesDrug Discov Today, Vol. 25, Issue 3, Page 485-490, Year 2020
Publish dateDec 23, 2019
AuthorsMichael Saur / Michael J Hartshorn / Jing Dong / Judith Reeks / Gabor Bunkoczi / Harren Jhoti / Pamela A Williams /
PubMed AbstractRecent advances in electron cryo-microscopy (cryo-EM) structure determination have pushed the resolutions obtainable by the method into the range widely considered to be of utility for drug discovery. ...Recent advances in electron cryo-microscopy (cryo-EM) structure determination have pushed the resolutions obtainable by the method into the range widely considered to be of utility for drug discovery. Here, we review the use of cryo-EM in fragment-based drug discovery (FBDD) based on in-house method development. We demonstrate not only that cryo-EM can reveal details of the molecular interactions between fragments and a protein, but also that the current reproducibility, quality, and throughput are compatible with FBDD. We exemplify this using the test system β-galactosidase (Bgal) and the oncology target pyruvate kinase 2 (PKM2).
External linksDrug Discov Today / PubMed:31877353
MethodsEM (single particle)
Resolution2.2 - 3.2 Å
Structure data

10563

6tsh

EMDB-10563, PDB-6tsh:
Beta-galactosidase in complex with deoxygalacto-nojirimycin
Method: EM (single particle) / Resolution: 2.3 Å

10564

6tsk

EMDB-10564, PDB-6tsk:
Beta-galactosidase in complex with L-ribose
Method: EM (single particle) / Resolution: 2.3 Å

10574

6tte

EMDB-10574, PDB-6tte:
Beta-galactosidase in complex with PETG
Method: EM (single particle) / Resolution: 2.2 Å

10575

6ttf

EMDB-10575, PDB-6ttf:
PKM2 in complex with Compound 5
Method: EM (single particle) / Resolution: 3.2 Å

10576

6tth

EMDB-10576, PDB-6tth:
PKM2 in complex with L-threonine
Method: EM (single particle) / Resolution: 2.6 Å

10577

6tti

EMDB-10577, PDB-6tti:
PKM2 in complex with Compound 6
Method: EM (single particle) / Resolution: 2.5 Å

10584

6ttq

EMDB-10584, PDB-6ttq:
PKM2 in complex with Compound 10
Method: EM (single particle) / Resolution: 2.7 Å

Chemicals

ChemComp-MG:
Unknown entry

ChemComp-DGJ:
(2R,3S,4R,5S)-2-(hydroxymethyl)piperidine-3,4,5-triol / medication, Galafold*YM / Migalastat

ChemComp-HOH:
WATER / Water

ChemComp-0MK:
beta-L-ribopyranose / Ribose

ChemComp-PTQ:
2-phenylethyl 1-thio-beta-D-galactopyranoside

ChemComp-LZ2:
5-hydroxynaphthalene-1-sulfonamide

ChemComp-FBP:
1,6-di-O-phosphono-beta-D-fructofuranose / Fructose 1,6-bisphosphate

ChemComp-THR:
THREONINE / Threonine

ChemComp-NXE:
~{N}-[3-(trifluoromethyl)-1,2-oxazol-5-yl]ethanamide

ChemComp-DMS:
DIMETHYL SULFOXIDE / DMSO, precipitant*YM / Dimethyl sulfoxide

ChemComp-NXH:
1-propan-2-yl-3-pyridin-4-yl-urea

Source
  • escherichia coli (E. coli)
  • Human alphaherpesvirus 1 strain RH2
  • homo sapiens (human)
KeywordsSUGAR BINDING PROTEIN / Bgal / nojirimycin / L-ribose / PETG / CYTOSOLIC PROTEIN / PKM2 / FBDD / L-threonine

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