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- EMDB-4590: Leishmania tarentolae proteasome 20S subunit complexed with GSK3494245 -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-4590 | |||||||||
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Title | Leishmania tarentolae proteasome 20S subunit complexed with GSK3494245 | |||||||||
![]() | This is the sharpened EM map which was used for building the protein coordinates | |||||||||
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![]() | Proteasome 20S subunit / hydrolase | |||||||||
Function / homology | ![]() proteasome core complex / proteasome endopeptidase complex / proteasome core complex, beta-subunit complex / proteasome core complex, alpha-subunit complex / proteasomal protein catabolic process / threonine-type endopeptidase activity / proteolysis involved in protein catabolic process / ubiquitin-dependent protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process / hydrolase activity ...proteasome core complex / proteasome endopeptidase complex / proteasome core complex, beta-subunit complex / proteasome core complex, alpha-subunit complex / proteasomal protein catabolic process / threonine-type endopeptidase activity / proteolysis involved in protein catabolic process / ubiquitin-dependent protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process / hydrolase activity / nucleus / cytoplasm Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.8 Å | |||||||||
![]() | Rowland P / Goswami P | |||||||||
![]() | ![]() Title: Preclinical candidate for the treatment of visceral leishmaniasis that acts through proteasome inhibition. Authors: Susan Wyllie / Stephen Brand / Michael Thomas / Manu De Rycker / Chun-Wa Chung / Imanol Pena / Ryan P Bingham / Juan A Bueren-Calabuig / Juan Cantizani / David Cebrian / Peter D Craggs / ...Authors: Susan Wyllie / Stephen Brand / Michael Thomas / Manu De Rycker / Chun-Wa Chung / Imanol Pena / Ryan P Bingham / Juan A Bueren-Calabuig / Juan Cantizani / David Cebrian / Peter D Craggs / Liam Ferguson / Panchali Goswami / Judith Hobrath / Jonathan Howe / Laura Jeacock / Eun-Jung Ko / Justyna Korczynska / Lorna MacLean / Sujatha Manthri / Maria S Martinez / Lydia Mata-Cantero / Sonia Moniz / Andrea Nühs / Maria Osuna-Cabello / Erika Pinto / Jennifer Riley / Sharon Robinson / Paul Rowland / Frederick R C Simeons / Yoko Shishikura / Daniel Spinks / Laste Stojanovski / John Thomas / Stephen Thompson / Elisabet Viayna Gaza / Richard J Wall / Fabio Zuccotto / David Horn / Michael A J Ferguson / Alan H Fairlamb / Jose M Fiandor / Julio Martin / David W Gray / Timothy J Miles / Ian H Gilbert / Kevin D Read / Maria Marco / Paul G Wyatt / ![]() ![]() Abstract: Visceral leishmaniasis (VL), caused by the protozoan parasites and , is one of the major parasitic diseases worldwide. There is an urgent need for new drugs to treat VL, because current therapies ...Visceral leishmaniasis (VL), caused by the protozoan parasites and , is one of the major parasitic diseases worldwide. There is an urgent need for new drugs to treat VL, because current therapies are unfit for purpose in a resource-poor setting. Here, we describe the development of a preclinical drug candidate, GSK3494245/DDD01305143/compound 8, with potential to treat this neglected tropical disease. The compound series was discovered by repurposing hits from a screen against the related parasite Subsequent optimization of the chemical series resulted in the development of a potent cidal compound with activity against a range of clinically relevant and isolates. Compound 8 demonstrates promising pharmacokinetic properties and impressive in vivo efficacy in our mouse model of infection comparable with those of the current oral antileishmanial miltefosine. Detailed mode of action studies confirm that this compound acts principally by inhibition of the chymotrypsin-like activity catalyzed by the β5 subunit of the proteasome. High-resolution cryo-EM structures of apo and compound 8-bound 20S proteasome reveal a previously undiscovered inhibitor site that lies between the β4 and β5 proteasome subunits. This induced pocket exploits β4 residues that are divergent between humans and kinetoplastid parasites and is consistent with all of our experimental and mutagenesis data. As a result of these comprehensive studies and due to a favorable developability and safety profile, compound 8 is being advanced toward human clinical trials. | |||||||||
History |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 9.5 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 26 KB 26 KB | Display Display | ![]() |
Images | ![]() | 177.2 KB | ||
Filedesc metadata | ![]() | 8.8 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6qm7MC ![]() 4591C ![]() 6qm8C M: atomic model generated by this map C: citing same article ( |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Annotation | This is the sharpened EM map which was used for building the protein coordinates | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.07 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
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Sample components
+Entire : Proteasome 20S subunit
+Supramolecule #1: Proteasome 20S subunit
+Macromolecule #1: Proteasome alpha1 chain
+Macromolecule #2: Proteasome alpha2 chain
+Macromolecule #3: Proteasome alpha3 chain
+Macromolecule #4: Proteasome alpha4 chain
+Macromolecule #5: Proteasome alpha5 chain
+Macromolecule #6: Proteasome alpha6 chain
+Macromolecule #7: Proteasome alpha7 chain
+Macromolecule #8: Proteasome beta1 chain
+Macromolecule #9: Proteasome beta2 chain
+Macromolecule #10: Proteasome beta3 chain
+Macromolecule #11: Proteasome beta4 chain
+Macromolecule #12: Proteasome beta5 chain
+Macromolecule #13: Proteasome beta6 chain
+Macromolecule #14: Proteasome beta7 chain
+Macromolecule #15: ~{N}-[4-fluoranyl-3-(3-morpholin-4-ylimidazo[1,2-a]pyrimidin-7-yl...
+Macromolecule #16: water
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 7.5 |
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Vitrification | Cryogen name: ETHANE |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: FEI FALCON III (4k x 4k) / Detector mode: COUNTING / Average electron dose: 30.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
Startup model | Type of model: PDB ENTRY |
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Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2.1) / Number images used: 182775 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |