Detailed view for LdBPK_312710.1

Basic information

TDR Targets ID: 822791
Leishmania donovani, 2-oxoglutarate dehydrogenase, e3 component, lipoamidedehydrogenase-like protein
Source Database / ID: 

pI: 7.1802 | Length (AA): 478 | MW (Da): 52027 | Paralog Number: 0

Signal peptide: N | GPI Anchor: N | Predicted trans-membrane segments: 0

Druggability Group : DG

Targets have been classified into druggability groups (DG) according to their druggability score in network driven prioritizations. DGs range from 1 to 5; the higher the group number, the higher the chance of the target to be druggable

Pfam domains

PF02852   Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain
PF07992   Pyridine nucleotide-disulphide oxidoreductase

Gene Ontology

Mouse over links to read term descriptions.
GO:0050660   FAD binding  
GO:0016491   oxidoreductase activity  
GO:0055114   oxidation reduction  
GO:0045454   cell redox homeostasis  

Structural information

Modbase 3D models:

There are 4 models calculated for this protein. More info on these models, including the models themselves is available at: Modbase

Target Beg Target End Template Template Beg Template End Identity Evalue Model Score MPQS zDope
1 452 2yqu (A) 18 446 30.00 0 1 1.25321 0.03
1 450 1zx9 (A) 21 452 20.00 0 1 1.12462 0.4
1 462 6awa (A) 21 474 19.00 0 1 1.15113 0.35
112 319 2gqw (A) 90 301 32.00 0.015 0.93 0.531746 0.77

Help me make sense of these data.

Target Beg: first modeled residue
Target End: last modeled residue
Template: template structure used for modelling (PDB accession and chain)
Template Beg: first template residue in target-template alignment
Template End: last template residue in target-template alignment
Identity: sequence identity
Evalue: E value for target-template hit
Model Score: GA341 score (>0.7 for reliable model)
MPQS: ModPipe Quality Score (>1.1 for reliable model)
zDope: zDope Score (negative for reliable model)

A more detailed description of these scores is available at the Modbase Model Evaluation Help Pages, and in the papers referenced therein.

PDB Structures:

No structure availble in the PDB for this protein

Expression

No expression data available for this gene

Orthologs

Ortholog group members (OG5_143064)

Species Accession Gene Product
Leishmania braziliensis LbrM.31.2980   2-oxoglutarate dehydrogenase, e3 component, lipoamidedehydrogenase-like protein
Leishmania donovani LdBPK_312710.1   2-oxoglutarate dehydrogenase, e3 component, lipoamidedehydrogenase-like protein
Leishmania infantum LinJ.31.2710   2-oxoglutarate dehydrogenase, e3 component, lipoamidedehydrogenase-like protein
Leishmania major LmjF.31.2640   2-oxoglutarate dehydrogenase, e3 component, lipoamidedehydrogenase-like protein
Leishmania mexicana LmxM.30.2640   2-oxoglutarate dehydrogenase, e3 component, lipoamidedehydrogenase-like protein
Trypanosoma brucei gambiense Tbg972.4.5230   dihydrolipoamide dehydrogenase, putative
Trypanosoma brucei Tb927.4.5040   dihydrolipoamide dehydrogenase
Trypanosoma congolense TcIL3000_0_00470   dihydrolipoamide dehydrogenase, putative
Trypanosoma congolense TcIL3000_4_4300   dihydrolipoamide dehydrogenase, putative
Trypanosoma cruzi TcCLB.507757.60   dihydrolipoamide dehydrogenase, putative
Trypanosoma cruzi TcCLB.508933.10   dihydrolipoamide dehydrogenase, putative

Essentiality

LdBPK_312710.1 has one or more orthologs with essentiality data
Gene/Ortholog Organism Phenotype Source Study
Tb927.4.5040 Trypanosoma brucei no significant loss or gain of fitness in bloodstream forms (3 days) alsford
Tb927.4.5040 Trypanosoma brucei significant gain of fitness in bloodstream forms (6 days) alsford
Tb927.4.5040 Trypanosoma brucei significant gain of fitness in procyclic forms alsford
Tb927.4.5040 Trypanosoma brucei no significant loss or gain of fitness in differentiation of procyclic to bloodstream forms alsford
Show/Hide essentiality data references
  • wormbase C. elegans RNAi experiments WormBase web site, http://www.wormbase.org, release WS170
  • gerdes Experimental determination and system-level analysis of essential genes in E. coli MG1655 Gerdes et al., J Bacteriol. 2003 185:5673-84
  • nmpdr Genome-scale essentiality datasets from published studies (M. tuberculosis) National Microbial Pathogen Data Resource
  • keio Systematic single-gene knock-out mutants of E. coli K12 The Keio Collection
  • yeastgenome Systematic deletion of yeast genes Saccharomyces Genome Database
  • goodall The Essential Genome of Escherichia coli K-12 (Transposon directed high-throughput mutagenesis) Goodall, Emily CA, et al. "The essential genome of Escherichia coli K-12." mBio 9.1 (2018): e02096-17.
  • alsford High-throughput phenotyping using parallel sequencing of RNA interference targets in the African trypanosome Genome Res 2011, 21:915-924
  • sidik A Genome-wide CRISPR Screen in Toxoplasma Identifies Essential Apicomplexan Genes. Sidik, Saima M., et al. "A genome-wide CRISPR screen in toxoplasma identifies essential apicomplexan genes." Cell 166.6 (2016): 1423-1435.
  • blattner Systematic mutagenesis of the E. coli (MG1655) genome J Bacteriol 2004, 186:4921-4930
  • plasmo Functional Profiling of a Plasmodium Genome Reveals an Abundance of Essential Genes. Bushell, Ellen, et al. "Functional profiling of a Plasmodium genome reveals an abundance of essential genes." Cell 170.2 (2017): 260-272.
  • shigen Profiling of E. coli Chromosome (PEC) National Institute of Genetics, Japan
  • neb C. elegans RNAi phenotypes Data obtained from Wormbase WS150, curated by K. Chaudary and T. Carlow, New England Biolabs

Phenotypes and Validation (curated)

We have no manually annotated phenotypes for this target. What does this mean? / Care to help?

In TDR Targets, information about phenotypes that are caused by drugs, or by genetic manipulation of cells (e.g. gene knockouts or knockdowns) is manually curated from the literature. These descriptions help to describe the potential of the target for drug development. If no information is available for this gene or if the information is incomplete, this may mean that i) the papers containing this information either appeared after the curation effort for this organism was carried out or they were inadvertently missed by curators; or that ii) the curation effort for this organism has not yet started.

In any case, if you have information about papers containing relevant validation data for this target, please contact us.

Annotated validation

No validation data for this target

Associated compounds / Druggability

Known modulators for this target

No chemical compounds associated to this gene

Predicted associations

By orthology with druggable targets
Species Known druggable target Linked compounds Reference
Trypanosoma cruzi dihydrolipoamide dehydrogenase, putative Compounds References
Trypanosoma cruzi dihydrolipoamide dehydrogenase, putative Compounds References
By sequence similarity to non orthologous druggable targets
Species Target Length Identity Alignment span Linked Drugs Reference
Rattus norvegicus Glutathione reductase 424 aa 21.4% 397 aa Compounds References
Obtained from network model
No druggable targets predicted through repurposing network model

Assayability

Assay information

No assay information for this target.

Reagent availability

No reagent availability information for this target.

Bibliographic References

No literature references available for this target.

If you have references for this gene, please enter them in a user comment (below) or Contact us.

User comments

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Gene identifier LdBPK_312710.1 (Leishmania donovani), 2-oxoglutarate dehydrogenase, e3 component, lipoamidedehydrogenase-like protein
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