Detailed view for LmjF.06.0560

Basic information

TDR Targets ID: 29483
Leishmania major, deoxyuridine triphosphatase, putative,dUTP diphosphatase
Source Database / ID:  TriTrypDB  GeneDB

pI: 4.878 | Length (AA): 268 | MW (Da): 30354 | Paralog Number: 0

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

Druggability Group : DG3

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

PF08761   dUTPase

Gene Ontology

Mouse over links to read term descriptions.
No GO information for this protein.

Metabolic Pathways

Pyrimidine metabolism (KEGG)
Global map (KEGG)

Structural information

Modbase 3D models:

There are 2 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
8 260 1ogl (A) 9 278 54.00 0 1 1.77 -2.15
8 264 2yay (A) 8 264 99.99 0 1 2.22916 -1.76

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:

PDB tag
  • 2CJE:
  • Resolution Method # Atoms # Residues Dep. Date Pub. Date Mod. Date
PDB tag
  • 2YAY:
  • Resolution Method # Atoms # Residues Dep. Date Pub. Date Mod. Date
PDB tag
  • 2YAZ:
  • Resolution Method # Atoms # Residues Dep. Date Pub. Date Mod. Date
PDB tag
  • 2YB0:
  • Resolution Method # Atoms # Residues Dep. Date Pub. Date Mod. Date

Expression

Upregulation Percent Ranking Stage Dataset
Upper 80-100% percentile amastigotes. Fernandes MC
Upregulation Percent Ranking Stage Dataset
Upper 60-80% percentile metacyclic. Fernandes MC
Show/Hide expression data references
  • Fernandes MC Dual Transcriptome Profiling of Leishmania-Infected Human Macrophages Reveals Distinct Reprogramming Signatures.

Orthologs

Ortholog group members (OG5_143192)

Species Accession Gene Product
Leishmania braziliensis LbrM.06.0570   deoxyuridine triphosphatase, putative,dUTP diphosphatase
Leishmania donovani LdBPK_060580.1   deoxyuridine triphosphatase, putative
Leishmania infantum LinJ.06.0580   deoxyuridine triphosphatase, putative,dUTP diphosphatase
Leishmania major LmjF.06.0560   deoxyuridine triphosphatase, putative,dUTP diphosphatase
Leishmania mexicana LmxM.06.0560   deoxyuridine triphosphatase, putative,dUTP diphosphatase
Trypanosoma brucei gambiense Tbg972.7.5940   deoxyuridine triphosphatase, putative,dUTP diphosphatase, putative
Trypanosoma brucei Tb927.7.5160   deoxyuridine triphosphatase, putative
Trypanosoma congolense TcIL3000_7_4360   deoxyuridine triphosphatase, putative
Trypanosoma cruzi TcCLB.508175.160   deoxyuridine triphosphatase, putative
Trypanosoma cruzi TcCLB.509151.130   deoxyuridine triphosphatase, putative

Essentiality

LmjF.06.0560 has one or more orthologs with essentiality data
Gene/Ortholog Organism Phenotype Source Study
Tb927.7.5160 Trypanosoma brucei no significant loss or gain of fitness in bloodstream forms (3 days) alsford
Tb927.7.5160 Trypanosoma brucei no significant loss or gain of fitness in bloodstream forms (6 days) alsford
Tb927.7.5160 Trypanosoma brucei no significant loss or gain of fitness in procyclic forms alsford
Tb927.7.5160 Trypanosoma brucei significant loss 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
  • keio Systematic single-gene knock-out mutants of E. coli K12 The Keio Collection
  • nmpdr Genome-scale essentiality datasets from published studies (M. tuberculosis) National Microbial Pathogen Data Resource
  • 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.
  • 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.
  • blattner Systematic mutagenesis of the E. coli (MG1655) genome J Bacteriol 2004, 186:4921-4930
  • 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

Druggability index (range: 0 to 1): 0.2

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 deoxyuridine triphosphatase, putative Compounds References
By sequence similarity to non orthologous druggable targets
No additional associated druggable targets
Obtained from network model

Ranking Plot

Putative Drugs List

Compound Raw Global Species
0.0362 0.2518 0.2667
0.0346 0.265 0.2649
0.0346 0.3051 0.304
0.035 0.4669 0
0.0357 0.3038 0.3022
0.0352 0.5435 0.5316
0.0348 0.3019 0.3003
0.048285 0.746538 0.746498
0.0348 0.3517 0.3497
0.0362 0.2675 0.2672
0.0352 0.3027 0.3013
0.048285 0.746538 0.746498
0.0346 0.2669 0.2669
0.0346 0.2669 0.2669
0.0355 0.2676 0.2638
0.0348 0.3005 0.3003
0.0352 0.3037 0.301
0.0355 0.3064 0.3021
0.035 0.3569 0.3568
0.0348 0.3553 0.3539
0.0348 0.3019 0.3003
0.0369 0.3745 0.3697
0.0352 0.3037 0.301
0.0352 0.3021 0.3021
0.0355 0.3538 0.3531
0.035 0.3063 0.3021
0.0348 0.3537 0.3537
0.0347 0.5523 0.5523
0.0357 0.3038 0.3022
0.0349 0.2665 0.2665
0.0352 0.5134 0.55
0.0362 0.2594 0.3044
0.0346 0.3021 0.3003
0.0346 0.5319 0.5319
0.0353 0.2735 0.5393
0.048285 0.746538 0.746498
0.0348 0.3021 0.3002
0.0359 0.2692 0.2682
0.035 0.3023 0.3004
0.0362 0.2675 0.2672

Assayability

Assay information

  • Inhibitory constant against Leishmania major deoxyuridine 5'-triphosphate nucleotidohydrolase; nd = not determined ChEMBL
  • Inhibitory constant against Leishmania major deoxyuridine 5'-triphosphate nucleotidohydrolase; nd = not determined
  • Inhibitory constant against Leishmania major deoxyuridine 5'-triphosphate nucleotidohydrolase ChEMBL
  • Inhibitory constant against Leishmania major deoxyuridine 5'-triphosphate nucleotidohydrolase
  • BRENDA Assay
  • An enzyme with this EC number or name or sequence has been assayed in Leishmania major ( 3 )

Reagent availability

  • Reagent:
  • Target Type Source Notes
    LmjF.06.0560 purified protein BRENDA A protein with this EC number or name or sequence has been purified from Leishmania major ( 3 )

Bibliographic References

7 literature references were collected for this gene.

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

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Gene identifier LmjF.06.0560 (Leishmania major), deoxyuridine triphosphatase, putative,dUTP diphosphatase
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