Detailed view for Tb927.11.12310

Basic information

TDR Targets ID: 14742
Trypanosoma brucei, cdc2-related kinase 12
Source Database / ID:  TriTrypDB  GeneDB

pI: 8.2355 | Length (AA): 769 | MW (Da): 84571 | Paralog Number: 0

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

Druggability Group : DG4

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

PF00069   Protein kinase domain

Gene Ontology

Mouse over links to read term descriptions.
GO:0008150   biological_process  
GO:0005575   cellular_component  
GO:0003674   molecular_function  
GO:0005524   ATP binding  
GO:0004713   protein tyrosine kinase activity  
GO:0004674   protein serine/threonine kinase activity  
GO:0004672   protein kinase activity  
GO:0006468   protein amino acid phosphorylation  

Structural information

Modbase 3D models:

There are 9 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
195 252 2enz (A) 221 278 19.00 0.035 0.03 0.293823 -0.46
211 252 1ptq (A) 236 277 21.00 0.13 0.05 0.337016 -0.88
256 360 2f2u (A) 31 123 28.00 0 0.11 0.172041 0.43
271 611 4idt (A) 341 657 23.00 0 0.88 0.597833 0.03
285 545 3bkb (A) 521 754 26.00 0.000076 0.54 0.407702 0.69
311 756 3oy1 (A) 46 400 23.00 0 1 0.435374 0.74
316 604 2qkw (B) 32 298 25.00 0.0015 0.95 0.416113 0.68
325 628 5j1w (C) 157 477 20.00 0 1 0.534719 -0.3
436 555 4j7b (A) 123 243 42.00 0 0.91 0.507347 0.23

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

Upregulation Percent Ranking Stage Dataset
Upper 60-80% percentile Procyclic, Bloodstream Form. Siegel TN
Show/Hide expression data references
  • Siegel TN Genome-wide analysis of mRNA abundance in two life-cycle stages of Trypanosoma brucei and identification of splicing and polyadenylation sites.

Orthologs

Ortholog group members (OG5_151464)

Species Accession Gene Product
Leishmania braziliensis LbrM.09.0300   protein kinase, putative
Leishmania donovani LdBPK_090270.1   cdc2-related kinase 12
Leishmania infantum LinJ.09.0270   protein kinase, putative
Leishmania major LmjF.09.0310   protein kinase, putative
Leishmania mexicana LmxM.09.0310   protein kinase, putative
Trypanosoma brucei gambiense Tbg972.11.13750   protein kinase, putative
Trypanosoma brucei Tb927.11.12310   cdc2-related kinase 12
Trypanosoma congolense TcIL3000.11.12940   cdc2-related kinase 12
Trypanosoma cruzi TcCLB.511127.220   cdc2-related kinase 12
Trypanosoma cruzi TcCLB.509023.200   cdc2-related kinase 12

Essentiality

Tb927.11.12310 has direct evidence of essentiality
Gene/Ortholog Organism Phenotype Source Study
Tb11.01.4130 this record Trypanosoma brucei significant loss of fitness in bloodstream forms (3 days) alsford
Tb11.01.4130 this record Trypanosoma brucei significant loss of fitness in bloodstream forms (6 days) alsford
Tb11.01.4130 this record Trypanosoma brucei no significant loss or gain of fitness in procyclic forms alsford
Tb11.01.4130 this record Trypanosoma brucei no significant loss or gain of fitness in differentiation of procyclic to bloodstream forms alsford
Show/Hide essentiality data references
  • keio Systematic single-gene knock-out mutants of E. coli K12 The Keio Collection
  • neb C. elegans RNAi phenotypes Data obtained from Wormbase WS150, curated by K. Chaudary and T. Carlow, New England Biolabs
  • gerdes Experimental determination and system-level analysis of essential genes in E. coli MG1655 Gerdes et al., J Bacteriol. 2003 185:5673-84
  • 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.
  • shigen Profiling of E. coli Chromosome (PEC) National Institute of Genetics, Japan
  • alsford High-throughput phenotyping using parallel sequencing of RNA interference targets in the African trypanosome Genome Res 2011, 21:915-924
  • wormbase C. elegans RNAi experiments WormBase web site, http://www.wormbase.org, release WS170
  • blattner Systematic mutagenesis of the E. coli (MG1655) genome J Bacteriol 2004, 186:4921-4930
  • 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.
  • nmpdr Genome-scale essentiality datasets from published studies (M. tuberculosis) National Microbial Pathogen Data Resource
  • 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.
  • yeastgenome Systematic deletion of yeast genes Saccharomyces Genome Database

Phenotypes and Validation (curated)

Annotated phenotypes:

Affected Entity Phenotypic quality Occurs in Occurs at Evidence Observed in Drugs/Inhibitors
cell proliferation (GO:0008283) decreased (PATO:0000468) bloodstream stage trypomastigotes (PLO:0027) inferred from RNAi experiment (ECO:0000019) No drug identifiers listed for this gene.
Annotator: fernan@iib.unsam.edu.ar. Comment: decreased cell proliferation (significant loss of fitness) in bloodstream forms (stage 6 days). References: 21363968
cell proliferation (GO:0008283) normal (PATO:0000461) procyclic (PLO:0034) inferred from RNAi experiment (ECO:0000019) No drug identifiers listed for this gene.
Annotator: fernan@iib.unsam.edu.ar. Comment: normal cell proliferation (no significant loss or gain of fitness) in differentiation of procyclic to bloodstream forms . References: 21363968

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): 0.4

Known modulators for this target

No chemical compounds associated to this gene

Predicted associations

By orthology with druggable targets
Non orthologous druggable targets
By sequence similarity to non orthologous druggable targets
Species Target Length Identity Alignment span Linked Drugs Reference
Oryctolagus cuniculus Cyclin-dependent kinase 4 189 aa 31.9% 207 aa Compounds References
Plasmodium falciparum (isolate 3D7) Cell division control protein 2 homolog 288 aa 31.1% 254 aa Compounds References
Schizosaccharomyces pombe 972h- Casein kinase II subunit alpha 332 aa 21.5% 396 aa Compounds References
Obtained from network model

Ranking Plot

Putative Drugs List

Compound Raw Global Species
0.0056 1 0.5
0.0023 0.5 0.5
0.0088 0.4477 0.5
0.0092 1 0.5
0.0039 0.9485 0.5
0.0012 0.5 0.5
0.0007 0.5 0.5
0.0042 0.5 0.5
0.0007 0.5 0.5
0.0063 1 0.5
0.0093 0.8828 0
0.0039 0.5 0.5
0.0061 0.6883 0.5304
0.0018 0.5 0.5
0.0027 1 0.5
0.0022 0.5 0.5
0.0069 0.3067 1
0.0064 0.3377 0
0.0008 0.5 0.5
0.0062 0.6935 0
0.0004 0.5 0.5
0.0033 1 0.5
0.0026 0.5 0.5
0.0063 0.7244 0.2543
0.0003 0.5 0.5
0.0032 0.5 0.5
0.0059 1 1
0.0039 0.5 0.5
0.0032 0.5 0.5
0.0029 0.5 0.5
0.0033 0.5 0.5
0.0059 1 1
0.0016 0.5 0.5
0.0012 0.5 0.5
0.0036 0.5 0.5
0.0081 0.5 0.5
0.0007 0.5 0.5
0.0016 0.5 0.5
0.0098 0.3242 0.2614
0.0081 1 0.5
0.0066 0.3101 0
0.0059 1 1
0.0037 1 0.5
0.0091 1 0.5
0.0067 0.5 0.5
0.0012 0.5 0.5
0.0011 1 0.5

Assayability

Assay information

No assay information for this target.

Reagent availability

No reagent availability information for this target.

Bibliographic References

27 literature references were collected for this gene.

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Gene identifier Tb927.11.12310 (Trypanosoma brucei), cdc2-related kinase 12
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