Detailed view for PVX_089980

Basic information

TDR Targets ID: 269925
Plasmodium vivax, cdc2-related protein kinase 1, putative
Source Database / ID:  PlasmoDB 

pI: 9.447 | Length (AA): 612 | MW (Da): 71264 | Paralog Number: 0

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

Druggability Group : DG5

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: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  

Metabolic Pathways

This gene is not mapped to any metabolic pathway in KEGG.

Structural information

Modbase 3D models:

There are 13 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
170 609 2acx (A) 89 508 19.00 0.00000047 1 0.83 0.39
264 575 1unl (A) 1 292 42.00 0 1 1.04 -0.9
273 585 2b9h (A) 19 325 36.00 0 1 0.99 -1.25
66 229 2fkj (A) 111 279 16.00 0.8 0.02 0.340774 -0.3
154 522 4y93 (A) 65 651 22.00 0 1 0.777841 0.39
161 590 4wnk (A) 78 472 22.00 0 1 0.780414 0.63
246 611 4qtb (A) 25 372 37.00 0 1 0.957939 0.04
258 611 3n9x (A) 19 408 34.00 0 1 0.845231 -0.06
261 581 3mi9 (A) 13 327 43.00 0 1 1.00211 -0.23
265 608 2b9h (A) 11 351 34.00 0 1 0.927992 -0.32
266 472 1csn (A) 11 220 24.00 0.00000072 0.92 0.491135 0.63
270 571 2qkr (A) 26 306 47.00 0 1 0.857064 0.31
273 470 2eva (A) 42 229 37.00 0.00000000089 0.99 0.509129 0.58

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
Mid 40-60% percentile intraerythrocytic - 12 hs, intraerythrocytic - 18 hs, intraerythrocytic - 24 hs, intraerythrocytic - 30 hs, intraerythrocytic - 40 hs, intraerythrocytic - 48 hs. Zhu L
Upregulation Percent Ranking Stage Dataset
Lower 20-40% percentile intraerythrocytic - 6 hs, intraerythrocytic - 36 hs. Zhu L
Show/Hide expression data references
  • Zhu L New insights into the Plasmodium vivax transcriptome using RNA-Seq.

Orthologs

Ortholog group members (OG5_129183)

Species Accession Gene Product
Arabidopsis thaliana AT1G67580   putative serine/threonine protein kinase
Babesia bovis BBOV_II004380   cdc-related protein kinase I
Brugia malayi Bm1_17240   Protein kinase domain containing protein
Brugia malayi Bm1_13195   hypothetical protein
Caenorhabditis elegans CELE_ZC504.3   Protein ZC504.3
Caenorhabditis elegans CELE_B0495.2   Protein B0495.2
Dictyostelium discoideum DDB_G0283279   CDK family protein kinase
Drosophila melanogaster Dmel_CG4268   CG4268 gene product from transcript CG4268-RA
Echinococcus granulosus EgrG_000528200   cyclin dependent kinase 11B
Echinococcus multilocularis EmuJ_000528200   cyclin dependent kinase 11B
Homo sapiens ENSG00000248333   cyclin-dependent kinase 11B
Homo sapiens ENSG00000008128   cyclin-dependent kinase 11A
Loa Loa (eye worm) LOAG_01264   cmgc/cdk/pitslre protein kinase
Loa Loa (eye worm) LOAG_08905   hypothetical protein
Mus musculus ENSMUSG00000029062   cyclin-dependent kinase 11B
Neospora caninum NCLIV_001240   hypothetical protein
Oryza sativa 4329899   Os02g0602100
Oryza sativa 4336224   Os04g0488000
Plasmodium berghei PBANKA_0719900   cdc2-related protein kinase 1
Plasmodium falciparum PF3D7_0417800   cdc2-related protein kinase 1
Plasmodium knowlesi PKNH_0510200   cdc2-related protein kinase 1, putative
Plasmodium vivax PVX_089980   cdc2-related protein kinase 1, putative
Plasmodium yoelii PY03317   cdc-2 related kinase 1
Schistosoma japonicum Sjp_0082800   ko:K08818 cell division cycle 2-like, putative
Schistosoma mansoni Smp_176620   serine/threonine protein kinase
Schmidtea mediterranea mk4.003556.02   Serine/threonine-protein kinase PITSLRE
Schmidtea mediterranea mk4.007076.00   Serine/threonine-protein kinase PITSLRE
Schmidtea mediterranea mk4.010725.00   Serine/threonine-protein kinase PITSLRE
Schmidtea mediterranea mk4.044688.00   Serine/threonine-protein kinase PITSLRE
Schmidtea mediterranea mk4.003707.02   Serine/threonine-protein kinase PITSLRE
Toxoplasma gondii TGME49_304970   cell-cycle-associated protein kinase CDK, putative
Theileria parva TP04_0551   cell division cycle 2 protein kinase, putative

Essentiality

PVX_089980 has one or more orthologs with essentiality data
Gene/Ortholog Organism Phenotype Source Study
CELE_ZC504.3 Caenorhabditis elegans embryonic lethal wormbase
CELE_B0495.2 Caenorhabditis elegans embryonic lethal wormbase
CELE_B0495.2 Caenorhabditis elegans slow growth wormbase
CELE_B0495.2 Caenorhabditis elegans sterile wormbase
TGME49_304970 Toxoplasma gondii Probably essential sidik
Show/Hide essentiality data references
  • wormbase C. elegans RNAi experiments WormBase web site, http://www.wormbase.org, release WS170
  • alsford High-throughput phenotyping using parallel sequencing of RNA interference targets in the African trypanosome Genome Res 2011, 21:915-924
  • 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.
  • 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.
  • keio Systematic single-gene knock-out mutants of E. coli K12 The Keio Collection
  • shigen Profiling of E. coli Chromosome (PEC) National Institute of Genetics, Japan
  • yeastgenome Systematic deletion of yeast genes Saccharomyces Genome Database
  • nmpdr Genome-scale essentiality datasets from published studies (M. tuberculosis) National Microbial Pathogen Data Resource
  • neb C. elegans RNAi phenotypes Data obtained from Wormbase WS150, curated by K. Chaudary and T. Carlow, New England Biolabs
  • blattner Systematic mutagenesis of the E. coli (MG1655) genome J Bacteriol 2004, 186:4921-4930
  • gerdes Experimental determination and system-level analysis of essential genes in E. coli MG1655 Gerdes et al., J Bacteriol. 2003 185:5673-84
  • 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.

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): 0.7

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
Homo sapiens cyclin-dependent kinase 11A Compounds References
By sequence similarity to non orthologous druggable targets
Species Target Length Identity Alignment span Linked Drugs Reference
Rattus norvegicus Mitogen-activated protein kinase 1 358 aa 36.6% 369 aa Compounds References
Patiria pectinifera Cdc2 300 aa 39.0% 310 aa Compounds References
Xenopus laevis Aurora kinase B-A 361 aa 26.8% 299 aa Compounds References
Oryctolagus cuniculus Cyclin-dependent kinase 4 189 aa 39.8% 171 aa Compounds References
Rattus norvegicus Cell division protein kinase 5 292 aa 40.3% 313 aa Compounds References
Rattus norvegicus Mitogen-activated protein kinase 8 411 aa 32.2% 342 aa Compounds References
Schizosaccharomyces pombe 972h- Casein kinase II subunit alpha 332 aa 26.8% 310 aa Compounds References
Rattus norvegicus MAP kinase p38 alpha 360 aa 34.4% 320 aa Compounds References
Plasmodium falciparum (isolate 3D7) Cell division control protein 2 homolog 288 aa 40.5% 316 aa Compounds References
Homo sapiens Cyclin-dependent kinase 1/cyclin B1 297 aa 40.2% 311 aa Compounds References
Xenopus laevis Aurora kinase B-B 368 aa 26.8% 299 aa Compounds References
Obtained from network model

Ranking Plot

Putative Drugs List

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

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.

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Gene identifier PVX_089980 (Plasmodium vivax), cdc2-related protein kinase 1, putative
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