Detailed view for PVX_124045

Basic information

TDR Targets ID: 266655
Plasmodium vivax, NIMA-related protein kinase (Pfnek-1), putative
Source Database / ID:  PlasmoDB 

pI: 9.9288 | Length (AA): 998 | MW (Da): 111326 | 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:0004713   protein tyrosine kinase activity  
GO:0004674   protein serine/threonine kinase activity  
GO:0004672   protein kinase activity  
GO:0005524   ATP binding  
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 10 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
2 363 1kob (A) 41 373 21.00 0.00000000019 1 0.56 -0.03
10 298 2cl1 (A) 3 271 43.00 0 1 0.65 -0.5
8 299 4an3 (A) 61 362 31.00 0 1 0.580885 -0.36
10 298 2w5a (A) 3 271 43.00 0 1 0.699879 -0.28
15 378 4lgd (A) 27 477 24.00 0 1 0.527629 0.35
62 293 4u6r (A) 612 827 32.00 0.000000000066 1 0.453765 0.21
62 274 2i6l (A) 65 263 37.00 0 0.91 0.406727 0.2
434 508 4hse (A) 389 476 44.00 0.023 0.11 0.47845 -1.9
440 513 3q8t (A) 174 242 33.00 0.19 0.05 0.547448 -2.56
852 974 4wik (A) 468 597 13.00 0.51 0 0.176546 -0.51

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 intraerythrocytic - 24 hs, intraerythrocytic - 30 hs, intraerythrocytic - 36 hs, intraerythrocytic - 40 hs, intraerythrocytic - 48 hs. Zhu L
Upregulation Percent Ranking Stage Dataset
Mid 40-60% percentile intraerythrocytic - 6 hs. Zhu L
Upregulation Percent Ranking Stage Dataset
Lower 20-40% percentile intraerythrocytic - 12 hs, intraerythrocytic - 18 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_129446)

Species Accession Gene Product
Babesia bovis BBOV_III010080   protein kinase domain containing protein
Candida albicans CaO19.5325   likely protein kinase similar to S. cerevisiae KIN3 (YAR018C)
Candida albicans CaO19.12785   likely protein kinase similar to S. cerevisiae KIN3 (YAR018C)
Cryptosporidium hominis Chro.10172   NEK2 protein
Cryptosporidium parvum cgd1_1490   NEK2 protein, putative
Dictyostelium discoideum DDB_G0270814   NEK family protein kinase
Drosophila melanogaster Dmel_CG17256   CG17256 gene product from transcript CG17256-RA
Giardia lamblia GL50803_5375   Kinase, NEK
Giardia lamblia GL50803_95593   Kinase, NEK
Giardia lamblia GL50803_11311   Kinase, NEK
Homo sapiens ENSG00000117650   NIMA-related kinase 2
Mus musculus ENSMUSG00000026622   NIMA (never in mitosis gene a)-related expressed kinase 2
Neospora caninum NCLIV_043340   MGC81305 protein, related
Plasmodium berghei PBANKA_1443000   NIMA related kinase 1, putative
Plasmodium falciparum PF3D7_1228300   NIMA related kinase 1
Plasmodium knowlesi PKNH_1447700   NIMA related kinase 1, putative
Plasmodium vivax PVX_124045   NIMA-related protein kinase (Pfnek-1), putative
Plasmodium yoelii PY04005   NIMA-related protein kinase
Saccharomyces cerevisiae YAR018C   Kin3p
Schmidtea mediterranea mk4.011291.01  
Toxoplasma gondii TGME49_292140   NIMA-related protein kinase NIMA1
Theileria parva TP02_0139   NIMA-related protein kinase, putative
Trichomonas vaginalis TVAG_025740   AGC family protein kinase
Trichomonas vaginalis TVAG_050700   STE family protein kinase

Essentiality

PVX_124045 has one or more orthologs with essentiality data
Gene/Ortholog Organism Phenotype Source Study
PBANKA_1443000 Plasmodium berghei Essential plasmo
TGME49_292140 Toxoplasma gondii Probably essential sidik
Show/Hide essentiality data references
  • 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
  • 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.
  • wormbase C. elegans RNAi experiments WormBase web site, http://www.wormbase.org, release WS170
  • keio Systematic single-gene knock-out mutants of E. coli K12 The Keio Collection
  • 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
  • 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

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): 0.9

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 NIMA-related kinase 2 Compounds References
Plasmodium falciparum NIMA related kinase 1 Compounds References
By sequence similarity to non orthologous druggable targets
Species Target Length Identity Alignment span Linked Drugs Reference
Rattus norvegicus Cell division protein kinase 5 292 aa 31.6% 247 aa Compounds References
Homo sapiens Cyclin-dependent kinase 1/cyclin B1 297 aa 30.2% 245 aa Compounds References
Oryctolagus cuniculus Cyclin-dependent kinase 4 189 aa 28.4% 190 aa Compounds References
Patiria pectinifera Cdc2 300 aa 28.0% 254 aa Compounds References
Plasmodium falciparum (isolate 3D7) Cell division control protein 2 homolog 288 aa 31.6% 244 aa Compounds References
Schizosaccharomyces pombe 972h- Casein kinase II subunit alpha 332 aa 23.7% 266 aa Compounds References
Rattus norvegicus Jak1 protein 210 aa 24.2% 190 aa Compounds References
Rattus norvegicus Serine/threonine-protein kinase pim-3 326 aa 24.6% 305 aa Compounds References
Obtained from network model

Ranking Plot

Putative Drugs List

Compound Raw Global Species
0.0039 0.5 0.5
0.0663 0.7904 1
0.0125 1 0.5
0.0063 0.7244 0.7244
0.0436 1 0.5
0.1149 1 0.5
0.0078 0.2718 1
0.0323 1 1
0.0888 0.6211 0.6208
0.0189 0.3784 0.9308
0.1275 1 1
0.0003 0.5 0.5
0.0061 0.6883 1
0.0023 0.5 0.5
0.0356 1 1
0.0448 0.623 1
0.0098 0.3242 0.2614
0.0125 0.4077 1
0.0682 1 0.5
0.0818 1 1
0.1081 0.3282 1
0.0029 0.5 0.5
0.0346 0.8811 0.8974
0.0125 1 0.5
0.0004 0.5 0.5
0.0105 0.357 1
0.0125 1 0.5
0.0325 0.3444 1
0.0437 0.5115 1
0.0039 0.9485 0.5
0.0012 0.5 0.5
0.0888 0.6211 0.6208
0.1105 1 1
0.0125 0.3676 1
0.0057863 0.320697 0.420068
0.0448 0.623 1
0.0037 1 0.5
0.1333 0.2571 1
0.0367 1 0.5
0.0365 1 0.5
0.0447 0.8521 0.5
0.0027 1 0.5
0.1257 1 0.5
0.169477 1 1
0.0128 0.4046 0.6284
0.0067 0.5 0.5
0.0125 1 0.5
0.0128 0.4046 0.6284
0.0125 1 0.5
0.0105 0.357 1
0.013 0.2609 1
0.0091 1 0.5
0.0039 0.5 0.5
0.0008 0.5 0.5
0.0126 0.5909 1
0.0064 0.3377 0.5
0.0125 1 1
0.0733 0.4435 1
0.1173 1 0.5
0.0665 1 0.5
0.0125 1 1
0.0283 0.2908 1
0.0759 1 1
0.0033 0.5 0.5
0.0904 1 1
0.0032 0.5 0.5
0.0125 1 0.5
0.0016 0.5 0.5
0.0452 0.4154 1
0.0032 0.5 0.5
0.0066 0.3101 0.5
0.0016 0.5 0.5
0.1285 1 0.5
0.0124 0.3418 1
0.1404 0.5578 1
0.0007 0.5 0.5
0.1333 0.2571 1
0.0088 0.4477 0.5
0.0107 0.2918 0.8608
0.0124 1 0.5
0.0007 0.5 0.5
0.0124 0.6271 1
0.0213 1 1
0.0126 0.324 1
0.0069 0.3067 1
0.1242 1 1
0.0482 0.5397 1
0.0033 1 1
0.0103 0.278 1
0.0012 0.5 0.5
0.0042 0.5 0.5
0.0124 0.7261 1
0.0109 0.3558 0.5
0.0437 0.5115 1
0.0993 0.485 1
0.0603 0.3274 1
0.0117 0.3724 1
0.034 0.8586 1
0.0081 1 0.5
0.0692 1 1
0.0106 0.3718 1
0.0011 1 0.5
0.0356 0.9563 1
0.0127 0.4224 0.3779
0.0603 0.3274 1
0.0093 0.8828 0
0.0007 0.5 0.5
0.0026 0.5 0.5
0.1289 1 0.5
0.169477 1 1
0.1506 0.2974 1
0.0743 1 0.5
0.0103 0.278 1
0.0213 1 1
0.0102 0.3506 1
0.0357 0.4342 1
0.0059 1 1
0.0036 0.5 0.5
0.0104 0.3181 1
0.0129 0.4581 1
0.0059 1 1
0.0124 1 1
0.0059 1 1
0.0326 1 0.5
0.0322 0.9739 1
0.0223 0.371 1
0.0062 0.6935 0.5
0.1046 1 1
0.1203 1 0.5
0.0363 0.4277 0.5
0.0124 1 0.5
0.0124 0.4183 1
0.0235 0.4902 0.5
0.1081 1 1
0.0125 1 0.5
0.0665 0.6772 1
0.0105 0.357 1
0.0056 1 0.5
0.0875 1 1
0.0124 0.32 1
0.1168 1 1
0.0081 0.5 0.5
0.1218 1 0.5
0.1218 1 0.5
0.0125 1 0.5
0.0018 0.5 0.5
0.0356 0.9563 1
0.0108 0.3702 0.5
0.1213 1 1
0.0559 0.3993 1
0.0012 0.5 0.5
0.0128 0.4046 0.6284
0.0648 1 0.5
0.0124 0.8903 0.5
0.0092 1 0.5
0.0063 1 1
0.0022 0.5 0.5
0.0678 0.6446 1
0.1263 1 1

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.

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Gene identifier PVX_124045 (Plasmodium vivax), NIMA-related protein kinase (Pfnek-1), putative
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