Detailed view for PVX_002805

Basic information

TDR Targets ID: 268407
Plasmodium vivax, calcium-dependent protein kinase 4, putative
Source Database / ID:  PlasmoDB 

pI: 9.9085 | Length (AA): 1615 | MW (Da): 177294 | 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 12 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
942 1414 2acx (A) 24 470 12.00 0.0000000012 0.91 0.3 0.97
1110 1306 1x8b (A) 293 509 20.00 0 1 0.44 -0.69
1121 1370 1t4h (A) 226 464 23.00 0 1 0.33 0.24
1503 1611 2c30 (A) 552 658 25.00 0.000000006 0.16 0.34 -0.73
1517 1615 1phk () 196 291 31.00 0.0000000036 0.99 0.47 -0.7
754 882 3zfw (A) 308 454 16.00 0.92 0.01 0.246976 -0.26
1107 1449 3pfq (A) 291 632 20.00 0 1 0.195484 1.07
1114 1273 4d2w (A) 9 176 29.00 0.0000000011 1 0.366771 0.55
1116 1323 1csn (A) 12 220 20.00 0 0.81 0.266893 0.63
1120 1247 2nru (A) 198 318 31.00 0.00013 0.5 0.178957 1.53
1172 1273 5dbx (A) 130 227 37.00 0.0000046 0.94 0.235858 1.04
1512 1600 4d28 (A) 170 254 45.00 0.000000043 0.97 0.539808 -0.45

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 - 40 hs, intraerythrocytic - 48 hs. Zhu L
Upregulation Percent Ranking Stage Dataset
Mid 40-60% percentile intraerythrocytic - 36 hs. Zhu L
Upregulation Percent Ranking Stage Dataset
Lower 20-40% percentile intraerythrocytic - 12 hs, intraerythrocytic - 18 hs, intraerythrocytic - 24 hs, intraerythrocytic - 30 hs. Zhu L
Upregulation Percent Ranking Stage Dataset
Lower 0-20% percentile intraerythrocytic - 6 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_162068)

Species Accession Gene Product
Plasmodium berghei PBANKA_0311400   serine/threonine protein kinase, putative
Plasmodium falciparum PF3D7_0214600   serine/threonine protein kinase, putative
Plasmodium knowlesi PKNH_0406200   serine/threonine protein kinase, putative
Plasmodium vivax PVX_002805   calcium-dependent protein kinase 4, putative
Plasmodium yoelii PY06391   Protein kinase domain, putative
Plasmodium yoelii PY03306   hypothetical protein

Essentiality

PVX_002805 has one or more orthologs with essentiality data
Gene/Ortholog Organism Phenotype Source Study
PBANKA_0311400 Plasmodium berghei Essential plasmo
Show/Hide essentiality data references
  • 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.
  • 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
  • keio Systematic single-gene knock-out mutants of E. coli K12 The Keio Collection
  • yeastgenome Systematic deletion of yeast genes Saccharomyces Genome Database
  • nmpdr Genome-scale essentiality datasets from published studies (M. tuberculosis) National Microbial Pathogen Data Resource
  • shigen Profiling of E. coli Chromosome (PEC) National Institute of Genetics, Japan
  • 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.
  • blattner Systematic mutagenesis of the E. coli (MG1655) genome J Bacteriol 2004, 186:4921-4930
  • 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): 0.1

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
No additional associated druggable targets
Obtained from network model

Ranking Plot

Putative Drugs List

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

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Gene identifier PVX_002805 (Plasmodium vivax), calcium-dependent protein kinase 4, putative
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