Detailed view for PBANKA_1419800

Basic information

TDR Targets ID: 827470
Plasmodium berghei, 3',5'-cyclic nucleotide phosphodiesterase, putative
Source Database / ID: 

pI: 8.6946 | Length (AA): 1158 | MW (Da): 136748 | Paralog Number: 0

Signal peptide: N | GPI Anchor: N | Predicted trans-membrane segments: 6

Druggability Group : DG

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

PF00233   3'5'-cyclic nucleotide phosphodiesterase

Gene Ontology

Mouse over links to read term descriptions.
GO:0004114   3',5'-cyclic-nucleotide phosphodiesterase activity  
GO:0008081   phosphoric diester hydrolase activity  
GO:0007165   signal transduction  

Metabolic Pathways

Purine metabolism (KEGG)

Structural information

Modbase 3D models:

There are 4 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
707 1108 4wzi (B) 226 656 25.00 0 1 0.48855 -0.03
805 1110 2r8q (A) 619 930 25.00 0 1 0.559649 -1.03
805 1106 1zkl (A) 151 453 28.00 0 1 0.556194 -0.85
811 1104 5b25 (A) 156 496 34.00 0 1 0.598786 -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
Mid 40-60% percentile 4 hs Ring. Otto TD
Upregulation Percent Ranking Stage Dataset
Lower 20-40% percentile 16 hs Trophozoite, Erthyrocytic stages, Female gametocyte, Male gametocyte. Otto TD Yeoh LM
Upregulation Percent Ranking Stage Dataset
Lower 0-20% percentile Gametocyte, Ookinete, 22 hs Schizont. Otto TD
Show/Hide expression data references
  • Otto TD A comprehensive evaluation of rodent malaria parasite genomes and gene expression.
  • Yeoh LM Comparative transcriptomics of female and male gametocytes in Plasmodium berghei and the evolution of sex in alveolates.

Orthologs

Ortholog group members (OG5_130344)

Species Accession Gene Product
Babesia bovis BBOV_IV006510   3'5'-cyclic nucleotide phosphodiesterase, putative
Dictyostelium discoideum DDB_G0284331   cAMP phosphodiesterase
Drosophila melanogaster Dmel_CG42276   Phosphodiesterase 9
Echinococcus granulosus EgrG_000416500   high affinity cgmp specific 3' 5' cyclic
Echinococcus multilocularis EmuJ_000416500   high affinity cgmp specific 3' 5' cyclic
Homo sapiens ENSG00000160191   phosphodiesterase 9A
Mus musculus ENSMUSG00000041119   phosphodiesterase 9A
Neospora caninum NCLIV_022390   hypothetical protein
Plasmodium berghei PBANKA_1419800   3',5'-cyclic nucleotide phosphodiesterase, putative
Plasmodium falciparum PF3D7_1321500   3',5'-cyclic nucleotide phosphodiesterase, putative
Plasmodium knowlesi PKNH_1422100   3',5'-cyclic nucleotide phosphodiesterase, putative
Plasmodium yoelii PY03988   cGMP phosphodiesterase A4, putative
Plasmodium yoelii PY07634   asparagine-rich protein
Schistosoma japonicum Sjp_0050430   ko:K06927 endoribonuclease, putative
Schistosoma japonicum Sjp_0044930   ko:K01120 3',5'-cyclic-nucleotide phosphodiesterase [EC3.1.4.17], putative
Schistosoma japonicum Sjp_0044940   High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A, putative
Schistosoma mansoni Smp_163100   high-affinity cgmp-specific 35-cyclic phosphodiesterase
Schmidtea mediterranea mk4.001337.03   High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A
Schmidtea mediterranea mk4.001337.01  
Schmidtea mediterranea mk4.001337.02  
Schmidtea mediterranea mk4.010110.00   Phosphodiesterase 9
Toxoplasma gondii TGME49_202540   3'5'-cyclic nucleotide phosphodiesterase domain-containing protein

Essentiality

PBANKA_1419800 has direct evidence of essentiality
Gene/Ortholog Organism Phenotype Source Study
PBANKA_1419800 this record Plasmodium berghei Essential plasmo
TGME49_202540 Toxoplasma gondii Probably essential sidik
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.
  • 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
  • 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.
  • 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
  • yeastgenome Systematic deletion of yeast genes Saccharomyces Genome Database
  • blattner Systematic mutagenesis of the E. coli (MG1655) genome J Bacteriol 2004, 186:4921-4930
  • alsford High-throughput phenotyping using parallel sequencing of RNA interference targets in the African trypanosome Genome Res 2011, 21:915-924
  • 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.
  • wormbase C. elegans RNAi experiments WormBase web site, http://www.wormbase.org, release WS170

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

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
Rattus norvegicus High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A Compounds References
Homo sapiens phosphodiesterase 9A Compounds References
By sequence similarity to non orthologous druggable targets
No additional associated druggable targets
Obtained from network model
No druggable targets predicted through repurposing network model

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.

User comments

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Gene identifier PBANKA_1419800 (Plasmodium berghei), 3',5'-cyclic nucleotide phosphodiesterase, putative
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