Detailed view for Smp_020030

Basic information

TDR Targets ID: 295916
Schistosoma mansoni, parkin (ubiquitin E3 ligase prkn)
Source Database / ID:  GeneDB

pI: 6.8618 | Length (AA): 403 | MW (Da): 45937 | Paralog Number: 0

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

Druggability Group : DG1

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

No Pfam domain information for this protein.

Gene Ontology

Mouse over links to read term descriptions.
GO:0005829   cytosol  
GO:0005739   mitochondrion  
GO:0016881   acid-amino acid ligase activity  
GO:0004842   ubiquitin-protein ligase activity  
GO:0016567   protein ubiquitination  

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
2 71 2kdi (A) 12 77 17.00 0.000000049 0.88 0.349797 -0.07
74 402 5c1z (A) 79 462 34.00 0 1 0.952377 0.74
78 402 5caw (A) 144 459 36.00 0 1 0.925452 1.01
343 396 2m9y (A) 327 382 33.00 0.014 0.55 0.472095 -0.12

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

No expression data available for this gene

Orthologs

Ortholog group members (OG5_133223)

Species Accession Gene Product
Brugia malayi Bm1_57385   IBR domain containing protein
Caenorhabditis elegans CELE_K08E3.7   Protein PDR-1
Drosophila melanogaster Dmel_CG10523   parkin
Echinococcus granulosus EgrG_000108200   e3 ubiquitin protein ligase parkin
Echinococcus multilocularis EmuJ_000108200   e3 ubiquitin protein ligase parkin
Homo sapiens ENSG00000185345   parkin RBR E3 ubiquitin protein ligase
Loa Loa (eye worm) LOAG_05984   IBR domain-containing protein
Mus musculus ENSMUSG00000023826   Parkinson disease (autosomal recessive, juvenile) 2, parkin
Schistosoma japonicum Sjp_0051670   ko:K04556 parkin, putative
Schistosoma mansoni Smp_020030   parkin (ubiquitin E3 ligase prkn)

Essentiality

Smp_020030 has one or more orthologs with essentiality data
Gene/Ortholog Organism Phenotype Source Study
CELE_K08E3.7 Caenorhabditis elegans embryonic lethal wormbase
Show/Hide essentiality data references
  • gerdes Experimental determination and system-level analysis of essential genes in E. coli MG1655 Gerdes et al., J Bacteriol. 2003 185:5673-84
  • alsford High-throughput phenotyping using parallel sequencing of RNA interference targets in the African trypanosome Genome Res 2011, 21:915-924
  • neb C. elegans RNAi phenotypes Data obtained from Wormbase WS150, curated by K. Chaudary and T. Carlow, New England Biolabs
  • nmpdr Genome-scale essentiality datasets from published studies (M. tuberculosis) National Microbial Pathogen Data Resource
  • yeastgenome Systematic deletion of yeast genes Saccharomyces Genome Database
  • keio Systematic single-gene knock-out mutants of E. coli K12 The Keio Collection
  • 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
  • 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.
  • 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.
  • shigen Profiling of E. coli Chromosome (PEC) National Institute of Genetics, Japan
  • 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

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
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 Smp_020030 (Schistosoma mansoni), parkin (ubiquitin E3 ligase prkn)
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