Detailed view for Smp_072110.2

Basic information

TDR Targets ID: 289131
Schistosoma mansoni, programmed cell death protein
Source Database / ID:  GeneDB

pI: 5.3557 | Length (AA): 518 | MW (Da): 57139 | Paralog Number: 1

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

Druggability Group : DG2

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

PF02847   MA3 domain

Gene Ontology

Mouse over links to read term descriptions.
GO:0005488   binding  

Metabolic Pathways

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

Structural information

Modbase 3D models:

There are 3 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
23 102 5hwk (A) 14 91 33.00 0.8 0.1 0.25814 0.9
126 497 3eij (A) 155 450 38.00 0 1 0.758147 0.57
374 481 3l6a (A) 7 114 27.00 0.00021 1 0.724194 -1.72

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_129731)

Species Accession Gene Product
Arabidopsis thaliana AT5G63190   MA3 domain-containing protein
Arabidopsis thaliana AT3G48390   MA3 domain-containing protein
Arabidopsis thaliana AT1G22730   MA3 domain-containing protein
Arabidopsis thaliana AT4G24800   MA3 domain-containing protein
Cryptosporidium hominis Chro.20252   hypothetical protein
Cryptosporidium parvum cgd2_2350   MA3 domain containing protein
Drosophila melanogaster Dmel_CG10990   Programmed cell death 4 ortholog
Echinococcus granulosus EgrG_000802600   programmed cell death protein 4
Echinococcus multilocularis EmuJ_000802600   programmed cell death protein 4
Homo sapiens ENSG00000150593   programmed cell death 4 (neoplastic transformation inhibitor)
Mus musculus ENSMUSG00000024975   programmed cell death 4
Neospora caninum NCLIV_013910   Pdcd4-prov protein, related
Oryza sativa 4332101   Os03g0222100
Oryza sativa 4336196   Os04g0482800
Oryza sativa 4344544   Os08g0120500
Plasmodium berghei PBANKA_1321000   conserved Plasmodium protein, unknown function
Plasmodium falciparum PF3D7_1457300   conserved Plasmodium protein, unknown function
Plasmodium knowlesi PKNH_1224500   conserved Plasmodium protein, unknown function
Plasmodium vivax PVX_117600   hypothetical protein, conserved
Plasmodium yoelii PY04186   Arabidopsis thaliana At4g24800/F6I7_10
Schistosoma japonicum Sjp_0076950   Programmed cell death protein 4, putative
Schistosoma mansoni Smp_072110.2   programmed cell death protein
Schistosoma mansoni Smp_072110.3   programmed cell death protein
Schmidtea mediterranea mk4.003807.02   Programmed cell death protein 4
Toxoplasma gondii TGME49_286750   MA3 domain-containing protein

Essentiality

Smp_072110.2 has one or more orthologs with essentiality data
Gene/Ortholog Organism Phenotype Source Study
PBANKA_1321000 Plasmodium berghei Dispensable plasmo
TGME49_286750 Toxoplasma gondii Probably non-essential sidik
Show/Hide essentiality data references
  • 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
  • shigen Profiling of E. coli Chromosome (PEC) National Institute of Genetics, Japan
  • nmpdr Genome-scale essentiality datasets from published studies (M. tuberculosis) National Microbial Pathogen Data Resource
  • 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
  • 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
  • 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.
  • 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.

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
Homo sapiens programmed cell death 4 (neoplastic transformation inhibitor) Compounds References
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
0.0072 0.5 0.5
0.0123 0.7326 0.7326
0.0058 1 1
0.0061 0.2783 0.2783
0.0118 0.5718 0.5718
0.0061 0.2753 0.2753
0.0059 0.2866 0.2866
0.0119 1 1
0.0123 1 1
0.0118 0.5718 0.5718
0.0323 0.8018 1
0.0058 0.2866 0.2866
0.0061 0.312 0.312
0.0072 0.5 0.5
0.006 0.2866 0.2866
0.0072 0.5 0.5
0.0058 0.2528 0.2528
0.024 0.319 0.5702

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_072110.2 (Schistosoma mansoni), programmed cell death protein
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