Detailed view for Smp_039640.1

Basic information

TDR Targets ID: 285376
Schistosoma mansoni, retinoblastoma binding protein
Source Database / ID:  GeneDB

pI: 9.053 | Length (AA): 970 | MW (Da): 108720 | Paralog Number: 1

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

PF08783   DWNN domain
PF13696   Zinc knuckle

Gene Ontology

Mouse over links to read term descriptions.
GO:0005634   nucleus  
GO:0008270   zinc ion binding  
GO:0005515   protein binding  
GO:0003676   nucleic acid binding  

Metabolic Pathways

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

Structural information

Modbase 3D models:

There are 5 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
3 76 2c7h (A) 7 81 43.00 0.000000014 1 0.717889 -1.27
232 323 2y43 (A) 10 94 22.00 0 0.98 0.366745 -0.69
235 320 4gb0 (A) 3 89 21.00 0 0.99 0.27356 -0.49
241 320 2yu4 (A) 4 85 20.00 0 0.41 0.265374 0
243 290 5olm (A) 12 54 45.00 0.54 0.55 0.296085 0.53

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_127188)

Species Accession Gene Product
Arabidopsis thaliana AT5G47430   DWNN domain, a CCHC-type zinc finger
Arabidopsis thaliana AT4G17410   DWNN domain-containing protein
Babesia bovis BBOV_III006140   conserved hypothetical protein
Brugia malayi Bm1_30420   Zinc knuckle family protein
Candida albicans CaO19.4628   poss. member of chaperonin-cont. T-complex
Candida albicans CaO19.12098   poss. member of chaperonin-cont. T-complex
Caenorhabditis elegans CELE_F36F2.3   Protein TAG-214, isoform B
Cryptosporidium hominis Chro.80429   development protein DG1124
Cryptosporidium parvum cgd8_3720   D441/Mpe1p like protein with a zinc knuckle (C2HC) and PhD Zn finger domain
Dictyostelium discoideum DDB_G0279003   hypothetical protein
Drosophila melanogaster Dmel_CG3231   something that sticks like glue
Echinococcus granulosus EgrG_000776200   retinoblastoma binding protein
Entamoeba histolytica EHI_014000   Retinoblatoma-binding protein 6, putative
Echinococcus multilocularis EmuJ_000776200   retinoblastoma binding protein
Homo sapiens ENSG00000122257   retinoblastoma binding protein 6
Leishmania braziliensis LbrM.34.2960   hypothetical protein, conserved
Leishmania donovani LdBPK_353100.1   nucleic acid binding protein, putative
Leishmania infantum LinJ.35.3100   hypothetical protein, conserved
Leishmania major LmjF.35.3050   hypothetical protein, conserved
Leishmania mexicana LmxM.34.3050   hypothetical protein, conserved
Loa Loa (eye worm) LOAG_04740   hypothetical protein
Mus musculus ENSMUSG00000030779   retinoblastoma binding protein 6
Neospora caninum NCLIV_062930   hypothetical protein
Oryza sativa 4348695   Os10g0431000
Oryza sativa 4333626   Os03g0659400
Oryza sativa 4332754   Os03g0335100
Plasmodium berghei PBANKA_1028600   conserved Plasmodium protein, unknown function
Plasmodium falciparum PF3D7_1414100   conserved Plasmodium protein, unknown function
Plasmodium knowlesi PKNH_1344000   hypothetical protein, conserved in Apicomplexan species
Plasmodium vivax PVX_085745   hypothetical protein, conserved
Plasmodium yoelii PY03290   development protein DG1124
Saccharomyces cerevisiae YKL059C   Mpe1p
Schistosoma japonicum Sjp_0084270   Retinoblastoma-binding protein 6, putative
Schistosoma mansoni Smp_039640.2   retinoblastoma binding protein
Schistosoma mansoni Smp_039640.1   retinoblastoma binding protein
Schmidtea mediterranea mk4.005912.04   E3 ubiquitin-protein ligase RBBP6
Schmidtea mediterranea mk4.002560.01   E3 ubiquitin-protein ligase RBBP6
Schmidtea mediterranea mk4.006467.01   E3 ubiquitin-protein ligase RBBP6
Schmidtea mediterranea mk4.001379.02   E3 ubiquitin-protein ligase RBBP6
Schmidtea mediterranea mk4.002373.04   E3 ubiquitin-protein ligase RBBP6
Schmidtea mediterranea mk4.002373.05  
Schmidtea mediterranea mk4.017734.00   E3 ubiquitin-protein ligase RBBP6
Schmidtea mediterranea mk4.001800.00   E3 ubiquitin-protein ligase RBBP6
Schmidtea mediterranea mk4.000457.06  
Schmidtea mediterranea mk4.001379.03   E3 ubiquitin-protein ligase RBBP6
Schmidtea mediterranea mk4.002032.00   E3 ubiquitin-protein ligase RBBP6
Trypanosoma brucei gambiense Tbg972.9.7730   nucleic acid binding protein, putative,predicted zinc finger protein
Trypanosoma brucei Tb927.9.12670   predicted zinc finger protein
Trypanosoma congolense TcIL3000_9_5220   predicted zinc finger protein
Trypanosoma cruzi TcCLB.510743.20   hypothetical protein, conserved
Trypanosoma cruzi TcCLB.510659.279   nucleic acid binding protein, putative
Toxoplasma gondii TGME49_245660   hypothetical protein
Theileria parva TP02_0349   hypothetical protein

Essentiality

Smp_039640.1 has one or more orthologs with essentiality data
Gene/Ortholog Organism Phenotype Source Study
Tb09.211.3620 Trypanosoma brucei no significant loss or gain of fitness in bloodstream forms (3 days) alsford
Tb09.211.3620 Trypanosoma brucei no significant loss or gain of fitness in bloodstream forms (6 days) alsford
Tb09.211.3620 Trypanosoma brucei no significant loss or gain of fitness in procyclic forms alsford
Tb09.211.3620 Trypanosoma brucei significant gain of fitness in differentiation of procyclic to bloodstream forms alsford
CELE_F36F2.3 Caenorhabditis elegans embryonic lethal wormbase
YKL059C Saccharomyces cerevisiae inviable yeastgenome
TGME49_245660 Toxoplasma gondii Probably essential sidik
Show/Hide essentiality data references
  • alsford High-throughput phenotyping using parallel sequencing of RNA interference targets in the African trypanosome Genome Res 2011, 21:915-924
  • 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.
  • neb C. elegans RNAi phenotypes Data obtained from Wormbase WS150, curated by K. Chaudary and T. Carlow, New England Biolabs
  • keio Systematic single-gene knock-out mutants of E. coli K12 The Keio Collection
  • 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.
  • nmpdr Genome-scale essentiality datasets from published studies (M. tuberculosis) National Microbial Pathogen Data Resource
  • blattner Systematic mutagenesis of the E. coli (MG1655) genome J Bacteriol 2004, 186:4921-4930
  • shigen Profiling of E. coli Chromosome (PEC) National Institute of Genetics, Japan
  • yeastgenome Systematic deletion of yeast genes Saccharomyces Genome Database
  • 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
  • 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.

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Gene identifier Smp_039640.1 (Schistosoma mansoni), retinoblastoma binding protein
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