Detailed view for PY03877

Basic information

TDR Targets ID: 537754
Plasmodium yoelii, histone deacetylase
Source Database / ID: 

pI: 6.3331 | Length (AA): 447 | MW (Da): 50974 | Paralog Number: 0

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

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

PF00850   Histone deacetylase domain

Gene Ontology

Mouse over links to read term descriptions.
GO:0004407   histone deacetylase activity  
GO:0016575   histone deacetylation  

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
4 376 4bkx (B) 8 376 63.00 0 1 1.69985 -1.53
5 374 4a69 (A) 3 370 58.00 0 1 1.64804 -1.62
8 407 5td7 (A) 6 451 19.00 0 1 1.12945 -0.34

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_126742)

Species Accession Gene Product
Arabidopsis thaliana AT3G44680   histone deacetylase 9
Arabidopsis thaliana AT4G38130   histone deacetylase 19
Arabidopsis thaliana AT5G63110   RPD3-like histone deacetylase
Babesia bovis BBOV_III011020   histone deacetylase
Brugia malayi Bm1_09295   Histone deacetylase 1
Brugia malayi Bm1_18270   histone deacetylase 3 (HD3)
Brugia malayi Bm1_14350   histone deacetylase 1 (HD1)
Candida albicans CaO19.6801   one of two distinct genes with strong similarity to S. cerevisiae RPD3 (YNL330C) SIN3 histone deacetylase complex component
Candida albicans CaO19.10352   one of two distinct genes with strong similarity to S. cerevisiae RPD3 (YNL330C) SIN3 histone deacetylase complex component
Candida albicans CaO19.2834   one of two distinct genes with strong similarity to S. cerevisiae RPD3 (YNL330C) SIN3 histone deacetylase complex component
Candida albicans CaO19.14093   one of two distinct genes with strong similarity to S. cerevisiae RPD3 (YNL330C) SIN3 histone deacetylase complex component
Caenorhabditis elegans CELE_C53A5.3   Protein HDA-1
Caenorhabditis elegans CELE_R06C1.1   Protein HDA-3
Cryptosporidium hominis Chro.60173   histone deacetylase
Cryptosporidium hominis Chro.60019   histone deacetylase
Cryptosporidium parvum cgd6_1380   histone deacetylase HDA2/Rpd3p
Cryptosporidium parvum cgd6_80   RPD3/HD1 histone deacetylase
Dictyostelium discoideum DDB_G0270338   histone deacetylase family protein
Dictyostelium discoideum DDB_G0268024   histone deacetylase family protein
Drosophila melanogaster Dmel_CG2128   Histone deacetylase 3
Drosophila melanogaster Dmel_CG7471   CG7471 gene product from transcript CG7471-RA
Echinococcus granulosus EgrG_001114800   histone deacetylase 3
Echinococcus granulosus EgrG_001102300   histone deacetylase 1
Entamoeba histolytica EHI_119320   histone deacetylase, putative
Echinococcus multilocularis EmuJ_001102300   histone deacetylase 1
Echinococcus multilocularis EmuJ_001114800   histone deacetylase 3
Giardia lamblia GL50803_3281   Histone deacetylase
Homo sapiens ENSG00000171720   histone deacetylase 3
Homo sapiens ENSG00000116478   histone deacetylase 1
Homo sapiens 3066   histone deacetylase 2
Leishmania braziliensis LbrM.24.1510   histone deacetylase, putative
Leishmania braziliensis LbrM.21.0740   histone deacetylase, putative
Leishmania donovani LdBPK_210740.1   histone deacetylase, putative
Leishmania donovani LdBPK_241410.1   histone deacetylase, putative
Leishmania infantum LinJ.21.0740   histone deacetylase, putative
Leishmania infantum LinJ.24.1410   histone deacetylase, putative
Leishmania major LmjF.21.0680   histone deacetylase, putative
Leishmania major LmjF.24.1370   histone deacetylase, putative
Leishmania mexicana LmxM.21.0680   histone deacetylase, putative
Leishmania mexicana LmxM.24.1370   histone deacetylase, putative
Loa Loa (eye worm) LOAG_00213   hypothetical protein
Loa Loa (eye worm) LOAG_05318   histone deacetylase 1
Loa Loa (eye worm) LOAG_00876   histone deacetylase 3
Mus musculus ENSMUSG00000028800   histone deacetylase 1
Mus musculus ENSMUSG00000024454   histone deacetylase 3
Mus musculus ENSMUSG00000019777   histone deacetylase 2
Neospora caninum NCLIV_065780   histone deacetylase, putative
Neospora caninum NCLIV_045860   hypothetical protein
Oryza sativa 4328720   Os02g0215200
Oryza sativa 4350006   Os11g0200000
Oryza sativa 4328717   Os02g0214900
Oryza sativa 4345332   Os08g0344100
Oryza sativa 9270728   Os11g0201400
Oryza sativa 4341387   Os06g0583400
Plasmodium berghei PBANKA_0826500   histone deacetylase 1, putative
Plasmodium falciparum PF3D7_0925700   histone deacetylase 1
Plasmodium knowlesi PKNH_0723600   histone deacetylase 1, putative
Plasmodium vivax PVX_099700   histone deacetylase 1, putative
Plasmodium yoelii PY03877   histone deacetylase
Saccharomyces cerevisiae YNL330C   Rpd3p
Schistosoma japonicum Sjp_0204480   ko:K06067 histone deacetylase 1/2, putative
Schistosoma japonicum Sjp_0012980   ko:K01463 Hdac3 [EC:3.5.1.-], putative
Schistosoma mansoni Smp_093280   histone deacetylase
Schistosoma mansoni Smp_005210   histone deacetylase
Schmidtea mediterranea mk4.022000.01   Histone deacetylase Rpd3
Schmidtea mediterranea mk4.005967.01  
Schmidtea mediterranea mk4.007639.01   Histone deacetylase 3
Schmidtea mediterranea mk4.008527.02   Histone deacetylase 3
Schmidtea mediterranea mk4.019651.00   Histone deacetylase
Schmidtea mediterranea mk4.013163.00   Histone deacetylase
Trypanosoma brucei gambiense Tbg972.10.2000   histone deacetylase 1,histone deacetylase-like 1 protein, putative
Trypanosoma brucei Tb927.10.1680   histone deacetylase 1
Trypanosoma congolense TcIL3000_10_1420   histone deacetylase-like 1 protein, putative
Trypanosoma cruzi TcCLB.511911.159   histone deacetylase 1, putative
Trypanosoma cruzi TcCLB.508637.114   histone deacetylase 1, putative
Toxoplasma gondii TGME49_227290   histone deacetylase HDAC3
Toxoplasma gondii TGME49_249620   histone deacetylase HDAC2
Theileria parva TP02_0039   histone deacetylase, putative
Trichomonas vaginalis TVAG_185870   histone deacetylase, putative
Trichomonas vaginalis TVAG_464210   histone deacetylase 1, 2 ,3, putative
Trichomonas vaginalis TVAG_390760   histone deacetylase, putative
Trichomonas vaginalis TVAG_426760   histone deacetylase, putative
Trichomonas vaginalis TVAG_178760   histone deacetylase, putative
Trichomonas vaginalis TVAG_166720   histone deacetylase 1, 2 ,3, putative
Trichomonas vaginalis TVAG_059170   histone deacetylase, putative
Trichomonas vaginalis TVAG_226910   histone deacetylase, putative
Trichomonas vaginalis TVAG_182970   histone deacetylase 1, 2 ,3, putative

Essentiality

PY03877 has one or more orthologs with essentiality data
Gene/Ortholog Organism Phenotype Source Study
Tb927.10.1680 Trypanosoma brucei no significant loss or gain of fitness in bloodstream forms (3 days) alsford
Tb927.10.1680 Trypanosoma brucei significant loss of fitness in bloodstream forms (6 days) alsford
Tb927.10.1680 Trypanosoma brucei no significant loss or gain of fitness in procyclic forms alsford
Tb927.10.1680 Trypanosoma brucei no significant loss or gain of fitness in differentiation of procyclic to bloodstream forms alsford
CELE_C53A5.3 Caenorhabditis elegans embryonic arrest wormbase
CELE_C53A5.3 Caenorhabditis elegans embryonic lethal wormbase
CELE_C53A5.3 Caenorhabditis elegans larval arrest wormbase
CELE_C53A5.3 Caenorhabditis elegans sterile wormbase
PBANKA_0826500 Plasmodium berghei Essential plasmo
TGME49_249620 Toxoplasma gondii Probably essential sidik
TGME49_227290 Toxoplasma gondii Probably essential sidik
Show/Hide essentiality data references
  • yeastgenome Systematic deletion of yeast genes Saccharomyces Genome Database
  • 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
  • alsford High-throughput phenotyping using parallel sequencing of RNA interference targets in the African trypanosome Genome Res 2011, 21:915-924
  • gerdes Experimental determination and system-level analysis of essential genes in E. coli MG1655 Gerdes et al., J Bacteriol. 2003 185:5673-84
  • 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
  • neb C. elegans RNAi phenotypes Data obtained from Wormbase WS150, curated by K. Chaudary and T. Carlow, New England Biolabs
  • 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
  • wormbase C. elegans RNAi experiments WormBase web site, http://www.wormbase.org, release WS170
  • 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 histone deacetylase 1 Compounds References
Mus musculus histone deacetylase 1 Compounds References
Mus musculus histone deacetylase 3 Compounds References
Rattus norvegicus Histone deacetylase 1 Compounds References
Cryptosporidium parvum RPD3/HD1 histone deacetylase Compounds References
Rattus norvegicus Histone deacetylase Compounds References
Mycoplana ramosa Acetylpolyamine aminohydrolase Compounds References
Plasmodium falciparum histone deacetylase 1 Compounds References
Mus musculus histone deacetylase 2 Compounds References
Cryptosporidium parvum histone deacetylase HDA2/Rpd3p Compounds References
Homo sapiens histone deacetylase 3 Compounds References
Homo sapiens histone deacetylase 2 Compounds References
Zea mays Histone deacetylase HD1B Compounds References
By sequence similarity to non orthologous druggable targets
Species Target Length Identity Alignment span Linked Drugs Reference
Schistosoma mansoni histone deacetylase 1 2 3 440 aa 31.7% 398 aa Compounds References
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

No user comments are available for this gene. Log in to add comments, or register.

Enter your comment

User ()
Gene identifier PY03877 (Plasmodium yoelii), histone deacetylase
Title for this comment
Comment