Detailed view for PVX_084610

Basic information

TDR Targets ID: 266046
Plasmodium vivax, lysine-specific histone demethylase 1, putative
Source Database / ID:  PlasmoDB 

pI: 9.2143 | Length (AA): 2857 | MW (Da): 324759 | Paralog Number: 0

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

Druggability Group : DG5

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

PF01593   Flavin containing amine oxidoreductase
PF13450   NAD(P)-binding Rossmann-like domain

Gene Ontology

Mouse over links to read term descriptions.
GO:0016491   oxidoreductase activity  
GO:0009055   electron carrier activity  
GO:0008270   zinc ion binding  
GO:0055114   oxidation reduction  

Metabolic Pathways

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

Structural information

Modbase 3D models:

There are 11 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
2075 2286 1b37 (A) 259 460 32.00 0.00000057 0.99 0.3 0.17
27 113 4b1z (M) 431 517 18.00 0.63 0.04 0.174152 -0.5
326 1492 4rh7 (A) 1255 2343 10.00 0 0.85 -0.0677296 1.54
342 473 1y4c (A) 349 653 17.00 0.072 0.28 0.304902 -1.01
1090 1126 3bog (C) 3 79 51.00 0.018 0.06 0.594651 -0.86
1176 1216 4i59 (A) 32 72 56.00 0.0084 0.61 0.573051 0.55
1177 1216 1i8t (A) 3 42 53.00 0.034 0.41 0.527701 0.5
2075 2286 1b37 (A) 259 460 32.00 0.0000021 0.93 0.225904 0.94
2746 2798 1wes (A) 12 62 29.00 0.07 0.4 0.0214509 1.28
2747 2801 2l5u (A) 9 58 38.00 0.0026 0.95 0.272151 0.83
2747 2809 2ke1 (A) 294 351 40.00 0.079 0.78 0.287751 1.25

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 intraerythrocytic - 36 hs. Zhu L
Upregulation Percent Ranking Stage Dataset
Lower 20-40% percentile intraerythrocytic - 6 hs, intraerythrocytic - 12 hs, intraerythrocytic - 18 hs, intraerythrocytic - 24 hs, intraerythrocytic - 30 hs, intraerythrocytic - 40 hs, intraerythrocytic - 48 hs. Zhu L
Show/Hide expression data references
  • Zhu L New insights into the Plasmodium vivax transcriptome using RNA-Seq.

Orthologs

Ortholog group members (OG5_146824)

Species Accession Gene Product
Babesia bovis BBOV_IV010050   amine oxidase, putative
Homo sapiens 6698   small proline-rich protein 1A
Plasmodium berghei PBANKA_0610100   lysine-specific histone demethylase 1, putative
Plasmodium falciparum PF3D7_1211600   lysine-specific histone demethylase 1, putative
Plasmodium knowlesi PKNH_1311700   lysine-specific histone demethylase 1, putative
Plasmodium vivax PVX_084610   lysine-specific histone demethylase 1, putative
Plasmodium yoelii PY03791   amine oxidase, flavin-containing, putative
Theileria parva TP01_0723   hypothetical protein

Essentiality

PVX_084610 has one or more orthologs with essentiality data
Gene/Ortholog Organism Phenotype Source Study
PBANKA_0610100 Plasmodium berghei Dispensable plasmo
Show/Hide essentiality data references
  • keio Systematic single-gene knock-out mutants of E. coli K12 The Keio Collection
  • 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
  • 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.
  • gerdes Experimental determination and system-level analysis of essential genes in E. coli MG1655 Gerdes et al., J Bacteriol. 2003 185:5673-84
  • neb C. elegans RNAi phenotypes Data obtained from Wormbase WS150, curated by K. Chaudary and T. Carlow, New England Biolabs
  • 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
  • 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.
  • nmpdr Genome-scale essentiality datasets from published studies (M. tuberculosis) National Microbial Pathogen Data Resource
  • 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

Druggability index (range: 0 to 1): 0.4

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

Ranking Plot

Putative Drugs List

Compound Raw Global Species
0.0262 1 0.5
0.0041 1 0.5
0.0048 0.6551 0.6354
0.0419 1 0.5
0.0217 1 1
0.0025 0.4128 0.5
0.0137 0.7284 0.5
0.0282 0.5 0.5
0.0065 1 0.5
0.0064 1 0.5
0.0272 1 0.5
0.0108 1 0.5
0.0023 0.5 0.5
0.0255 0.6236 0.5
0.0063 1 0.5
0.0087 0.3247 0.5
0.0439 0.3516 0.5
0.0262 1 0.5
0.013 1 0.5
0.0478 0.2943 0.399
0.0064 1 0.5
0.014 0.9532 1
0.0051 1 1
0.0042 0.2805 0.5
0.0135 0.4325 0.5
0.0062 1 0.5
0.0153 1 0.5
0.011 0.3084 0.5
0.0109 1 0.5
0.0085 1 0.5
0.0239 0.2732 0.5
0.0086 0.5 0.5
0.0023 0.5 0.5
0.0063 1 0.5
0.0131 0.5 0.5
0.0177 0.4028 1
0.0042 0.5 0.5

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 PVX_084610 (Plasmodium vivax), lysine-specific histone demethylase 1, putative
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