Detailed view for PVX_117100

Basic information

TDR Targets ID: 265856
Plasmodium vivax, 1-deoxy-D-xylulose 5-phosphate reductoisomerase, putative
Source Database / ID:  PlasmoDB 

pI: 9.1628 | Length (AA): 528 | MW (Da): 58555 | 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

PF02670   1-deoxy-D-xylulose 5-phosphate reductoisomerase
PF08436   1-deoxy-D-xylulose 5-phosphate reductoisomerase C-terminal
PF13288   DXP reductoisomerase C-terminal domain

Gene Ontology

Mouse over links to read term descriptions.
GO:0070402   GO:NADPH binding  

GO:0046872   metal ion binding  
GO:0030604   1-deoxy-D-xylulose-5-phosphate reductoisomerase activity  
GO:0005515   protein binding  
GO:0005488   binding  
GO:0003824   catalytic activity  
GO:0055114   oxidation reduction  
GO:0008299   isoprenoid biosynthetic process  
GO:0008152   metabolic process  

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
78 479 2c82 (A) 13 383 39.00 0 1 1.36 -1.38
79 487 1q0q (A) 3 398 39.00 0 1 1.32 -1.68
15 110 2lqg (A) 920 1023 7.00 0.026 0 0.218718 -0.54
115 520 3au8 (A) 77 482 74.00 0 1 1.74424 -1.63

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 - 12 hs, intraerythrocytic - 18 hs, intraerythrocytic - 24 hs, intraerythrocytic - 30 hs. Zhu L
Upregulation Percent Ranking Stage Dataset
Lower 20-40% percentile intraerythrocytic - 6 hs, intraerythrocytic - 36 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_130462)

Species Accession Gene Product
Arabidopsis thaliana AT5G62790   1-deoxy-D-xylulose 5-phosphate reductoisomerase
Babesia bovis BBOV_III010740   1-deoxy-D-xylulose 5-phosphate reductoisomerase family protein
Chlamydia trachomatis CT_071   1-deoxy-D-xylulose 5-phosphate reductoisomerase
Escherichia coli b0173   1-deoxy-D-xylulose 5-phosphate reductoisomerase
Mycobacterium leprae ML1583c   PROBABLE 1-DEOXY-D-XYLULOSE 5-PHOSPHATE REDUCTOISOMERASE DXR (DXP REDUCTOISOMERASE) (1-DEOXYXYLULOSE-5-PHOSPHATE REDUCTOISOMERAS
Mycobacterium tuberculosis Rv2870c   Probable 1-deoxy-D-xylulose 5-phosphate reductoisomerase Dxr (DXP reductoisomerase) (1-deoxyxylulose-5-phosphate reductoisomeras
Mycobacterium ulcerans MUL_2085   1-deoxy-D-xylulose 5-phosphate reductoisomerase
Neospora caninum NCLIV_051900   1-deoxy-D-xylulose 5-phosphate reductoisomerase, putative
Oryza sativa 4326153   Os01g0106900
Plasmodium berghei PBANKA_1330600   1-deoxy-D-xylulose 5-phosphate reductoisomerase, putative
Plasmodium falciparum PF3D7_1467300   1-deoxy-D-xylulose 5-phosphate reductoisomerase
Plasmodium knowlesi PKNH_1214000   1-deoxy-D-xylulose 5-phosphate reductoisomerase, putative
Plasmodium vivax PVX_117100   1-deoxy-D-xylulose 5-phosphate reductoisomerase, putative
Plasmodium yoelii PY05578   1-deoxy-D-xylulose 5-phosphate reductoisomerase
Toxoplasma gondii TGME49_214850   1-deoxy-D-xylulose 5-phosphate reductoisomerase, putative
Treponema pallidum TP0601   1-deoxy-D-xylulose 5-phosphate reductoisomerase
Theileria parva TP02_0073   1-deoxy-D-xylulose 5-phosphate reductoisomerase, putative
Wolbachia endosymbiont of Brugia malayi Wbm0179   1-deoxy-D-xylulose 5-phosphate reductoisomerase

Essentiality

PVX_117100 has one or more orthologs with essentiality data
Gene/Ortholog Organism Phenotype Source Study
b0173 Escherichia coli essential goodall
PBANKA_1330600 Plasmodium berghei Essential plasmo
TGME49_214850 Toxoplasma gondii Probably essential sidik
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
  • nmpdr Genome-scale essentiality datasets from published studies (M. tuberculosis) National Microbial Pathogen Data Resource
  • 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
  • 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.
  • 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.
  • shigen Profiling of E. coli Chromosome (PEC) National Institute of Genetics, Japan
  • wormbase C. elegans RNAi experiments WormBase web site, http://www.wormbase.org, release WS170
  • yeastgenome Systematic deletion of yeast genes Saccharomyces Genome Database

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): 0.6

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
Arabidopsis thaliana 1-deoxy-D-xylulose 5-phosphate reductoisomerase Compounds References
Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) 1-deoxy-D-xylulose 5-phosphate reductoisomerase Compounds References
Plasmodium falciparum 1-deoxy-D-xylulose 5-phosphate reductoisomerase Compounds References
Escherichia coli 1-deoxy-D-xylulose 5-phosphate reductoisomerase Compounds References
Mycobacterium tuberculosis Probable 1-deoxy-D-xylulose 5-phosphate reductoisomerase Dxr (DXP reductoisomerase) (1-deoxyxylulose-5-phosphate reductoisomeras Compounds References
Synechocystis sp. (strain PCC 6803 / Kazusa) 1-deoxyxylulose-5-phosphate reductoisomerase 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
0.0444 1 0.5
0.1462 1 1
0.0519737 1 0.5
0.1007 0.5 0.5
0.0476 1 1
0.0923 0.5 0.5
0.1539 1 1
0.395036 1 1
0.1287 0.9357 1
0.0902 1 0.5
0.0519821 1 1
0.1011 0.7261 1
0.266 1 1
0.312 0.3795 1
0.3534 0.5 0.5
0.052 1 0.5
0.2215 1 1
2.5678 1 1
0.143 1 0.5
0.101974 0.5 0.5
0.102 0.5 0.5
0.6418 0.5 0.5
0.052 0.2966 1
0.052 0.5843 1
0.0431 0.3109 1
0.052 0.3955 1
0.1807 0.5 0.5
0.052 0.4287 1
0.052 0.4747 1
0.0519737 1 0.5
0.101974 0.5 0.5
0.7907 1 1
0.101974 0.5 0.5
0.4058 1 1
0.086 1 1
0.2286 1 1
0.0416 0.4235 1
0.0971 1 1
0.045 0.3051 1
2.1901 1 1
0.052 0.2578 1
0.05 1 1
0.2496 1 1
1.5123 1 1
0.052 0.2966 1
0.052 1 1
0.0267 1 1
0.052 0.6401 1
0.179 0.8522 1
1.7089 1 1
0.052 0.2747 1
0.5352 0.8174 1
1.0606 0.6346 1
0.5352 0.8174 1
0.1818 1 0.5
0.0519737 1 1
0.224 1 0.5
2.0201 1 1
1.0606 0.6346 1
0.3019 1 1
0.0487 0.3203 1
0.052 0.5513 1
0.05 0.3578 1
0.3723 1 1
0.8376 0.8305 1
0.1739 1 1
0.2521 1 0.5
0.2199 1 0.5
0.102 0.5 0.5
0.052 0.2747 1
0.5352 0.8174 1
0.1394 1 1
0.052 0.3076 1
0.3099 1 0.5
0.0488 0.2967 1
0.05 1 0.5
0.1265 1 0.5
0.134 1 1
0.052 0.3004 1
0.052 1 1
1.9715 0.9097 1
0.1351 0.5 0.5
0.052 0.6082 1
0.0971 1 1
0.0907 1 1
0.1467 0.788 0.5
0.102 1 1
0.5258 1 1
0.0873 1 0.5
0.0519737 0.5 0.5
0.0953 0.5 0.5
0.05 1 0.5
0.2641 0.2763 1
0.3579 1 1
0.102 0.5 0.5
0.2795 0.5 0.5
0.044 0.2958 1
0.0448 0.4496 1
0.0519737 1 0.5
1.4565 1 1
0.1782 1 0.5
0.2276 1 1
0.05 1 0.5
0.1242 0.8096 1
0.052 0.5037 1
0.1541 1 1
0.1467 1 1
0.0449 0.6488 1
0.042 0.2719 1
0.4035 1 1
0.4514 1 1
0.5095 0.5 0.5
2.5678 1 1
0.2304 1 1
0.0452 0.652 1
0.0923 0.5 0.5
0.052 0.312 1
2.1901 1 1
0.052 1 1
0.0606 0.3545 1
0.102 0.5 0.5
0.0983 1 0.5
0.4514 1 1
0.052 0.3794 1
2.3657 1 1
0.1394 1 1
0.2641 0.2763 1
0.4566 0.5874 1
0.4514 1 1
0.4517 1 0.5
0.5352 0.8174 1
0.1467 0.3483 1
0.052 1 1
0.1351 0.4753 0.5
0.0519737 1 1
0.102 1 1
0.5225 1 0.5
0.1738 1 0.5
0.052 0.6122 1
0.0519737 1 1
0.052 1 1
0.0443 0.5404 1
0.1008 1 1
0.052 0.4287 1
0.0971 1 1
0.1299 1 1
0.0833 0.5 0.5
0.225 1 1
0.104 0.3216 1
0.052 0.5843 1
0.1177 0.2895 1
0.2803 1 1
0.1279 1 1
1.5123 1 1
0.6464 1 1
0.052 0.3815 0.5
0.052 0.5513 1
0.1292 0.5 0.5
0.2641 0.2763 1
0.7907 1 1
0.052 0.6082 1
0.5352 1 0.5
0.0519737 1 1
0.052 0.3004 1
0.086 0.5 0.5
0.052 1 1
0.052 0.4726 1
0.4514 1 1
0.05 1 0.5
0.1768 0.6008 1
0.0452 0.3063 1
0.4514 1 1
0.5268 0.5 0.5
0.052 0.6077 1
0.0418 0.518 1
0.6842 1 0.5
0.0375 1 0.5
0.5352 1 0.5
0.3579 1 1
0.2655 0.5 0.5
0.0837 1 0.5
0.0416 1 1
0.0519737 0.5 0.5
0.4517 1 0.5
0.0971 1 1
0.1385 1 1
0.172 0.5 0.5
0.0983 1 0.5
0.052 0.6401 1
0.1861 0.6465 1
0.0449 0.2706 1
0.2423 1 1
0.1373 1 0.5
0.052 0.6082 1
2.3657 1 1
0.052 0.3794 1
0.0446 0.4753 1
0.2988 1 1
0.0446 0.6447 1
0.0698 0.5801 1
2.5678 1 1
0.0331 0.3487 0.3376
0.05 0.3076 1
0.2563 1 0.5
1.0505 1 1
0.101974 1 0.5
0.052 0.6453 1
0.0846 0.616 1
1.8917 1 1
0.1762 0.5 0.5
0.4514 1 1
0.6563 0.5 0.5
0.3723 1 1
1.5763 0.8325 1
0.0885 0.5698 0.5
0.3099 1 0.5
0.052 0.3076 1
0.7481 1 1
0.1118 1 1
0.2804 0.3922 1
0.0899 0.3021 0.4972
0.101974 0.5 0.5
0.0662 1 1
0.0427 0.6236 1
0.3165 1 0.5
0.052 0.312 1
0.0821 0.5 0.5
0.0425 0.573 0.5
0.052 1 1
0.0428 1 1
0.05 0.3803 0.5495
0.4514 1 1
0.0845 0.5 0.5
0.083 0.5 0.5
0.0519737 0.5 0.5
0.052 1 1
0.0431 0.6187 1
0.1676 0.5 0.5
1.1192 1 1
0.1746 0.7634 1
0.135 1 1
0.0366 0.3554 1
0.0836 0.3741 1
0.0899 0.3021 0.4972
0.5352 0.8174 1
0.3165 1 0.5
0.3788 1 1
0.225729 0.5 0.5
0.0886 1 0.5
0.0421 1 0.5
0.052 0.6122 1
1.5763 0.8325 1
0.101974 1 1
0.101974 1 0.5
0.0888 1 0.5
0.7882 1 1
0.3528 0.5 0.5
0.052 0.3955 1
0.0938918 1 0.5
0.2743 1 1
0.4093 1 1
0.2159 0.5 0.5
0.052 1 1
0.101974 0.5 0.5
0.1394 1 1
2.3657 1 1
0.0445 0.2608 1
0.1746 0.7634 1
0.0416 0.4235 1
0.1118 1 1
0.1424 0.9627 1
0.2743 1 1
0.3092 1 0.5
0.101974 0.5 0.5
0.0857 0.2887 1
0.0426543 0.5 0.5
0.089 0.9067 1
0.2679 1 1
0.1265 1 0.5
0.0437 0.5571 1
0.0364 1 1
0.8128 0.8305 1
0.052 1 1
0.1739 1 1
0.1242 0.8096 1
0.5352 0.8174 1
0.0971 1 1
0.1907 1 1
0.1796 0.5 0.5
0.0469 0.3191 1
0.1279 1 1
0.05 1 1
0.05 1 1
0.6464 1 1
0.0249 0.972 0.5
0.3866 1 0.5
0.05 0.2984 1
0.044 0.5339 1
0.089 0.9067 1
0.2743 1 1
0.2496 1 1
0.4514 1 1
0.052 0.6453 1
0.1682 1 0.5
0.052 0.6077 1
0.052 1 1
0.0456 0.6515 1
0.4385 1 1
2.5678 1 1
0.4379 1 1
0.0449 0.6488 1
0.1778 0.5 0.5
1.5763 0.8325 1
1.0988 0.517 0.9832
0.0433 0.4316 1
0.052 0.3076 1
0.089 0.9069 0.5
0.3515 0.5 0.5
0.089 0.9067 1
0.2743 1 1
0.0906 1 0.5
0.0896 1 0.5
0.0971 1 1
0.3125 0.5 0.5
0.0449 0.6488 1
0.0168 0.4528 1
0.052 0.5037 1
0.052 1 1
0.1719 1 1
0.0496 1 1
0.052 0.2578 1

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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User comments

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Gene identifier PVX_117100 (Plasmodium vivax), 1-deoxy-D-xylulose 5-phosphate reductoisomerase, putative
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