Detailed view for PF3D7_0605600

Basic information

TDR Targets ID: 4410
Plasmodium falciparum, nucleoside diphosphate kinase, putative
Source Database / ID:  PlasmoDB   |   GeneDB   |   MPMP

pI: 7.5678 | Length (AA): 1828 | MW (Da): 219869 | Paralog Number: 0

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

PF00334   Nucleoside diphosphate kinase

Gene Ontology

Mouse over links to read term descriptions.
GO:0006165   nucleoside diphosphate phosphorylation  
GO:0005524   ATP binding  
GO:0004550   nucleoside diphosphate kinase activity  
GO:0006241   CTP biosynthetic process  
GO:0006228   UTP biosynthetic process  
GO:0006183   GTP biosynthetic process  

Structural information

Modbase 3D models:

There are 19 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
146 288 1nhk (R) 2 140 29.00 0 1 0.44 -1.77
146 301 1nue (A) 3 152 27.00 0 1 0.52 -1.26
143 291 4w98 (A) 0 143 26.00 0 1 0.47571 -1.08
146 288 3vgv (N) 2 140 34.00 0.00000000032 1 0.133228 0.32
146 289 1nhk (R) 2 141 30.00 0 1 0.483775 -1.08
147 302 1vya (A) 1 149 23.00 0 1 0.145039 0
264 1367 1epw (A) 138 1253 16.00 0 0.94 0.496939 1.78
469 650 4uos (A) 2 183 20.00 0.037 0.28 0.339562 -1.05
787 1202 4jra (B) 883 1262 29.00 0.66 0.11 -0.0646289 2.53
1205 1440 4tql (A) 10 238 24.00 0.00011 0.72 0.316303 -0.19
1440 1612 3na7 (A) 5 167 21.00 0.1 0.07 0.225839 -0.08
1 148 4dz6 (A) 3 159 16.00 0.000000022 0.73 0.281942 -0.75
1 141 3r9l (A) 1 135 19.00 0.0000000042 0.94 -0.0108769 0.45
147 302 1vya (A) 1 149 23.00 0 1 0.159806 -0.16
147 298 1xiq (A) 1 149 22.00 0 1 0.377124 -0.41
476 665 4uos (A) 2 183 23.00 0.019 0.46 0.334855 -0.88
638 1207 2nyy (A) 688 1262 25.00 0.55 0.88 0.168766 2
792 1207 4jra (B) 883 1262 29.00 0.68 0.11 -0.0652496 2.53
1210 1445 4tql (A) 10 238 24.00 0.000088 0.72 0.322951 -0.19

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
Upper 80-100% percentile Male Gametocyte. Lasonder E
Upregulation Percent Ranking Stage Dataset
Upper 60-80% percentile Female Gametocyte. Lasonder E
Upregulation Percent Ranking Stage Dataset
Lower 20-40% percentile intra-erythrocytic - 32 hs, Oocyst, Sporozoite. Otto TD Zanghi G
Upregulation Percent Ranking Stage Dataset
Lower 0-20% percentile intra-erythrocytic - 0 hs, intra-erythrocytic - 8 hs, intra-erythrocytic - 16 hs, intra-erythrocytic - 24 hs, intra-erythrocytic - 40 hs, intra-erythrocytic - 48 hs, Ring. Otto TD Zanghi G
Show/Hide expression data references
  • Otto TD New insights into the blood-stage transcriptome of Plasmodium falciparum using RNA-Seq.
  • Zanghi G A Specific PfEMP1 Is Expressed in P. falciparum Sporozoites and Plays a Role in Hepatocyte Infection.
  • Lasonder E Integrated transcriptomic and proteomic analyses of P. falciparum gametocytes. Molecular insight into sex-specific processes and translational repression.

Orthologs

Ortholog group members (OG5_133897)

Species Accession Gene Product
Echinococcus granulosus EgrG_000713200   thioredoxin domain containing protein 3
Echinococcus multilocularis EmuJ_000713200   thioredoxin domain containing protein 3
Homo sapiens ENSG00000086288   NME/NM23 family member 8
Mus musculus ENSMUSG00000041138   NME/NM23 family member 8
Neospora caninum NCLIV_037320   MGC78790 protein, related
Plasmodium berghei PBANKA_0104400   nucleoside diphosphate kinase, putative
Plasmodium falciparum PF3D7_0605600   nucleoside diphosphate kinase, putative
Plasmodium knowlesi PKNH_1144900   nucleoside diphosphate kinase, putative
Plasmodium vivax PVX_113450   nucleoside diphosphate kinase, putative
Plasmodium yoelii PY01721   hypothetical protein
Schistosoma japonicum Sjp_0300510   Thioredoxin domain-containing protein 3 homolog, putative
Schistosoma mansoni Smp_168270   nucleoside diphosphate kinase
Schmidtea mediterranea mk4.016211.01   Nucleoside diphosphate kinase
Schmidtea mediterranea mk4.001063.07   Nucleoside diphosphate kinase
Schmidtea mediterranea mk4.003598.03   Nucleoside diphosphate kinase
Schmidtea mediterranea mk4.004334.03   TXNDC6 protein
Toxoplasma gondii TGME49_269035   nucleoside diphosphate kinase

Essentiality

PF3D7_0605600 has one or more orthologs with essentiality data
Gene/Ortholog Organism Phenotype Source Study
TGME49_269035 Toxoplasma gondii Essentiality uncertain sidik
Show/Hide essentiality data references
  • nmpdr Genome-scale essentiality datasets from published studies (M. tuberculosis) National Microbial Pathogen Data Resource
  • 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
  • neb C. elegans RNAi phenotypes Data obtained from Wormbase WS150, curated by K. Chaudary and T. Carlow, New England Biolabs
  • 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.
  • 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
  • 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.
  • yeastgenome Systematic deletion of yeast genes Saccharomyces Genome Database
  • keio Systematic single-gene knock-out mutants of E. coli K12 The Keio Collection
  • 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

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

  • Assay for Nucleoside 5'-Diphosphate Kinase (2.7.4.6 ) Sigma-Aldrich
  • Automatic link to known assays based on EC numbers.

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 PF3D7_0605600 (Plasmodium falciparum), nucleoside diphosphate kinase, putative
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