Detailed view for PF3D7_1366500

Basic information

TDR Targets ID: 2323
Plasmodium falciparum, nucleoside diphosphate kinase

Source Database / ID:  PlasmoDB   |   GeneDB   |   MPMP

pI: 9.4165 | Length (AA): 149 | MW (Da): 17012 | 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 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
1 149 1xiq (A) 1 149 99.99 0 1 2.26 -1.67
2 139 1ehw (A) 5 142 51.00 0 1 1.73 -2.05
1 149 1xiq (A) 1 149 99.99 0 1 2.2418 -1.49

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:

  • 1XIQ:
  • Resolution Method # Atoms # Residues Dep. Date Pub. Date Mod. Date

Expression

Upregulation Percent Ranking Stage Dataset
Upper 80-100% percentile intra-erythrocytic - 32 hs, gametocyte, early schizont, early trophozoite, late schizont, late trophozoite, Oocyst, Female Gametocyte. Otto TD PlasmoDB Zanghi G Lasonder E
Upregulation Percent Ranking Stage Dataset
Upper 60-80% percentile intra-erythrocytic - 8 hs, intra-erythrocytic - 16 hs, intra-erythrocytic - 24 hs, intra-erythrocytic - 40 hs, intra-erythrocytic - 48 hs, Ring, Male Gametocyte. Otto TD Zanghi G Lasonder E
Upregulation Percent Ranking Stage Dataset
Mid 40-60% percentile intra-erythrocytic - 0 hs. Otto TD
Upregulation Percent Ranking Stage Dataset
Lower 20-40% percentile Sporozoite. Zanghi G
Show/Hide expression data references
  • Zanghi G A Specific PfEMP1 Is Expressed in P. falciparum Sporozoites and Plays a Role in Hepatocyte Infection.
  • Otto TD New insights into the blood-stage transcriptome of Plasmodium falciparum using RNA-Seq.
  • PlasmoDB Data on upregulation of P. falciparum genes in different life cycle stages, combined from several microarray experiments available in PlasmoDB
  • 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_126708)

Species Accession Gene Product
Arabidopsis thaliana AT4G23900   nucleoside diphosphate kinase IV
Arabidopsis thaliana AT4G11010   nucleoside diphosphate kinase 3
Arabidopsis thaliana AT5G63310   nucleoside diphosphate kinase II
Arabidopsis thaliana AT4G09320   nucleoside diphosphate kinase 1
Babesia bovis BBOV_III005290   nucleoside diphosphate kinase family protein
Brugia malayi Bm1_50135   Nucleoside diphosphate kinase
Candida albicans CaO19.11786   Nucleoside diphosphate kinase-like orf
Candida albicans CaO19.4311   Nucleoside diphosphate kinase-like orf
Caenorhabditis elegans CELE_F25H2.5   Protein NDK-1
Cryptosporidium hominis Chro.40219   nucleoside diphosphate kinase
Cryptosporidium hominis Chro.50237   nucleoside-diphosphate kinase
Cryptosporidium parvum cgd4_1940   putative nucleoside-diphosphate kinase
Cryptosporidium parvum cgd5_1470   signal peptide containing protein having a NDK (nucleoside-diphosphate kinase) domain
Chlamydia trachomatis CT_500   nucleoside diphosphate kinase
Dictyostelium discoideum DDB_G0273069   NDP kinase
Dictyostelium discoideum DDB_G0279911   NDP kinase
Dictyostelium discoideum DDB_G0273805   NDP kinase
Drosophila melanogaster Dmel_CG2210   abnormal wing discs
Escherichia coli b2518   multifunctional nucleoside diphosphate kinase and apyrimidinic endonuclease and 3'-phosphodiesterase
Echinococcus granulosus EgrG_001117000   nucleoside diphosphate kinase
Entamoeba histolytica EHI_104360   nucleoside diphosphate kinase, putative
Echinococcus multilocularis EmuJ_001117000   nucleoside diphosphate kinase
Giardia lamblia GL50803_11301   Nucleoside diphosphate kinase
Homo sapiens ENSG00000239672   NME/NM23 nucleoside diphosphate kinase 1
Homo sapiens ENSG00000011052   NME1-NME2 readthrough
Homo sapiens ENSG00000103024   NME/NM23 nucleoside diphosphate kinase 3
Homo sapiens ENSG00000243678   NME/NM23 nucleoside diphosphate kinase 2
Leishmania braziliensis LbrM.32.3200   nucleoside diphosphate kinase b
Leishmania braziliensis LbrM.32.3210   nucleoside diphosphate kinase b
Leishmania donovani LdBPK_323110.1   nucleoside diphosphate kinase b
Leishmania infantum LinJ.32.3100   nucleoside diphosphate kinase b
Leishmania infantum LinJ.32.3110   nucleoside diphosphate kinase b
Leishmania major LmjF.32.2950   nucleoside diphosphate kinase b
Leishmania mexicana LmxM.31.2951   nucleoside diphosphate kinase b
Loa Loa (eye worm) LOAG_04137   nucleoside diphosphate kinase
Mycobacterium leprae ML1469c   PROBABLE NUCLEOSIDE DIPHOSPHATE KINASE NDK (NDK) (NDP KINASE) (NUCLEOSIDE-2-P KINASE)
Mus musculus 229879   predicted gene 4862
Mus musculus ENSMUSG00000073435   NME/NM23 nucleoside diphosphate kinase 3
Mus musculus ENSMUSG00000024177   NME/NM23 nucleoside diphosphate kinase 4
Mus musculus 18102   NME/NM23 nucleoside diphosphate kinase 1
Mus musculus 102641423   nucleoside diphosphate kinase B-like
Mus musculus ENSMUSG00000020857   NME/NM23 nucleoside diphosphate kinase 2
Mycobacterium tuberculosis Rv2445c   Probable nucleoside diphosphate kinase NdkA (NDK) (NDP kinase) (nucleoside-2-P kinase)
Mycobacterium ulcerans MUL_3716   nucleoside diphosphate kinase
Neospora caninum NCLIV_002390   Nucleoside diphosphate kinase (EC 2.7.4.6), related
Oryza sativa 4349403   Os10g0563700
Oryza sativa 4343275   Os07g0492000
Oryza sativa 4352460   Os12g0548300
Oryza sativa 4339815   Os05g0595400
Plasmodium berghei PBANKA_1142400   nucleoside diphosphate kinase b, putative
Plasmodium falciparum PF3D7_1366500   nucleoside diphosphate kinase
Plasmodium knowlesi PKNH_1104800   nucleoside diphosphate kinase b, putative
Plasmodium vivax PVX_115285   nucleoside diphosphate kinase A, putative
Plasmodium yoelii PY04911   nucleoside diphosphate kinase
Saccharomyces cerevisiae YKL067W   nucleoside diphosphate kinase
Schistosoma japonicum Sjp_0210660   ko:K00940 nucleoside-diphosphate kinase [EC2.7.4.6], putative
Schistosoma japonicum Sjp_0308570   Nucleoside diphosphate kinase, putative
Schistosoma mansoni Smp_092750   nucleoside diphosphate kinase
Schmidtea mediterranea mk4.000098.07   Nucleoside diphosphate kinase
Schmidtea mediterranea mk4.041404.00   Nucleoside diphosphate kinase
Schmidtea mediterranea mk4.016108.00   Nucleoside diphosphate kinase
Trypanosoma brucei gambiense Tbg972.11.18090   nucleoside diphosphate kinase, putative
Trypanosoma brucei Tb927.11.16130   nucleoside diphosphate kinase
Trypanosoma congolense TcIL3000.11.16070   nucleoside diphosphate kinase
Trypanosoma cruzi TcCLB.508707.200   Nucleoside diphosphate kinase 1
Toxoplasma gondii TGME49_295350   nucleoside diphosphate kinase, putative
Treponema pallidum TP1010   nucleoside-diphosphate kinase (ndk)
Theileria parva TP02_0422   nucleoside diphosphate kinase, putative
Wolbachia endosymbiont of Brugia malayi Wbm0717   nucleoside diphosphate kinase

Essentiality

PF3D7_1366500 has one or more orthologs with essentiality data
Gene/Ortholog Organism Phenotype Source Study
Tb11.01.7800 Trypanosoma brucei no significant loss or gain of fitness in bloodstream forms (3 days) alsford
Tb11.01.7800 Trypanosoma brucei significant gain of fitness in bloodstream forms (6 days) alsford
Tb11.01.7800 Trypanosoma brucei no significant loss or gain of fitness in procyclic forms alsford
Tb11.01.7800 Trypanosoma brucei no significant loss or gain of fitness in differentiation of procyclic to bloodstream forms alsford
b2518 Escherichia coli non-essential goodall
CELE_F25H2.5 Caenorhabditis elegans embryonic lethal wormbase
CELE_F25H2.5 Caenorhabditis elegans larval arrest wormbase
CELE_F25H2.5 Caenorhabditis elegans larval lethal wormbase
CELE_F25H2.5 Caenorhabditis elegans sterile wormbase
PBANKA_1142400 Plasmodium berghei Slow plasmo
TGME49_295350 Toxoplasma gondii Probably non-essential sidik
Show/Hide essentiality data references
  • keio Systematic single-gene knock-out mutants of E. coli K12 The Keio Collection
  • 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.
  • 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.
  • nmpdr Genome-scale essentiality datasets from published studies (M. tuberculosis) National Microbial Pathogen Data Resource
  • yeastgenome Systematic deletion of yeast genes Saccharomyces Genome Database
  • 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.
  • neb C. elegans RNAi phenotypes Data obtained from Wormbase WS150, curated by K. Chaudary and T. Carlow, New England Biolabs
  • alsford High-throughput phenotyping using parallel sequencing of RNA interference targets in the African trypanosome Genome Res 2011, 21:915-924
  • blattner Systematic mutagenesis of the E. coli (MG1655) genome J Bacteriol 2004, 186:4921-4930
  • 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
  • shigen Profiling of E. coli Chromosome (PEC) National Institute of Genetics, Japan

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): 0.2


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

  • Pfal006645AAA;
  • Type Source Notes
    soluble recombinant protein Structural Genomics for Pathogenic Protozoa (SGPP) Pfal006645; Recombinant protein: full-length; Source: P falciparum; nucleoside diphosphate kinase b; putative ;

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.

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Gene identifier PF3D7_1366500 (Plasmodium falciparum), nucleoside diphosphate kinase
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