Detailed view for PF3D7_0503100

Basic information

TDR Targets ID: 4061
Plasmodium falciparum, 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase, putative
Source Database / ID:  PlasmoDB   |   GeneDB   |   MPMP

pI: 9.6293 | Length (AA): 537 | MW (Da): 63376 | Paralog Number: 0

Signal peptide: N | GPI Anchor: N | Predicted trans-membrane segments: 1

Druggability Group : DG3

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

No Pfam domain information for this protein.

Gene Ontology

Mouse over links to read term descriptions.
GO:0050515   4-(cytidine 5'-diphospho)-2-C-methyl-D-erythritol kinase activity  
GO:0020011   apicoplast  
GO:0016301   kinase activity  
GO:0005524   ATP binding  
GO:0016310   phosphorylation  
GO:0016114   terpenoid biosynthetic process  

Structural information

Modbase 3D models:

There are 5 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
132 493 1uek (A) 1 256 24.00 0 1 0.4 0.54
216 513 1h72 (C) 22 299 17.00 0 0.98 0.52 -0.06
132 514 4ed4 (A) 14 308 20.00 0 1 0.605522 0.91
136 349 2ww4 (A) 7 161 34.00 0.0092 0.6 0.22681 1.03
254 361 2v8p (A) 59 159 30.00 0.3 0.48 0.505417 -0.25

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

Orthologs

Ortholog group members (OG5_130885)

Species Accession Gene Product
Arabidopsis thaliana AT2G26930   4-diphosphocytidyl-2-C-methyl-D-erythritol kinase
Babesia bovis BBOV_II007070   hypothetical protein
Chlamydia trachomatis CT_804   4-diphosphocytidyl-2-C-methyl-D-erythritol kinase
Escherichia coli b1208   4-diphosphocytidyl-2-C-methylerythritol kinase
Mycobacterium leprae ML0242   Probable 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase IspE (CMK) (4-(cytidine-5'-diphospho)-2-C-methyl-D-erythritol kinase)
Mycobacterium tuberculosis Rv1011   Probable 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase IspE (CMK) (4-(cytidine-5'-diphospho)-2-C-methyl-D-erythritol kinase)
Mycobacterium ulcerans MUL_4649   4-diphosphocytidyl-2-C-methyl-D-erythritol kinase
Oryza sativa 4327968   Os01g0802100
Plasmodium berghei PBANKA_1102800   4-diphosphocytidyl-2-C-methyl-D-erythritol kinase, putative
Plasmodium falciparum PF3D7_0503100   4-diphosphocytidyl-2-C-methyl-D-erythritol kinase, putative
Plasmodium knowlesi PKNH_1030800   4-diphosphocytidyl-2-C-methyl-D-erythritol kinase, putative
Plasmodium vivax PVX_097660   4-diphosphocytidyl-2-C-methyl-D-erythritol kinase, putative
Plasmodium yoelii PY04665   4-diphosphocytidyl-2-c-methyl-d-erythritol kinase (ec 2.7.1.148) (cmk) (4-(cytidine-5'-diphospho)-2-c-methyl-d-erythritol kinase
Treponema pallidum TP0371   hypothetical protein
Theileria parva TP02_0681   4-diphosphocytidyl-2C-methyl-D-erythritol kinase, putative
Wolbachia endosymbiont of Brugia malayi Wbm0173   4-diphosphocytidyl-2-C-methyl-D-erythritol kinase

Essentiality

PF3D7_0503100 has one or more orthologs with essentiality data
Gene/Ortholog Organism Phenotype Source Study
b1208 Escherichia coli essential goodall
PBANKA_1102800 Plasmodium berghei Essential plasmo
Show/Hide essentiality data references
  • 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
  • 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.
  • 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
  • wormbase C. elegans RNAi experiments WormBase web site, http://www.wormbase.org, release WS170
  • nmpdr Genome-scale essentiality datasets from published studies (M. tuberculosis) National Microbial Pathogen Data Resource
  • 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.
  • blattner Systematic mutagenesis of the E. coli (MG1655) genome J Bacteriol 2004, 186:4921-4930

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
Yersinia pestis 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase Compounds References
Solanum lycopersicum 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase, chloroplastic/chromoplastic Compounds References
Arabidopsis thaliana 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase Compounds References
Escherichia coli 4-diphosphocytidyl-2-C-methylerythritol kinase 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
0.0143 0.3151 0.5
0.0314 0.4093 0.5
0.0164 0.7842 0
0.0297 0.6879 1
0.0291 0.6951 0.5
0.0145 0.474 0.5
0.0175 0.3684 0.5
0.0289 0.6694 1
0.0141 0.5569 0.5
0.0151 0.4879 1
0.0144 0.5964 0.5
0.0145 0.474 0.5
0.0144 0.3104 1
0.0142 0.8515 0.5
0.0172 0.4262 0.3579
0.0169 0.5261 1
0.0138 0.586 0.5
0.0175 0.299 0.5
0.0146 0.313 1
0.0296 0.611 0.5
0.0242 0.3646 1

Assayability

Assay information

No assay information for this target.

Reagent availability

No reagent availability information for this target.

Bibliographic References

56 literature references were collected for this gene.

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_0503100 (Plasmodium falciparum), 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase, putative
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