Detailed view for PF3D7_1368800

Basic information

TDR Targets ID: 267
Plasmodium falciparum, DNA repair endonuclease, putative
Source Database / ID:  PlasmoDB   |   GeneDB   |   MPMP

pI: 7.7653 | Length (AA): 1700 | MW (Da): 204533 | Paralog Number: 0

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

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:0005515   protein binding  
GO:0004518   nuclease activity  
GO:0003677   DNA binding  
GO:0019058   viral infectious cycle  
GO:0008037   cell recognition  
GO:0007155   cell adhesion  
GO:0006281   DNA repair  
GO:0006259   DNA metabolic process  

Metabolic Pathways

Nucleotide excision repair (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
1345 1424 2bgw (A) 18 97 35.00 0.0000092 1 0.68 -1.97
1346 1480 1j23 (A) 5 134 25.00 0 0.96 0.61 -2.3
160 350 2p6r (A) 4 184 11.00 0.18 0.05 0.0224529 0.22
530 751 4o87 (A) 18 264 29.00 0.38 0.98 0.209988 1
995 1180 4uos (A) 3 184 8.00 0.018 0 0.181512 -0.75
1349 1481 1j23 (A) 8 135 25.00 0.015 0.9 0.441035 -0.96
1638 1700 2aq0 (A) 11 74 30.00 0.00071 1 0.516159 -1.52
45 293 5czz (A) 626 923 29.00 0.44 0.64 0.085359 1.55
536 757 4o87 (A) 18 264 29.00 0.42 0.98 0.208597 1
1354 1486 1j23 (A) 8 135 25.00 0.036 0.9 0.441342 -0.96
1641 1713 2aq0 (A) 1 74 29.00 0.00045 1 0.523515 -1.53

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 60-80% percentile early schizont, late schizont, late trophozoite. PlasmoDB
Upregulation Percent Ranking Stage Dataset
Mid 40-60% percentile intra-erythrocytic - 32 hs, gametocyte, early trophozoite, Female Gametocyte, Male Gametocyte. Otto TD PlasmoDB Lasonder E
Upregulation Percent Ranking Stage Dataset
Lower 20-40% 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, Oocyst, Ring, Sporozoite. Otto TD Zanghi G
Show/Hide expression data references
  • Lasonder E Integrated transcriptomic and proteomic analyses of P. falciparum gametocytes. Molecular insight into sex-specific processes and translational repression.
  • 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
  • Zanghi G A Specific PfEMP1 Is Expressed in P. falciparum Sporozoites and Plays a Role in Hepatocyte Infection.

Orthologs

Ortholog group members (OG5_127977)

Species Accession Gene Product
Arabidopsis thaliana AT5G41150   DNA repair endonuclease UVH1
Babesia bovis BBOV_IV002550   DNA repair endonuclease, putative
Brugia malayi Bm1_46945   ERCC4 domain containing protein
Candida albicans CaO19.12779   UV endonuclease
Candida albicans CaO19.5319   UV endonuclease
Candida albicans CaO19.5318   UV endonuclease
Candida albicans CaO19.12778   UV endonuclease
Caenorhabditis elegans CELE_C47D12.8   Protein C47D12.8
Cryptosporidium hominis Chro.40338   UV endonuclease; Rad1p
Cryptosporidium parvum cgd4_2960   ERCC4/XP-G-type excision repair nuclease
Cryptosporidium parvum cgd4_2970   RAD1, NH2 terminal ERCC4-like helicase domain
Dictyostelium discoideum DDB_G0284419   DNA excision repair protein 4
Drosophila melanogaster Dmel_CG3697   meiotic 9
Echinococcus granulosus EgrG_000580700   dna repair endonuclease xpf
Entamoeba histolytica EHI_148310   DNA repair endonuclease, putative
Echinococcus multilocularis EmuJ_000580700   dna repair endonuclease xpf
Homo sapiens ENSG00000175595   excision repair cross-complementation group 4
Loa Loa (eye worm) LOAG_00528   ERCC4 domain-containing protein
Mus musculus 50505   excision repair cross-complementing rodent repair deficiency, complementation group 4
Neospora caninum NCLIV_043890   Protein C47D12.8, partially confirmed by transcript evidence, related
Oryza sativa 4331279   Os03g0100400
Plasmodium berghei PBANKA_1144700   DNA repair endonuclease, putative
Plasmodium falciparum PF3D7_1368800   DNA repair endonuclease, putative
Plasmodium knowlesi PKNH_1102400   DNA repair endonuclease, putative
Plasmodium vivax PVX_115400   DNA repair endonuclease, putative
Plasmodium yoelii PY04288   DNA repair endonuclease, subunit
Saccharomyces cerevisiae YPL022W   Rad1p
Schistosoma japonicum Sjp_0081630   ko:K01175 excision repair cross-complementing rodent repair deficiency, complementation group 4 [EC:3.1.-.-], putative
Schistosoma japonicum Sjp_0099170   ko:K01175 excision repair cross-complementing rodent repair deficiency, complementation group 4 [EC:3.1.-.-], putative
Schistosoma mansoni Smp_153770   DNA repair endonuclease xp-f / mei-9 / rad1
Schmidtea mediterranea mk4.000684.11   DNA repair endonuclease XPF
Schmidtea mediterranea mk4.000684.10  
Schmidtea mediterranea mk4.000684.07   DNA repair endonuclease XPF
Toxoplasma gondii TGME49_305310   ERCC4 domain-containing protein
Theileria parva TP03_0395   DNA repair endonuclease, putative
Trichomonas vaginalis TVAG_447530   nuclease Rad1

Essentiality

PF3D7_1368800 has one or more orthologs with essentiality data
Gene/Ortholog Organism Phenotype Source Study
CELE_C47D12.8 Caenorhabditis elegans embryonic lethal wormbase
CELE_C47D12.8 Caenorhabditis elegans slow growth wormbase
PBANKA_1144700 Plasmodium berghei Slow plasmo
TGME49_305310 Toxoplasma gondii Essentiality uncertain sidik
Show/Hide essentiality data references
  • alsford High-throughput phenotyping using parallel sequencing of RNA interference targets in the African trypanosome Genome Res 2011, 21:915-924
  • 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.
  • yeastgenome Systematic deletion of yeast genes Saccharomyces Genome Database
  • nmpdr Genome-scale essentiality datasets from published studies (M. tuberculosis) National Microbial Pathogen Data Resource
  • keio Systematic single-gene knock-out mutants of E. coli K12 The Keio Collection
  • 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
  • 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
  • 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.
  • 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

Druggability index (range: 0 to 1): 0.5

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
Homo sapiens excision repair cross-complementation group 4 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
0.0036 0.3379 0
0.00451601 0.334418 0
0.0035 0.3379 0.0301
0.0041 0.5661 0.5661
0.0041 0.3379 0
0.0041 0.5661 0.5661
0.0041 0.3379 0
0.0041 0.5661 0.5661
0.0033 0.3379 0
0.0041 0.4144 0.2739
0.0041 0.3379 0
0.0041 0.3379 0
0.0041 0.5661 0.5661
0.0041 0.3379 0
0.026 0.5661 0.5661
0.0041 0.5661 0.5661
0.00485664 0.563385 0.563385
0.0033 0.5661 0.5661
0.0041 0.3379 0
0.0034 0.3379 0
0.0036 0.5661 0.5661
0.0037 0.3379 0
0.0041 0.3379 0
0.0041 0.3379 0
0.0262 0.5661 0.5661
0.0041 0.3379 0
0.0041 0.3379 0
0.0041 0.5661 0.5661
0.0041 0.3379 0
0.0041 0.5661 0.5661
0.0034 0.5661 0.5661
0.0041 0.3379 0
0.0041 0.3379 0
0.0041 0.5661 0.5661
0.0243 0.5835 0.5835
0.0037 0.3379 0
0.0036 0.3379 0
0.0041 0.3379 0
0.0041 0.5661 0.5661
0.0298 0.4485 0.6038
0.0033 0.3379 0
0.0033 0.5793 0.5661
0.0101 0.5661 0.5661
0.0041 0.3379 0
0.0041 0.3379 0
0.0033 0.5661 0.5661
0.0041 0.3379 0
0.0041 0.5661 0.5661
0.00493821 0.52505 0.52505
0.0041 0.3379 0
0.0041 0.3379 0
0.0033 0.3379 0
0.0041 0.3379 0
0.0214 0.4652 0.6202
0.0298 0.4485 0.6038
0.0041 0.3379 0
0.0041 0.3379 0
0.0041 0.5661 0.5661
0.0041 0.3379 0
0.0033 0.3379 0
0.0041 0.3379 0
0.0041 0.3379 0
0.014 0.2562 0
0.0041 0.3379 0
0.0041 0.5661 0.5661
0.0101 0.3379 0
0.0135 0.579 0.5661
0.0041 0.3379 0
0.0041 0.3379 0
0.0041 0.3379 0
0.0041 0.3379 0
0.00478288 0.502511 0.123058
0.0257 0.5835 0.5835
0.0041 0.3379 0
0.0041 0.3379 0
0.0041 0.5661 0.5661
0.0041 0.3379 0
0.0041 0.3379 0
0.0261 0.5888 0.5888
0.0041 0.5661 0.5661
0.0041 0.5661 0.5661
0.0041 0.5661 0.5661
0.0041 0.3379 0
0.0041 0.3379 0
0.0041 0.3379 0
0.0033 0.5541 0.5541
0.0162 0.3526 0.5661
0.0041 0.3379 0
0.0072 0.3379 0
0.0041 0.3379 0

Assayability

Assay information

No assay information for this target.

Reagent availability

No reagent availability information for this target.

Bibliographic References

1 literature reference was collected for this gene.

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_1368800 (Plasmodium falciparum), DNA repair endonuclease, putative
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