Detailed view for PF3D7_0403900

Basic information

TDR Targets ID: 3815
Plasmodium falciparum, SET domain protein, putative
Source Database / ID:  PlasmoDB   |   GeneDB   |   MPMP

pI: 8.5462 | Length (AA): 1186 | MW (Da): 142738 | 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

PF00856   SET domain

Gene Ontology

Mouse over links to read term descriptions.
GO:0005515   protein binding  

Metabolic Pathways

Lysine degradation (KEGG)

Structural information

Modbase 3D models:

There are 17 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
32 956 1epw (A) 284 1284 20.00 0 0.83 0.67 1.64
1017 1186 1zkk (A) 201 352 39.00 0 1 0.33 -0.22
400 714 2fds (A) 22 324 21.00 0.014 0.76 0.419699 0.13
437 706 4hte (A) 262 557 29.00 0.98 0.29 0.193056 0.95
514 714 4tql (A) 27 228 13.00 0.22 0.04 0.357877 -0.86
951 1175 4ldg (A) 17 266 37.00 0 1 0.507813 0.13
997 1170 2r3a (A) 99 261 29.00 0.018 1 0.187112 0.71
1015 1186 3f9x (A) 199 352 40.00 0 1 0.484125 0.02
1032 1170 4h12 (A) 1550 1666 29.00 0.31 1 0.245601 0.73
1041 1170 4mi0 (A) 621 726 38.00 0.026 1 0.231012 0.8
21 265 4tql (A) 9 238 18.00 0.34 0.48 0.286265 -0.2
223 430 4kik (A) 451 659 11.00 0 0.03 -0.0182496 -0.23
444 713 4hte (A) 262 557 29.00 0.98 0.29 0.19012 0.95
510 1012 5czz (A) 483 1027 22.00 0.85 0.74 0.355426 1.6
925 1188 3k5k (A) 929 1165 24.00 0.0000000087 1 0.177191 1.47
958 1182 4ldg (A) 17 266 37.00 0 1 0.4985 0.13
1021 1193 3f9x (A) 199 352 41.00 0 1 0.451913 0.26

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, Sporozoite, Male Gametocyte. PlasmoDB Zanghi G Lasonder E
Upregulation Percent Ranking Stage Dataset
Mid 40-60% percentile intra-erythrocytic - 0 hs, intra-erythrocytic - 8 hs, intra-erythrocytic - 40 hs, intra-erythrocytic - 48 hs, gametocyte, merozoite, Female Gametocyte. Otto TD PlasmoDB Lasonder E
Upregulation Percent Ranking Stage Dataset
Lower 20-40% percentile intra-erythrocytic - 16 hs, intra-erythrocytic - 24 hs, intra-erythrocytic - 32 hs, early trophozoite, Oocyst, Ring. Otto TD PlasmoDB 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.
  • 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.
  • Zanghi G A Specific PfEMP1 Is Expressed in P. falciparum Sporozoites and Plays a Role in Hepatocyte Infection.

Orthologs

Ortholog group members (OG5_130816)

Species Accession Gene Product
Babesia bovis BBOV_IV004680   SET domain containing protein
Brugia malayi Bm1_00260   Protein set-1
Caenorhabditis elegans CELE_T26A5.7   Protein SET-1, isoform B
Cryptosporidium hominis Chro.40051   SET domain
Cryptosporidium parvum cgd4_370   protein with a SET domain within carboxy region
Drosophila melanogaster Dmel_CG3307   CG3307 gene product from transcript CG3307-RB
Echinococcus granulosus EgrG_001031500   histone lysine n methyltransferase setd8
Echinococcus multilocularis EmuJ_001031500   histone lysine n methyltransferase setd8
Homo sapiens ENSG00000183955   SET domain containing (lysine methyltransferase) 8
Loa Loa (eye worm) LOAG_02341   hypothetical protein
Mus musculus ENSMUSG00000049327   SET domain containing (lysine methyltransferase) 8
Neospora caninum NCLIV_011360   SET domain-containing protein, putative
Plasmodium berghei PBANKA_1001600   SET domain protein, putative
Plasmodium falciparum PF3D7_0403900   SET domain protein, putative
Plasmodium knowlesi PKNH_0301900   SET domain protein, putative
Plasmodium vivax PVX_001050   SET domain protein, putative
Plasmodium yoelii PY01349   SET domain, putative
Schistosoma japonicum Sjp_0109250   IPR001214,SET,domain-containing
Schistosoma japonicum Sjp_0018990   Histone-lysine N-methyltransferase SETD8, putative
Schistosoma mansoni Smp_055310   histone-lysine n-methyltransferase seto7
Schmidtea mediterranea mk4.004321.01   SETD8-1
Toxoplasma gondii TGME49_211730   histone lysine methyltransferase SET8
Theileria parva TP01_0281   hypothetical protein

Essentiality

PF3D7_0403900 has one or more orthologs with essentiality data
Gene/Ortholog Organism Phenotype Source Study
CELE_T26A5.7 Caenorhabditis elegans embryonic lethal wormbase
CELE_T26A5.7 Caenorhabditis elegans larval arrest wormbase
CELE_T26A5.7 Caenorhabditis elegans larval lethal wormbase
CELE_T26A5.7 Caenorhabditis elegans slow growth wormbase
PBANKA_1001600 Plasmodium berghei Slow plasmo
TGME49_211730 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
  • 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.
  • 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
  • yeastgenome Systematic deletion of yeast genes Saccharomyces Genome Database
  • shigen Profiling of E. coli Chromosome (PEC) National Institute of Genetics, Japan
  • blattner Systematic mutagenesis of the E. coli (MG1655) genome J Bacteriol 2004, 186:4921-4930
  • 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.
  • 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.
  • neb C. elegans RNAi phenotypes Data obtained from Wormbase WS150, curated by K. Chaudary and T. Carlow, New England Biolabs

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
Homo sapiens SET domain containing (lysine methyltransferase) 8 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
0.0403 1 1
0.0403 1 1
0.0079 0.5 0.5
0.0193 0.2616 1
0.0589 0.4049 1
0.0548 0.743 1
0.0394 0.8214 1
0.0578 0.3861 1
0.0146 1 1
0.0391 0.76 1
0.0579 0.7829 1
0.0496 0.5854 1
0.0588 0.295 1
0.0573 0.3891 1
0.0385 0.5 0.5
0.0579 0.3373 1
0.0391 0.76 1
0.0079 0.5 0.5
0.0193 0.4031 1
0.0079 0.5 0.5
0.0401 1 0.5
0.0583 0.395 1
0.0079 0.5 0.5
0.0479 0.5 0.5
0.0417 0.7389 0.5
0.0404 0.3283 1
0.0063 0.4053 1
0.0561 0.8186 1
0.0605 1 1
0.0565 0.7066 1
0.0548 0.743 1
0.0473 0.2915 1
0.0417 0.6888 1
0.0399 0.5423 0.8835
0.0473 0.2915 1
0.0371 0.5 0.5
0.0064 0.2983 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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Gene identifier PF3D7_0403900 (Plasmodium falciparum), SET domain protein, putative
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