Detailed view for PF3D7_1122800

Basic information

TDR Targets ID: 1708
Plasmodium falciparum, calcium-dependent protein kinase 6
Source Database / ID:  PlasmoDB   |   GeneDB   |   MPMP

pI: 5.166 | Length (AA): 1617 | MW (Da): 191814 | 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

PF00069   Protein kinase domain
PF13202   EF hand

Gene Ontology

Mouse over links to read term descriptions.
GO:0005524   ATP binding  
GO:0005509   calcium ion binding  
GO:0004713   protein tyrosine kinase activity  
GO:0004674   protein serine/threonine kinase activity  
GO:0004672   protein kinase activity  
GO:0006468   protein amino acid phosphorylation  

Metabolic Pathways

This gene is not mapped to any metabolic pathway in KEGG.

Structural information

Modbase 3D models:

There are 27 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
1004 1617 1omw (A) 45 651 17.00 0 1 0.19 0.16
1467 1539 1f54 (A) 1 75 27.00 0.00000014 0.99 0.54 -1.69
214 815 1vqq (A) 31 665 25.00 0.7 0.78 0.183394 1.78
285 426 3fby (A) 354 483 32.00 0.013 0.05 0.0869169 1.67
333 485 2ap3 (A) 26 184 25.00 0.95 0.15 0.31062 -0.54
980 1381 2j0k (A) 119 631 28.00 0.00000094 1 0.175709 1.24
1068 1443 2fo0 (A) 140 525 23.00 0 1 0.351529 0.98
1148 1616 3lij (A) 38 512 31.00 0 1 0.649043 -0.52
1169 1432 3is5 (A) 126 395 50.00 0.00000045 1 0.631165 -0.69
1184 1385 4clj (A) 1122 1342 31.00 0.00000017 1 0.434023 -0.08
1219 1375 4uya (A) 168 346 36.00 0.00002 1 0.335193 0.13
1231 1431 4x7q (B) 96 287 26.00 0.000073 1 0.456404 -0.81
1439 1617 3mse (B) 1 179 99.99 0 1 1.1998 -0.68
1475 1533 4gft (A) 141 199 21.00 0.72 1 0.491487 -1.98
138 888 3vuo (A) 244 1140 25.00 0.079 0.78 0.341597 1.76
306 501 1yo8 (A) 725 962 32.00 0.0038 0.02 -0.0746293 2
319 471 2ap3 (A) 26 184 26.00 0.9 0.1 0.342546 -0.76
966 1367 2j0k (A) 119 631 28.00 0.000001 1 0.17788 1.24
1002 1409 3vs1 (A) 92 511 20.00 0.16 1 0.257423 0.93
1134 1602 3lij (A) 38 512 31.00 0 1 0.651376 -0.52
1155 1418 3is5 (A) 126 395 50.00 0.0000021 1 0.619591 -0.69
1169 1362 4nst (A) 732 939 31.00 0.00000000061 1 0.467123 -0.05
1170 1371 4clj (A) 1122 1342 31.00 0.00000018 1 0.435114 -0.08
1205 1361 4uya (A) 168 346 36.00 0.000022 1 0.336041 0.13
1217 1417 4x7q (B) 96 287 26.00 0.000078 1 0.45749 -0.81
1425 1603 3mse (B) 1 179 99.99 0 1 1.20077 -0.68
1461 1519 4gft (A) 141 199 21.00 0.74 1 0.491606 -1.98

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:

PDB tag
  • 3MSE:
  • Resolution Method # Atoms # Residues Dep. Date Pub. Date Mod. Date

Expression

Upregulation Percent Ranking Stage Dataset
Upper 80-100% percentile sporozoite, early ring, late schizont, Sporozoite. PlasmoDB Zanghi G
Upregulation Percent Ranking Stage Dataset
Upper 60-80% percentile gametocyte, merozoite, early schizont, early trophozoite, late ring, late trophozoite, Ring. PlasmoDB Zanghi G
Upregulation Percent Ranking Stage Dataset
Mid 40-60% percentile intra-erythrocytic - 8 hs, intra-erythrocytic - 16 hs, Oocyst, Female Gametocyte. Otto TD Zanghi G Lasonder E
Upregulation Percent Ranking Stage Dataset
Lower 20-40% percentile intra-erythrocytic - 0 hs, intra-erythrocytic - 24 hs, intra-erythrocytic - 40 hs. Otto TD
Upregulation Percent Ranking Stage Dataset
Lower 0-20% percentile intra-erythrocytic - 32 hs, intra-erythrocytic - 48 hs, Male Gametocyte. Otto TD Lasonder E
Show/Hide expression data references
  • 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.
  • Lasonder E Integrated transcriptomic and proteomic analyses of P. falciparum gametocytes. Molecular insight into sex-specific processes and translational repression.
  • Zanghi G A Specific PfEMP1 Is Expressed in P. falciparum Sporozoites and Plays a Role in Hepatocyte Infection.

Orthologs

Ortholog group members (OG5_146625)

Species Accession Gene Product
Cryptosporidium hominis Chro.40377   hypothetical protein
Cryptosporidium parvum cgd4_3330   hypothetical protein
Neospora caninum NCLIV_061660   CAM kinase, CDPK family, putative
Plasmodium berghei PBANKA_0925500   calcium-dependent protein kinase 6
Plasmodium falciparum PF3D7_1122800   calcium-dependent protein kinase 6
Plasmodium knowlesi PKNH_0920600   calcium-dependent protein kinase 6, putative
Plasmodium vivax PVX_091755   calcium-dependent protein kinase 6, putative
Plasmodium yoelii PY04265   Plasmodium falciparum CDPK2 protein-related
Toxoplasma gondii TGME49_218720   calcium-dependent protein kinase CDPK6

Essentiality

PF3D7_1122800 has one or more orthologs with essentiality data
Gene/Ortholog Organism Phenotype Source Study
PBANKA_0925500 Plasmodium berghei Slow plasmo
TGME49_218720 Toxoplasma gondii Essentiality uncertain sidik
Show/Hide essentiality data references
  • 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.
  • wormbase C. elegans RNAi experiments WormBase web site, http://www.wormbase.org, release WS170
  • gerdes Experimental determination and system-level analysis of essential genes in E. coli MG1655 Gerdes et al., J Bacteriol. 2003 185:5673-84
  • 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
  • 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
  • alsford High-throughput phenotyping using parallel sequencing of RNA interference targets in the African trypanosome Genome Res 2011, 21:915-924
  • 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
  • shigen Profiling of E. coli Chromosome (PEC) National Institute of Genetics, Japan
  • 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

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
Non orthologous druggable targets
By sequence similarity to non orthologous druggable targets
Species Target Length Identity Alignment span Linked Drugs Reference
Patiria pectinifera Cdc2 300 aa 27.4% 241 aa Compounds References
Oryctolagus cuniculus Cyclin-dependent kinase 4 189 aa 30.1% 156 aa Compounds References
Rattus norvegicus MAP kinase p38 alpha 360 aa 28.8% 292 aa Compounds References
Rattus norvegicus Cell division protein kinase 5 292 aa 28.7% 244 aa Compounds References
Rattus norvegicus Mitogen-activated protein kinase 1 358 aa 27.7% 310 aa Compounds References
Plasmodium falciparum (isolate 3D7) Cell division control protein 2 homolog 288 aa 27.7% 289 aa Compounds References
Zea mays CaM kinase I alpha 492 aa 29.2% 414 aa Compounds References
Homo sapiens Cyclin-dependent kinase 1/cyclin B1 297 aa 30.0% 240 aa Compounds References
Obtained from network model

Ranking Plot

Putative Drugs List

Compound Raw Global Species
0.0016 0.5 0.5
0.0032 0.5 0.5
0.0059 1 1
0.0033 0.5 0.5
0.0007 0.5 0.5
0.0059 1 1
0.0064 0.3377 0
0.0007 0.5 0.5
0.0012 0.5 0.5
0.0011 1 0.5
0.0023 0.5 0.5
0.0037 1 0.5
0.0018 0.5 0.5
0.0029 0.5 0.5
0.0093 0.8828 0
0.0062 0.6935 0
0.0088 0.4477 0.5
0.0056 1 0.5
0.0063 1 1
0.0016 0.5 0.5
0.0012 0.5 0.5
0.0098 0.3242 0.2614
0.0067 0.5 0.5
0.0039 0.5 0.5
0.0042 0.5 0.5
0.0059 1 1
0.0081 0.5 0.5
0.0004 0.5 0.5
0.0066 0.3101 0
0.0081 1 0.5
0.0008 0.5 0.5
0.0036 0.5 0.5
0.0022 0.5 0.5
0.0033 1 1
0.0039 0.9485 0.5
0.0063 0.7244 0.7244
0.0039 0.5 0.5
0.0061 0.6883 1
0.0003 0.5 0.5
0.0007 0.5 0.5
0.0092 1 0.5
0.0091 1 0.5
0.0026 0.5 0.5
0.0032 0.5 0.5
0.0069 0.3067 1
0.0012 0.5 0.5
0.0027 1 0.5

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.

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_1122800 (Plasmodium falciparum), calcium-dependent protein kinase 6
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