Detailed view for LmjF.35.4770

Basic information

TDR Targets ID: 21204
Leishmania major, cyclophilin 40
Source Database / ID:  TriTrypDB  GeneDB

pI: 5.6468 | Length (AA): 354 | MW (Da): 38420 | Paralog Number: 0

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

Druggability Group : DG2

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

PF00160   Cyclophilin type peptidyl-prolyl cis-trans isomerase/CLD

Gene Ontology

Mouse over links to read term descriptions.
GO:0000413   protein peptidyl-prolyl isomerization  
GO:0005488   binding  
GO:0003755   peptidyl-prolyl cis-trans isomerase activity  
GO:0005515   protein binding  
GO:0006457   protein folding  

Metabolic Pathways

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

Structural information

Modbase 3D models:

There are 6 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
2 349 1ihg (A) 14 365 43.00 0 1 1.48 -0.6
3 175 1mzw (A) 10 177 51.00 0 1 1.22 -1.54
2 349 1ihg (A) 14 365 40.00 0 1 1.48065 -0.44
3 176 5f66 (A) 3 165 60.00 0 1 1.26693 -1.42
3 175 1mzw (A) 10 177 52.00 0 1 1.2371 -1.55
289 337 2vsy (A) 21 69 18.00 0 0.59 0.505118 -1.45

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 amastigotes, metacyclic. Fernandes MC
Show/Hide expression data references
  • Fernandes MC Dual Transcriptome Profiling of Leishmania-Infected Human Macrophages Reveals Distinct Reprogramming Signatures.

Orthologs

Ortholog group members (OG5_129059)

Species Accession Gene Product
Arabidopsis thaliana AT2G15790   peptidyl-prolyl cis-trans isomerase CYP40
Candida albicans CaO19.7654   likely cyclophilin type peptidyl-prolyl cis-trans isomerase similar to S. cerevisiae CPR6 (YLR216C)
Dictyostelium discoideum DDB_G0283663   cyclophilin-type peptidylprolyl cis-trans isomerase
Drosophila melanogaster Dmel_CG8336   CG8336 gene product from transcript CG8336-RB
Entamoeba histolytica EHI_125840   peptidyl-prolyl cis-trans isomerase, putative
Homo sapiens ENSG00000171497   peptidylprolyl isomerase D
Leishmania braziliensis LbrM.34.4730   cyclophilin 40
Leishmania donovani LdBPK_354830.1   peptidyl-prolyl cis-trans isomerase (cyclophilin- 40), putative
Leishmania infantum LinJ.35.4830   cyclophilin 40
Leishmania major LmjF.35.4770   cyclophilin 40
Leishmania mexicana LmxM.34.4770   peptidyl-prolyl cis-trans isomerase (cyclophilin- 40), putative
Mus musculus ENSMUSG00000027804   peptidylprolyl isomerase D (cyclophilin D)
Oryza sativa 4330806   Os02g0761100
Oryza sativa 4340493   Os06g0216800
Saccharomyces cerevisiae YLR216C   peptidylprolyl isomerase CPR6
Trypanosoma brucei gambiense Tbg972.9.5630   peptidyl-prolyl cis-trans isomerase (cyclophilin- 40), putative,cyclophilin-40, putative
Trypanosoma brucei Tb927.9.9780   peptidyl-prolyl cis-trans isomerase (cyclophilin- 40), putative
Trypanosoma cruzi TcCLB.506885.400   40 kDa cyclophilin, putative
Trypanosoma cruzi TcCLB.503687.40   rotamase, putative
Trichomonas vaginalis TVAG_004440   cyclophillin, putative

Essentiality

LmjF.35.4770 has one or more orthologs with essentiality data
Gene/Ortholog Organism Phenotype Source Study
Tb09.211.1350 Trypanosoma brucei no significant loss or gain of fitness in bloodstream forms (3 days) alsford
Tb09.211.1350 Trypanosoma brucei no significant loss or gain of fitness in bloodstream forms (6 days) alsford
Tb09.211.1350 Trypanosoma brucei no significant loss or gain of fitness in procyclic forms alsford
Tb09.211.1350 Trypanosoma brucei no significant loss or gain of fitness in differentiation of procyclic to bloodstream forms alsford
Show/Hide essentiality data references
  • 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.
  • shigen Profiling of E. coli Chromosome (PEC) National Institute of Genetics, Japan
  • 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
  • yeastgenome Systematic deletion of yeast genes Saccharomyces Genome Database
  • neb C. elegans RNAi phenotypes Data obtained from Wormbase WS150, curated by K. Chaudary and T. Carlow, New England Biolabs
  • 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
  • gerdes Experimental determination and system-level analysis of essential genes in E. coli MG1655 Gerdes et al., J Bacteriol. 2003 185:5673-84
  • 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
  • keio Systematic single-gene knock-out mutants of E. coli K12 The Keio Collection

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 peptidylprolyl isomerase D Compounds References
By sequence similarity to non orthologous druggable targets
Species Target Length Identity Alignment span Linked Drugs Reference
Plasmodium falciparum peptidyl-prolyl cis-trans isomerase 171 aa 50.9% 169 aa Compounds References
Rattus norvegicus Cyclophilin A 164 aa 54.3% 175 aa Compounds References
Obtained from network model

Ranking Plot

Putative Drugs List

Compound Raw Global Species
0.0064 0.3832 1
0.00691212 0.5 0.5
0.0063 0.5 0.5
0.0329 0.5424 1
0.0064 0.3832 1
0.0051 0.5 0.5
0.0056 0.3832 1
0.0277 0.3943 1
0.0103 0.9952 1
0.0052 1 0.5
0.0112 0.2729 0.9937
0.0165 0.4849 1
0.0063 0.4706 0.5
0.0179 0.4616 1
0.0064 0.3832 1
0.0178 0.4623 1
0.0064 0.3832 1
0.0181131 0.282723 0.282723

Assayability

Assay information

  • Assay for FK-Binding Protein Peptidyl-Prolyl Isomerase Activity (5.2.1.8 ) Sigma-Aldrich
  • Automatic link to known assays based on EC numbers.

Reagent availability

No reagent availability information for this target.

Bibliographic References

5 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.

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Gene identifier LmjF.35.4770 (Leishmania major), cyclophilin 40
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