Detailed view for Rv3315c

Basic information

TDR Targets ID: 5733
Mycobacterium tuberculosis, Probable cytidine deaminase Cdd (cytidine aminohydrolase) (cytidine nucleoside deaminase)
Source Database / ID:  Tuberculist 

pI: 6.0601 | Length (AA): 133 | MW (Da): 14072 | Paralog Number: 0

Signal peptide: N | GPI Anchor: | 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

PF00383   Cytidine and deoxycytidylate deaminase zinc-binding region

Gene Ontology

Mouse over links to read term descriptions.
GO:0016787   hydrolase activity  
GO:0008270   zinc ion binding  
GO:0004126   cytidine deaminase activity  
GO:0003824   catalytic activity  
GO:0046087   cytidine metabolic process  

Structural information

Modbase 3D models:

There are 2 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
3 128 4wig (A) 3 128 99.00 0 1 2.08757 -0.56
4 122 4f3w (A) 4 122 80.00 0 1 1.85894 -0.71

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
  • 3IJF:
  • Resolution Method # Atoms # Residues Dep. Date Pub. Date Mod. Date
PDB tag
  • 3MPZ:
  • Resolution Method # Atoms # Residues Dep. Date Pub. Date Mod. Date
PDB tag
  • 4WIF:
  • Resolution Method # Atoms # Residues Dep. Date Pub. Date Mod. Date
PDB tag
  • 4WIG:
  • Resolution Method # Atoms # Residues Dep. Date Pub. Date Mod. Date

Expression

Upregulation Percent Ranking Stage Dataset
Upper 80-100% percentile Dormant phase. murphy
Upregulation Percent Ranking Stage Dataset
Upper 60-80% percentile Dormant phase. hasan
Show/Hide expression data references
  • murphy Identification of gene targets against dormant phase Mycobacterium tuberculosis infections.
  • hasan Prioritizing genomic drug targets in pathogens: application to Mycobacterium tuberculosis.

Orthologs

Ortholog group members (OG5_127381)

Species Accession Gene Product
Arabidopsis thaliana AT2G19570   cytidine deaminase 1
Brugia malayi Bm1_11460   cytidine deaminase, identical
Caenorhabditis elegans CELE_C47D2.2   Protein CDD-1
Caenorhabditis elegans CELE_F49E8.4   Protein CDD-2
Dictyostelium discoideum DDB_G0288933   cytidine deaminase
Drosophila melanogaster Dmel_CG8349   CG8349 gene product from transcript CG8349-RA
Drosophila melanogaster Dmel_CG8353   CG8353 gene product from transcript CG8353-RB
Drosophila melanogaster Dmel_CG8360   CG8360 gene product from transcript CG8360-RC
Escherichia coli b2143   cytidine/deoxycytidine deaminase
Echinococcus granulosus EgrG_000572800   cytidine deaminase
Entamoeba histolytica EHI_012930   cytidine deaminase, putative
Echinococcus multilocularis EmuJ_000572800   cytidine deaminase
Giardia lamblia GL50803_2101   Cytidine deaminase
Homo sapiens ENSG00000158825   cytidine deaminase
Leishmania braziliensis LbrM.17.0340   cytidine deaminase-like protein
Leishmania donovani LdBPK_170410.1   cytidine deaminase-like protein
Leishmania infantum LinJ.17.0410   cytidine deaminase-like protein
Leishmania major LmjF.17.0360   cytidine deaminase-like protein
Leishmania mexicana LmxM.17.0360   cytidine deaminase-like protein
Mycobacterium leprae ML2174   PROBABLE CYTIDINE DEAMINASE CDD (CYTIDINE AMINOHYDROLASE) (CYTIDINE NUCLEOSIDE DEAMINASE)
Mus musculus ENSMUSG00000028755   cytidine deaminase
Mycobacterium tuberculosis Rv3315c   Probable cytidine deaminase Cdd (cytidine aminohydrolase) (cytidine nucleoside deaminase)
Mycobacterium ulcerans MUL_1366   cytidine deaminase
Neospora caninum NCLIV_016250   cytidine deaminase, putative
Oryza sativa 4325937   Os01g0712700
Onchocerca volvulus OVOC12559  
Onchocerca volvulus OVOC1862  
Saccharomyces cerevisiae YLR245C   cytidine deaminase
Schmidtea mediterranea mk4.029758.00   Cytidine deaminase
Schmidtea mediterranea mk4.001536.03   Cytidine deaminase
Schmidtea mediterranea mk4.026379.01   Cytidine deaminase
Schmidtea mediterranea mk4.003249.03   Cytidine deaminase
Trypanosoma brucei gambiense Tbg972.9.1500   cytidine deaminase, putative
Trypanosoma brucei Tb927.9.3000   cytidine deaminase
Trypanosoma congolense TcIL3000_9_900   cytidine deaminase, putative
Trypanosoma cruzi TcCLB.511321.23   cytidine deaminase-like protein
Trypanosoma cruzi TcCLB.510053.60   cytidine deaminase-like protein, putative
Toxoplasma gondii TGME49_239630   cytidine and deoxycytidylate deaminase zinc-binding region domain-containing protein
Trichomonas vaginalis TVAG_070480   cytidine deaminase, putative
Trichomonas vaginalis TVAG_135190   cytidine deaminase, putative

Essentiality

Rv3315c has direct evidence of essentiality
Gene/Ortholog Organism Phenotype Source Study
mtu3375 this record Mycobacterium tuberculosis non-essential nmpdr
Tb09.160.1680 Trypanosoma brucei no significant loss or gain of fitness in bloodstream forms (3 days) alsford
Tb09.160.1680 Trypanosoma brucei significant gain of fitness in bloodstream forms (6 days) alsford
Tb09.160.1680 Trypanosoma brucei significant gain of fitness in procyclic forms alsford
Tb09.160.1680 Trypanosoma brucei significant gain of fitness in differentiation of procyclic to bloodstream forms alsford
b2143 Escherichia coli non-essential goodall
TGME49_239630 Toxoplasma gondii Probably non-essential 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
  • neb C. elegans RNAi phenotypes Data obtained from Wormbase WS150, curated by K. Chaudary and T. Carlow, New England Biolabs
  • 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.

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
Mus musculus cytidine deaminase Compounds References
Homo sapiens cytidine deaminase 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
0.011 1 0.5
0.0226 0.5 0.5
0.0065 0.5 0.5
0.0264 0.5 0.5
0.0559 1 0.5
0.0065 0.5 0.5
0.0185 1 0.5
0.0218 1 0.5
0.0065 0.5 0.5
0.0519 1 1
0.048 1 0.5
0.0065 0.5 0.5
0.0065 0.5 0.5
0.0526 1 1
0.0065 0.5 0.5
0.0123 0.5755 1
0.0065 0.5 0.5
0.0065 0.5 0.5
0.0065 0.5 0.5
0.0335 0.5 0.5
0.0065 0.5 0.5
0.0669 1 1
0.0535 1 1
0.0535 1 1
0.0065 0.5 0.5
0.0065 0.5 0.5
0.0104 0.2574 0.5781
0.0065 0.5 0.5
0.0065 0.5 0.5
0.0118 1 0.5
0.0065 0.5 0.5
0.0186 1 0.5
0.0523 1 1
0.0121 1 1
0.0065 0.5 0.5
0.0122 1 0.5
0.018 1 0.5
0.0186 1 1
0.0161 1 1
0.0065 0.5 0.5
0.0065 0.5 0.5
0.0065 0.5 0.5
0.0057 1 1
0.0816 1 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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User comments

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Gene identifier Rv3315c (Mycobacterium tuberculosis), Probable cytidine deaminase Cdd (cytidine aminohydrolase) (cytidine nucleoside deaminase)
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