Detailed view for Rv1882c

Basic information

TDR Targets ID: 8196
Mycobacterium tuberculosis, Probable short-chain type dehydrogenase/reductase
Source Database / ID:  Tuberculist 

pI: 10.0757 | Length (AA): 277 | MW (Da): 30010 | Paralog Number: 1

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

PF00106   short chain dehydrogenase

Gene Ontology

Mouse over links to read term descriptions.
GO:0016491   oxidoreductase activity  
GO:0005488   binding  
GO:0003824   catalytic activity  
GO:0008152   metabolic process  

Structural information

Modbase 3D models:

There are 5 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 50 3vpx (A) 174 221 21.00 0.24 0.49 0.462495 -0.7
2 274 4yac (A) 7 294 25.00 0 1 1.20916 0.33
2 185 3tox (A) 9 194 39.00 0 1 1.10756 -0.36
2 50 1gpj (A) 168 216 29.00 0.66 0.66 0.511495 -0.42
3 257 3v8b (A) 7 259 30.00 0 1 1.25818 -0.01

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 Dormant phase. hasan
Upregulation Percent Ranking Stage Dataset
Lower 0-20% percentile Dormant phase. murphy
Show/Hide expression data references
  • hasan Prioritizing genomic drug targets in pathogens: application to Mycobacterium tuberculosis.
  • murphy Identification of gene targets against dormant phase Mycobacterium tuberculosis infections.

Orthologs

Ortholog group members (OG5_126778)

Species Accession Gene Product
Arabidopsis thaliana AT5G65205   Rossmann-fold NAD(P)-binding domain-containing protein
Arabidopsis thaliana AT5G10050   Rossmann-fold NAD(P)H/NAD(P)(+) binding (NADB) domain-containing protein
Arabidopsis thaliana AT5G50700   hydroxysteroid dehydrogenase 1
Arabidopsis thaliana AT5G50600   hydroxysteroid dehydrogenase 1
Candida albicans CaO19.5615   one of three genes similar to S. cerevisiae AYR1 (YIL124W) 1-Acyl dihydroxyacetone phosphate reductase involved in phosphatidic
Candida albicans CaO19.5879   one of three genes similar to S. cerevisiae AYR1 (YIL124W) 1-Acyl dihydroxyacetone phosphate reductase involved in phosphatidic
Candida albicans CaO19.13300   one of three genes similar to S. cerevisiae AYR1 (YIL124W) 1-Acyl dihydroxyacetone phosphate reductase involved in phosphatidic
Candida albicans CaO19.6167   one of three genes similar to S. cerevisiae AYR1 (YIL124W) 1-Acyl dihydroxyacetone phosphate reductase involved in phosphatidic
Caenorhabditis elegans CELE_F28H7.2   Protein F28H7.2
Dictyostelium discoideum DDB_G0294589   short-chain dehydrogenase/reductase family protein
Dictyostelium discoideum DDB_G0278655   glucose/ribitol dehydrogenase family protein
Dictyostelium discoideum DDB_G0284209   short-chain dehydrogenase/reductase family protein
Dictyostelium discoideum DDB_G0289127   glucose/ribitol dehydrogenase family protein
Dictyostelium discoideum DDB_G0281673   short-chain dehydrogenase/reductase family protein
Dictyostelium discoideum DDB_G0284277   hypothetical protein
Dictyostelium discoideum DDB_G0295807   glucose/ribitol dehydrogenase family protein
Dictyostelium discoideum DDB_G0284429   glucose/ribitol dehydrogenase family protein
Dictyostelium discoideum DDB_G0289129   glucose/ribitol dehydrogenase family protein
Dictyostelium discoideum DDB_G0283935   hypothetical protein
Dictyostelium discoideum DDB_G0286861   hypothetical protein
Dictyostelium discoideum DDB_G0289259   hypothetical protein
Dictyostelium discoideum DDB_G0291674   hypothetical protein
Dictyostelium discoideum DDB_G0285753   hypothetical protein
Dictyostelium discoideum DDB_G0271802   hypothetical protein
Dictyostelium discoideum DDB_G0279545   hypothetical protein
Dictyostelium discoideum DDB_G0275559   glucose/ribitol dehydrogenase family protein
Dictyostelium discoideum DDB_G0269340   short-chain dehydrogenase/reductase family protein
Dictyostelium discoideum DDB_G0292574   glucose/ribitol dehydrogenase family protein
Dictyostelium discoideum DDB_G0289167   hypothetical protein
Dictyostelium discoideum DDB_G0288591   short-chain dehydrogenase/reductase family protein
Dictyostelium discoideum DDB_G0286845   glucose/ribitol dehydrogenase family protein
Dictyostelium discoideum DDB_G0271748   hypothetical protein
Dictyostelium discoideum DDB_G0279783   hypothetical protein
Dictyostelium discoideum DDB_G0284207   short-chain dehydrogenase/reductase family protein
Dictyostelium discoideum DDB_G0272466   glucose/ribitol dehydrogenase family protein
Dictyostelium discoideum DDB_G0290659   short-chain dehydrogenase/reductase family protein
Dictyostelium discoideum DDB_G0291676   hypothetical protein
Dictyostelium discoideum DDB_G0290329   glucose/ribitol dehydrogenase family protein
Dictyostelium discoideum DDB_G0286849   hypothetical protein
Escherichia coli b0493   putative oxidoreductase
Homo sapiens ENSG00000080511   retinol dehydrogenase 8 (all-trans)
Mus musculus ENSMUSG00000053773   retinol dehydrogenase 8
Mycobacterium tuberculosis Rv1882c   Probable short-chain type dehydrogenase/reductase
Mycobacterium tuberculosis Rv3530c   Possible oxidoreductase
Mycobacterium ulcerans MUL_2977   short chain dehydrogenase
Mycobacterium ulcerans MUL_4092   short chain dehydrogenase
Mycobacterium ulcerans MUL_3423   short chain dehydrogenase
Mycobacterium ulcerans MUL_2794   short chain dehydrogenase
Oryza sativa 4335679   Os04g0390800
Oryza sativa 4336030   Os04g0457200
Saccharomyces cerevisiae YIL124W   acylglycerone-phosphate reductase
Schmidtea mediterranea mk4.052776.00  

Essentiality

Rv1882c has direct evidence of essentiality
Gene/Ortholog Organism Phenotype Source Study
this record Mycobacterium tuberculosis non-essential nmpdr
mtu3591 Mycobacterium tuberculosis non-essential nmpdr
b0493 Escherichia coli non-essential goodall
Show/Hide essentiality data references
  • blattner Systematic mutagenesis of the E. coli (MG1655) genome J Bacteriol 2004, 186:4921-4930
  • 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
  • shigen Profiling of E. coli Chromosome (PEC) National Institute of Genetics, Japan
  • 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
  • nmpdr Genome-scale essentiality datasets from published studies (M. tuberculosis) National Microbial Pathogen Data Resource
  • wormbase C. elegans RNAi experiments WormBase web site, http://www.wormbase.org, release WS170
  • 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
  • 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.
  • 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.

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): 0.1

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
Macaca mulatta Hydroxysteroid 11-beta dehydrogenase 1 140 aa 30.2% 139 aa Compounds References
Obtained from network model

Ranking Plot

Putative Drugs List

Compound Raw Global Species
0.0073 0.2873 0.3563
0.0021 0.5 0.5
0.0097 1 1
0.0035 1 0.5
0.0114 1 0.5
0.0009 0.5 0.5
0.0009 0.5 0.5
0.0102 0.7451 0.5
0.0088 0.6544 0.5
0.0132 0.3658 0.376
0.0073 0.3141 0.4101
0.0027 0.5 0.5
0.0097 0.4304 0.5
0.007 0.2916 1
0.0012 0.5 0.5
0.0118 1 0.5
0.0218 0.5 0.5
0.007 1 0.5
0.0165 1 0.5
0.007 0.2916 1
0.0012 0.5 0.5
0.0009 0.5 0.5
0.0073 0.3811 1
0.0057 0.284 0.6413
0.0082 1 0.5
0.0056 0.875 1
0.0056 1 0.5
0.0016 0.5 0.5
0.0013 1 0.5
0.0402 1 1
0.0131 0.5 0.5
0.0089 0.5 0.5
0.0162 1 0.5
0.0108 0.5 0.5
0.0009 0.5 0.5
0.016 0.577 1
0.0073 0.3811 1
0.0004 0.5 0.5
0.0171 0.4063 0.5
0.0021 0.3321 0.5
0.0046 0.3082 0.5
0.0009 0.7374 0.5
0.0119 0.2746 0
0.0196 0.8679 0.5
0.0196 0.8679 0.5
0.0123 0.5 0.5
0.0106 1 0.5
0.0106 0.5 0.5
0.0009 1 0.5
0.0005 0.5 0.5
0.0088 1 0.5
0.0113 1 1
0.0196 0.8679 0.5
0.007 1 0.5
0.008 0.5 0.5
0.0068 1 0.5
0.0019 0.4322 0.5
0.0004 0.5 0.5
0.0106 0.2872 0.4772
0.0004 0.5 0.5
0.0004 0.5 0.5
0.0068 0.2585 0.5
0.0005 0.5 0.5
0.011 0.3568 0.3299
0.0066 0.3586 0.5
0.0067 0.3468 0.5
0.0071 0.3141 0
0.0157 0.5 0.5
0.0222 0.5 0.5
0.016 0.577 1
0.0058 0.3931 1
0.0089 0.5 0.5
0.0085 1 0.5
0.007 0.2916 1
0.0013 0.5 0.5
0.0053 1 1
0.0084 0.4283 1
0.004 0.5 0.5
0.0076 1 0.5
0.0026 0.5 0.5
0.0021 0.3321 0.5
0.0408 0.5144 0.5
0.0009 0.5 0.5
0.0009 0.5 0.5
0.0009 0.5 0.5
0.0064 0.3508 0.5
0.0087 0.5 0.5
0.0004 0.5 0.5
0.0058 1 1
0.0032 1 1
0.0068 1 0.5
0.0009 0.5 0.5
0.0039 1 0.5
0.0045 1 0.5
0.0073 0.4546 1
0.0171 0.4063 0.5
0.0408 0.5144 0.5
0.0093 0.5 0.5
0.0114 1 0.5
0.007 1 0.5
0.0053 1 0.5
0.0408 0.5144 0.5
0.0004 0.5 0.5
0.0027 0.5 0.5
0.0004 0.5 0.5
0.0106 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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Gene identifier Rv1882c (Mycobacterium tuberculosis), Probable short-chain type dehydrogenase/reductase
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