Detailed view for Rv3559c

Basic information

TDR Targets ID: 9188
Mycobacterium tuberculosis, Probable oxidoreductase

Source Database / ID:  Tuberculist 

pI: 6.022 | Length (AA): 262 | MW (Da): 27430 | 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

PF00106  
PF13561   Enoyl-(Acyl carrier protein) reductase

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 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
2 261 3o38 (A) 2 261 85.00 0 1 1.89267 -0.37
20 195 3h7a (A) 8 178 25.00 0 1 1.04006 -0.65

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:

  • 3O38:
  • Resolution Method # Atoms # Residues Dep. Date Pub. Date Mod. Date

Expression

Upregulation Percent Ranking Stage Dataset
Upper 80-100% percentile Dormant phase. hasan
Upregulation Percent Ranking Stage Dataset
Mid 40-60% percentile Dormant phase. murphy
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_168406)

Species Accession Gene Product
Mycobacterium tuberculosis Rv3559c   Probable oxidoreductase
Mycobacterium ulcerans MUL_4124   short chain dehydrogenase

Essentiality

Rv3559c has direct evidence of essentiality
Gene/Ortholog Organism Phenotype Source Study
mtu3620 this record Mycobacterium tuberculosis essential nmpdr
Show/Hide essentiality data references
  • gerdes Experimental determination and system-level analysis of essential genes in E. coli MG1655 Gerdes et al., J Bacteriol. 2003 185:5673-84
  • 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
  • alsford High-throughput phenotyping using parallel sequencing of RNA interference targets in the African trypanosome Genome Res 2011, 21:915-924
  • keio Systematic single-gene knock-out mutants of E. coli K12 The Keio Collection
  • wormbase C. elegans RNAi experiments WormBase web site, http://www.wormbase.org, release WS170
  • blattner Systematic mutagenesis of the E. coli (MG1655) genome J Bacteriol 2004, 186:4921-4930
  • yeastgenome Systematic deletion of yeast genes Saccharomyces Genome Database
  • 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.
  • 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.
  • 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.
  • nmpdr Genome-scale essentiality datasets from published studies (M. tuberculosis) National Microbial Pathogen Data Resource

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): 0.7


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
Staphylococcus aureus (strain NCTC 8325) Enoyl-[acyl-carrier-protein] reductase [NADPH] FabI 256 aa 25.9% 259 aa Compounds References
Bacillus subtilis (strain 168) Enoyl-[acyl-carrier-protein] reductase [NADH] 258 aa 24.8% 258 aa Compounds References
Staphylococcus aureus Enoyl-[acyl-carrier-protein] reductase [NADPH] 256 aa 25.5% 259 aa Compounds References
Staphylococcus aureus subsp. aureus MRSA252 Enoyl-[acyl-carrier-protein] reductase 256 aa 25.5% 259 aa Compounds References
Macaca mulatta Hydroxysteroid 11-beta dehydrogenase 1 140 aa 24.5% 139 aa Compounds References
Staphylococcus aureus Enoyl-ACP reductase 243 aa 26.0% 231 aa Compounds References

Obtained from network model

Ranking Plot


Putative Drugs List


Compound Raw Global Species
0.0084 0.4283 1
0.0033 0.6302 1
0.0089 0.5 0.5
0.0108 0.5 0.5
0.0035 1 0.5
0.00146296 0.5 0.5
0.0106 1 0.5
0.0183 0.5 0.5
0.0102 0.7451 0.5
0.0009 1 0.5
0.0021 0.3321 0.5
0.0056 1 0.5
0.0157 0.5 0.5
0.0122 0.5 0.5
0.007 0.2916 1
0.0088 1 0.5
0.0004 0.5 0.5
0.004 0.5 0.5
0.0073 0.4546 1
0.0012 0.5 0.5
0.0045 1 0.5
0.0218 0.5 0.5
0.0004 0.5 0.5
0.0009 0.5 0.5
0.007 1 0.5
0.0408 0.5144 0.5
0.0197 1 1
0.0004 0.5 0.5
0.0088 0.4497 1
0.0146 1 1
0.0026 0.5 0.5
0.0097 0.4304 0.5
0.0118 1 0.5
0.0073 0.3141 0.4101
0.016 0.577 1
0.0408 0.5144 0.5
0.0027 0.5 0.5
0.0082 1 0.5
0.0068 1 0.5
0.0013 0.5 0.5
0.002 0.5 0.5
0.007 0.2916 1
0.0108 0.5 0.5
0.0012 0.5 0.5
0.0071 0.3141 0
0.0021 0.5 0.5
0.0106 0.5 0.5
0.0162 1 0.5
0.007 1 0.5
0.0073 0.2873 0.3563
0.0009 0.5 0.5
0.0277 0.3427 1
0.0009 0.5 0.5
0.0004 0.5 0.5
0.0085 1 0.5
0.0123 0.5 0.5
0.0132 0.3658 0.376
0.0004 0.5 0.5
0.008 0.5 0.5
0.016 0.577 1
0.0019 0.4322 0.5
0.007 1 0.5
0.002 0.5 0.5
0.0039 1 0.5
0.0058 0.3931 1
0.0005 0.5 0.5
0.0032 1 1
0.0076 1 0.5
0.0114 0.5 0.5
0.0222 0.5 0.5
0.0106 0.2872 0.4772
0.0277 0.3427 1
0.0097 1 1
0.0113 1 1
0.0286 0.5 0.5
0.0273 0.5 0.5
0.0057 0.284 0.6413
0.0009 0.5 0.5
0.0171 0.4063 0.5
0.0016 0.5 0.5
0.0196 0.8679 0.5
0.0066 0.3586 0.5
0.011 0.3568 0.3299
0.0093 0.5 0.5
0.0114 1 0.5
0.0073 0.3811 1
0.0056 0.875 1
0.0046 0.3082 0.5
0.0009 0.7374 0.5
0.0009 0.5 0.5
0.0087 0.5 0.5
0.0149 1 1
0.0013 1 0.5
0.0114 1 0.5
0.0179 0.5 0.5
0.0009 0.5 0.5
0.0004 0.5 0.5
0.0106 1 1
0.0119 0.2746 0
0.0021 0.3321 0.5
0.0068 1 0.5
0.0108 0.5 0.5
0.0027 0.5 0.5
0.0132 0.3248 1
0.0068 0.2585 0.5
0.0005 0.5 0.5
0.0408 0.5144 0.5
0.0251 1 1
0.0067 0.3468 0.5
0.0089 0.5 0.5
0.007 0.2916 1
0.0064 0.3508 0.5
0.0009 0.5 0.5
0.0196 0.8679 0.5
0.0222 0.5 0.5
0.0053 1 1
0.0402 1 1
0.0196 0.8679 0.5
0.023 1 1
0.0053 1 0.5
0.0058 1 1
0.0165 1 0.5
0.0131 0.5 0.5
0.0171 0.4063 0.5
0.0073 0.3811 1
0.0004 0.5 0.5
0.024 0.8536 0.8373
0.0192 0.5 0.5
0.0088 0.6544 0.5
0.0009 0.5 0.5
0.0164 0.5 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.

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User comments

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Gene identifier Rv3559c (Mycobacterium tuberculosis), Probable oxidoreductase
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