Detailed view for Rv2464c

Basic information

TDR Targets ID: 981478
Mycobacterium tuberculosis, Possible DNA glycosylase
Source Database / ID:  Tuberculist 

pI: 10.1624 | Length (AA): 268 | MW (Da): 29682 | 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

PF01149  
PF06827  
PF06831  

Gene Ontology

Mouse over links to read term descriptions.
GO:0016799   hydrolase activity, hydrolyzing N-glycosyl compounds  
GO:0003906   DNA-(apurinic or apyrimidinic site) lyase activity  
GO:0003824   catalytic activity  
GO:0003684   damaged DNA binding  
GO:0003676   nucleic acid binding  
GO:0008270   zinc ion binding  
GO:0006289   nucleotide-excision repair  
GO:0006284   base-excision repair  
GO:0006281   DNA repair  

Metabolic Pathways

Base excision repair (KEGG)

Structural information

Modbase 3D models:

There are 3 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
1 267 1kfv (B) 3 269 25.00 0 1 1.23607 0.02
2 268 1ee8 (A) 1 263 29.00 0 1 1.32157 -0.27
155 267 4mb7 (A) 172 273 36.00 0.000051 0.96 0.767442 -0.18

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

No expression data available for this gene

Orthologs

Ortholog group members (OG5_150515)

Species Accession Gene Product
Escherichia coli b0714   endonuclease VIII/5-formyluracil/5-hydroxymethyluracil DNA glycosylase
Mycobacterium tuberculosis Rv2464c   Possible DNA glycosylase
Mycobacterium ulcerans MUL_3737   formamidopyrimidine-DNA glycosylase

Essentiality

Rv2464c has one or more orthologs with essentiality data
Gene/Ortholog Organism Phenotype Source Study
b0714 Escherichia coli non-essential goodall
Show/Hide essentiality data references
  • 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
  • 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.
  • 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
  • wormbase C. elegans RNAi experiments WormBase web site, http://www.wormbase.org, release WS170
  • keio Systematic single-gene knock-out mutants of E. coli K12 The Keio Collection
  • 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
  • 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

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
No additional associated druggable targets
Obtained from network model

Ranking Plot

Putative Drugs List

Compound Raw Global Species
0.052 0.6592 1
0.0422 0.8518 1
0.0112 0.8903 1
0.0376 0.8151 1
0.0389 0.844 1
0.0274 0.3128 1
0.018 0.2788 1
0.062 0.6741 1
0.0096 0.5453 1
0.0627 0.7485 1
0.0366 0.3573 1
0.0581 0.574 1
0.0307 0.4313 1
0.0112 0.7472 1
0.0526 0.7396 1
0.0631 0.6542 1
0.0112 0.7092 1
0.0382 0.7182 1
0.0631 0.6542 1
0.0512 0.6511 1
0.0285 0.3942 1
0.0371 0.4287 1
0.0092 0.4929 0.5
0.0531 0.3275 1
0.0421 0.3549 0.5
0.0401 0.4735 1
0.0473 0.5497 1
0.009 0.2627 1
0.0274 0.2558 1
0.0112 0.4354 1
0.0526 0.7396 1
0.0329 0.8193 1
0.0183 0.4879 1
0.0274 0.2998 0.5787
0.0531 0.3275 1
0.0112 0.8853 0.5
0.0285 0.3942 1
0.0307 0.4313 1
0.0531 0.8628 1
0.009 0.2843 1
0.0381 0.5134 1
0.0652 0.4573 1
0.0112 0.4262 0.4213
0.0274 0.2998 0.5787
0.0531 0.3275 1
0.0531 0.3275 1
0.0468 0.8555 1
0.0274 0.3128 1
0.009 0.4661 1
0.0531 0.3275 1
0.0694 0.667 1
0.0721 0.6913 1
0.0396 0.742 1
0.0486 0.3291 1
0.0721 0.6913 1
0.0112 0.2936 0.4051
0.0652 0.4573 1
0.0568 0.673 1
0.0526 0.7396 1
0.0112 0.3609 0.3637
0.0203 0.4038 1
0.0274 0.8086 1
0.0526 0.7396 1
0.0104 0.8927 1
0.0272 0.8211 1
0.0264 0.2607 1
0.018 0.2788 1
0.009 0.7854 1
0.0473 0.5497 1
0.0366 0.3573 1
0.0245 0.3087 0.9964
0.0399 0.4481 1
0.0402 0.6954 1
0.018 0.5254 1
0.0192 0.3131 1
0.0729 0.7708 1
0.0245 0.3087 0.9964
0.0627 0.7485 1
0.0103 0.654 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.

If you have references for this gene, please enter them in a user comment (below) or Contact us.

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Gene identifier Rv2464c (Mycobacterium tuberculosis), Possible DNA glycosylase
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