Detailed view for Rv0548c

Basic information

TDR Targets ID: 980221
Mycobacterium tuberculosis, Naphthoate synthase MenB (dihydroxynaphthoic acid synthetase) (DHNA synthetase)
Source Database / ID:  Tuberculist 

pI: 6.4117 | Length (AA): 314 | MW (Da): 34657 | Paralog Number: 0

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

Druggability Group : DG1

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

PF00378  

Gene Ontology

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

Structural information

Modbase 3D models:

There is 1 model calculated for this protein. More info on this model, including the model itself is available at: Modbase

Target Beg Target End Template Template Beg Template End Identity Evalue Model Score MPQS zDope
15 314 4qii (A) 15 314 99.99 0 1 2.14871 -1.02

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_134385)

Species Accession Gene Product
Arabidopsis thaliana AT1G60550   1,4-Dihydroxy-2-naphthoyl-CoA synthase
Dictyostelium discoideum DDB_G0293354   enoyl Coenzyme A hydratase, cytosolic
Escherichia coli b2262   dihydroxynaphthoic acid synthetase
Mycobacterium leprae ML2263c   PROBABLE NAPHTHOATE SYNTHASE MENB (DIHYDROXYNAPHTHOIC ACID SYNTHETASE) (DHNA SYNTHETASE)
Mycobacterium tuberculosis Rv0548c   Naphthoate synthase MenB (dihydroxynaphthoic acid synthetase) (DHNA synthetase)
Mycobacterium ulcerans MUL_0648   naphthoate synthase
Oryza sativa 4327859   Os01g0662700

Essentiality

Rv0548c has one or more orthologs with essentiality data
Gene/Ortholog Organism Phenotype Source Study
b2262 Escherichia coli non-essential goodall
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
  • 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
  • blattner Systematic mutagenesis of the E. coli (MG1655) genome J Bacteriol 2004, 186:4921-4930
  • yeastgenome Systematic deletion of yeast genes Saccharomyces Genome Database
  • nmpdr Genome-scale essentiality datasets from published studies (M. tuberculosis) National Microbial Pathogen Data Resource
  • 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
  • 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.
  • 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

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

Compound Source Reference
References
References
References
References
References
References
References
References
References
References
References
References

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
0.0885 1 1
0.0693 0.7065 1
0.0376 0.7505 1
0.0893 1 1
0.0631 0.7715 1
0.0294 0.3821 0.5
0.0577 1 0.5
0.124 0.3916 1
0.0289 0.8499 0.5
0.0888 1 0.5
0.0582 0.8502 0.5
0.0796 1 0.5
0.0886 1 0.5
0.0796 1 0.5
0.0885 1 0.5
0.0894 0.5615 0.9629
0.0887 1 1
0.0967 1 1
0.0462 0.4625 1
0.0744 1 0.5
0.0459 0.4717 1
0.123 1 1
0.123 1 1
0.0288 1 0.5
0.123 1 1
0.0831 1 0.5
0.0357 0.514 1
0.0641 1 1
0.0887 1 1
0.095 1 0.5
0.0883 1 0.5
0.0928 0.28 1
0.0287 1 0.5
0.0624 1 1
0.0885 1 1
0.0922 0.2828 1
0.0288 1 0.5
0.0871 1 1
0.0301 0.9745 1
0.0388 0.9744 0.5
0.0388 0.9744 0.5
0.0796 1 0.5
0.0874 1 0.5
0.0917 1 0.5
0.0873 1 0.5
0.0624 1 1
0.1002 1 1
0.058 1 0.5
0.0744 1 0.5
0.0885 1 0.5
0.0462 0.4625 1
0.0287 0.9045 0.5
0.0875 1 0.5
0.0831 1 0.5
0.124 0.3916 1
0.0885 1 1
0.0612 1 1
0.0577 1 0.5
0.0581 1 0.5
0.0199 0.2744 0.1864
0.0549 1 1
0.1225 1 1
0.0376 0.7505 1
0.0928 0.28 1
0.0869 1 1
0.0698 0.6736 0.5
0.0698 1 1
0.124 0.3916 1
0.0873 1 0.5
0.123 1 1
0.0575 1 0.5
0.0893 1 1
0.124 0.3916 1
0.0902 1 1
0.0972 0.9926 1
0.0301 0.9745 1
0.1268 1 1
0.123 1 1
0.0884 1 0.5
0.0612 1 1
0.0226 0.4985 0.5
0.0892 1 0.5
0.0578 1 0.5
0.0445 0.6912 1
0.0887 1 1
0.0357 0.4364 1
0.113917 1 1
0.0885 1 1
0.0462 0.4625 1
0.1387 1 1
0.123 1 1
0.0961 1 0.5
0.096 1 1
0.0796 1 0.5
0.0581 1 0.5
0.124 0.3916 1
0.058 1 0.5
0.0578 1 1
0.0287 1 0.5
0.0381 0.4167 1
0.124 0.3916 1
0.058 1 0.5
0.0301 0.9745 1
0.0289 0.8499 0.5
0.0582 0.8502 0.5
0.0288 0.2745 0.5
0.0199 0.2744 0.1864
0.123 1 1
0.0332 1 0.5
0.0976 1 1
0.0578 1 0.5
0.0288 1 0.5
0.0885 1 1
0.0575 0.5041 1
0.098 1 1
0.0577 1 0.5
0.0902 1 1
0.0288 1 0.5

Assayability

Assay information

  • ChEMBL
  • Inhibition of Mycobacterium tuberculosis MenB expressed in Escherichia coli BL21 (DE3) at 125 ug/ml by double-reciprocal plot analysis
  • ChEMBL
  • Inhibition of Mycobacterium tuberculosis MenB expressed in Escherichia coli BL21 (DE3) by double-reciprocal plot analysis
  • ChEMBL
  • Non-competitive inhibition of Mycobacterium tuberculosis MenB expressed in Escherichia coli BL21 (DE3)
  • ChEMBL
  • Non-competitive inhibition of Mycobacterium tuberculosis MenB expressed in Escherichia coli BL21 (DE3) assessed as inhibition of enzyme-substrate complex formation
  • ChEMBL
  • Inhibition of Mycobacterium tuberculosis MenB expressed in Escherichia coli BL21 (DE3) up to 100 uM by double-reciprocal plot analysis
  • ChEMBL
  • Inhibition of Mycobacterium tuberculosis MenB expressed in Escherichia coli BL21 (DE3) assessed as formation of DHNA-CoA from OSB-CoA by enzyme coupled-assay in presence of Escherichia coli MenE preincubated for 1 hr
  • ChEMBL
  • Inhibition of Mycobacterium tuberculosis MenB expressed in Escherichia coli BL21 (DE3) assessed as formation of DHNA-CoA from OSB-CoA by enzyme coupled-assay in presence of Escherichia coli MenE
  • ChEMBL
  • Inhibition of Mycobacterium tuberculosis MenB expressed in Escherichia coli BL21 (DE3) assessed as formation of DHNA-CoA from OSB-CoA at 50 uM by enzyme coupled-assay in presence of Escherichia coli MenE
  • ChEMBL
  • Non-competitive inhibition of Mycobacterium tuberculosis MenB expressed in Escherichia coli BL21 (DE3) by Lineweaver-Burk plot analysis
  • ChEMBL
  • Inhibition of Mycobacterium tuberculosis MenB expressed in Escherichia coli BL21 (DE3) by Lineweaver-Burk plot analysis

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.

User comments

No user comments are available for this gene. Log in to add comments, or register.

Enter your comment

User ()
Gene identifier Rv0548c (Mycobacterium tuberculosis), Naphthoate synthase MenB (dihydroxynaphthoic acid synthetase) (DHNA synthetase)
Title for this comment
Comment