Detailed view for Rv1307

Basic information

TDR Targets ID: 5703
Mycobacterium tuberculosis, Probable ATP synthase delta chain AtpH
Source Database / ID:  Tuberculist 

pI: 5.2577 | Length (AA): 446 | MW (Da): 48806 | Paralog Number: 1

Signal peptide: Y | GPI Anchor: | Predicted trans-membrane segments: 1

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

PF00213   ATP synthase delta (OSCP) subunit
PF00430   ATP synthase B/B' CF(0)

Gene Ontology

Mouse over links to read term descriptions.
GO:0046933   hydrogen ion transporting ATP synthase activity, rotational mechanism  
GO:0045263   proton-transporting ATP synthase complex, coupling factor F(o)  
GO:0015078   hydrogen ion transmembrane transporter activity  
GO:0015986   ATP synthesis coupled proton transport  

Metabolic Pathways

Oxidative phosphorylation (KEGG)
Global map (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
59 118 1l2p (A) 62 121 28.00 0.67 0.02 0.559229 -1.5
62 298 5cwi (A) 3 234 17.00 0 0.78 0.71629 -0.2
63 139 5cwm (A) 144 216 37.00 0.29 0.53 0.581346 -1.03

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
Lower 0-20% percentile Dormant phase, Dormant phase. hasan 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_134191)

Species Accession Gene Product
Escherichia coli b3736   F0 sector of membrane-bound ATP synthase, subunit b
Mycobacterium leprae ML1141   PROBABLE ATP SYNTHASE B CHAIN ATPF
Mycobacterium tuberculosis Rv1306   Probable ATP synthase B chain AtpF
Mycobacterium tuberculosis Rv1307   Probable ATP synthase delta chain AtpH
Mycobacterium ulcerans MUL_3958   F0F1 ATP synthase subunit B

Essentiality

Rv1307 has direct evidence of essentiality
Gene/Ortholog Organism Phenotype Source Study
mtu1328 Mycobacterium tuberculosis essential nmpdr
mtu1329 this record Mycobacterium tuberculosis essential nmpdr
b3736 Escherichia coli non-essential goodall
Show/Hide essentiality data references
  • keio Systematic single-gene knock-out mutants of E. coli K12 The Keio Collection
  • 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
  • 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.
  • yeastgenome Systematic deletion of yeast genes Saccharomyces Genome Database
  • shigen Profiling of E. coli Chromosome (PEC) National Institute of Genetics, Japan
  • 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
  • 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.
  • 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
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Predicted associations

By orthology with druggable targets
Species Known druggable target Linked compounds Reference
Mycobacterium tuberculosis Probable ATP synthase B chain AtpF 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
1.1362 0.6342 0.6601
1.1362 0.6342 0.6601
1.1362 0.6342 0.6601
1.1362 0.6342 0.6601
1.1362 0.6342 0.6601
0.1707 0.6699 1
1.1362 0.6342 0.6601
0.1707 0.6699 1
1.1362 0.6342 0.6601
1.1362 0.6342 0.6601
1.1362 0.6342 0.6601
1.1362 0.6342 0.6601
1.1362 0.6342 0.6601
1.1362 0.6342 0.6601
0.1707 0.6699 1
1.1362 0.6342 0.6601
1.1362 0.6342 0.6601
1.1362 0.6342 0.6601
1.1362 0.6342 0.6601
1.1362 0.6342 0.6601
1.1362 0.6342 0.6601
1.1362 0.6342 0.6601
1.1362 0.6342 0.6601
1.1362 0.6342 0.6601
1.1362 0.6342 0.6601
1.1362 0.6342 0.6601
1.1362 0.6342 0.6601
1.1362 0.6342 0.6601
1.1362 0.6342 0.6601
1.1362 0.6342 0.6601
1.1362 0.6342 0.6601
1.1362 0.6342 0.6601
1.1362 0.6342 0.6601
1.1362 0.6342 0.6601
1.1362 0.6342 0.6601
1.1362 0.6342 0.6601
1.1362 0.6342 0.6601
1.1362 0.6342 0.6601
1.1362 0.6342 0.6601
1.1362 0.6342 0.6601
1.1362 0.6342 0.6601
1.1362 0.6342 0.6601
1.1362 0.6342 0.6601
1.1362 0.6342 0.6601
1.1362 0.6342 0.6601
1.1362 0.6342 0.6601
1.1362 0.6342 0.6601
1.1362 0.6342 0.6601
1.1362 0.6342 0.6601
1.1362 0.6342 0.6601
1.1362 0.6342 0.6601
1.1362 0.6342 0.6601
1.1362 0.6342 0.6601
1.1362 0.6342 0.6601
1.1362 0.6342 0.6601
1.1362 0.6342 0.6601
0.1707 0.6699 1
1.1362 0.6342 0.6601
1.1362 0.6342 0.6601
1.1362 0.6342 0.6601
1.1362 0.6342 0.6601
1.1362 0.6342 0.6601
1.1362 0.6342 0.6601
1.1362 0.6342 0.6601
1.1362 0.6342 0.6601
1.1362 0.6342 0.6601
1.1362 0.6342 0.6601
1.1362 0.6342 0.6601
1.1362 0.6342 0.6601

Assayability

Assay information

  • ChEMBL
  • Inhibition of Mycobacterium tuberculosis ATP synthase
  • ChEMBL
  • Inhibition of Mycobacterium tuberculosis H37Rv ATP synthase assessed as reduction in total ATP content at 100 uM after 18 hrs by bead-vortexing settling method

Reagent availability

  • Reagent:
  • Target Type Source Notes
    Rv1307 purified protein BRENDA A protein with this EC number or name or sequence has been purified from Mycobacterium phlei ( 1 )

Bibliographic References

15 literature references were collected for this gene.

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Gene identifier Rv1307 (Mycobacterium tuberculosis), Probable ATP synthase delta chain AtpH
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