Detailed view for Rv3080c

Basic information

TDR Targets ID: 6803
Mycobacterium tuberculosis, Serine/threonine-protein kinase transcriptional regulatory protein PknK (protein kinase K) (STPK K)

Source Database / ID:  Tuberculist 

pI: 5.6079 | Length (AA): 1110 | MW (Da): 119418 | 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

PF00069   Protein kinase domain
PF13191   AAA ATPase domain

Gene Ontology

Mouse over links to read term descriptions.
GO:0005524   ATP binding  
GO:0005515   protein binding  
GO:0004713   protein tyrosine kinase activity  
GO:0004674   protein serine/threonine kinase activity  
GO:0004672   protein kinase activity  
GO:0006468   protein amino acid phosphorylation  

Metabolic Pathways

This gene is not mapped to any metabolic pathway in KEGG.

Structural information

Modbase 3D models:

There are 7 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
5 272 1jpa (A) 612 879 23.00 0 1 0.466441 -0.39
19 443 4rer (A) 11 464 21.00 0 1 0.522883 0.96
24 280 5hu3 (A) 12 269 24.00 0 1 0.587532 -0.6
146 220 3vut (B) 226 303 50.00 0.21 0.08 0.0751676 1.76
326 600 2qen (A) 1 286 16.00 0 0.98 0.286048 0.43
361 689 1z6t (A) 147 471 17.00 0.021 0.98 0.312396 0.58
956 1107 5cwp (A) 8 160 23.00 0.15 0.1 0.303937 -0.31

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:

  • 1MRU:
  • Resolution Method # Atoms # Residues Dep. Date Pub. Date Mod. Date
  • 1O6Y:
  • Resolution Method # Atoms # Residues Dep. Date Pub. Date Mod. Date
  • 2FUM:
  • Resolution Method # Atoms # Residues Dep. Date Pub. Date Mod. Date
  • 2H34:
  • Resolution Method # Atoms # Residues Dep. Date Pub. Date Mod. Date
  • 3F61:
  • Resolution Method # Atoms # Residues Dep. Date Pub. Date Mod. Date
  • 3F69:
  • Resolution Method # Atoms # Residues Dep. Date Pub. Date Mod. Date
  • 3ORI:
  • Resolution Method # Atoms # Residues Dep. Date Pub. Date Mod. Date
  • 3ORK:
  • Resolution Method # Atoms # Residues Dep. Date Pub. Date Mod. Date
  • 3ORL:
  • Resolution Method # Atoms # Residues Dep. Date Pub. Date Mod. Date
  • 3ORM:
  • Resolution Method # Atoms # Residues Dep. Date Pub. Date Mod. Date
  • 3ORO:
  • Resolution Method # Atoms # Residues Dep. Date Pub. Date Mod. Date
  • 3ORP:
  • Resolution Method # Atoms # Residues Dep. Date Pub. Date Mod. Date
  • 3ORT:
  • Resolution Method # Atoms # Residues Dep. Date Pub. Date Mod. Date
  • 4OW8:
  • Resolution Method # Atoms # Residues Dep. Date Pub. Date Mod. Date
  • 4X3F:
  • Resolution Method # Atoms # Residues Dep. Date Pub. Date Mod. Date
  • 5U94:
  • Resolution Method # Atoms # Residues Dep. Date Pub. Date Mod. Date
  • 6B2P:
  • Resolution Method # Atoms # Residues Dep. Date Pub. Date Mod. Date
  • 6B2Q:
  • Resolution Method # Atoms # Residues Dep. Date Pub. Date Mod. Date

Expression

Upregulation Percent Ranking Stage Dataset
Upper 80-100% percentile Dormant phase. murphy
Upregulation Percent Ranking Stage Dataset
Mid 40-60% percentile Dormant phase. hasan
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_152919)

Species Accession Gene Product
Escherichia coli b3418   mal regulon transcriptional activator
Mycobacterium tuberculosis Rv3080c   Serine/threonine-protein kinase transcriptional regulatory protein PknK (protein kinase K) (STPK K)

Essentiality

Rv3080c has one or more orthologs with essentiality data
Gene/Ortholog Organism Phenotype Source Study
b3418 Escherichia coli non-essential goodall
Show/Hide essentiality data references
  • yeastgenome Systematic deletion of yeast genes Saccharomyces Genome Database
  • 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
  • shigen Profiling of E. coli Chromosome (PEC) National Institute of Genetics, Japan
  • blattner Systematic mutagenesis of the E. coli (MG1655) genome J Bacteriol 2004, 186:4921-4930
  • neb C. elegans RNAi phenotypes Data obtained from Wormbase WS150, curated by K. Chaudary and T. Carlow, New England Biolabs
  • 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.
  • nmpdr Genome-scale essentiality datasets from published studies (M. tuberculosis) National Microbial Pathogen Data Resource
  • alsford High-throughput phenotyping using parallel sequencing of RNA interference targets in the African trypanosome Genome Res 2011, 21:915-924
  • 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.
  • gerdes Experimental determination and system-level analysis of essential genes in E. coli MG1655 Gerdes et al., J Bacteriol. 2003 185:5673-84

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): 0.5


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
Patiria pectinifera Cdc2 300 aa 26.2% 271 aa Compounds References
Oryctolagus cuniculus Cyclin-dependent kinase 4 189 aa 27.6% 152 aa Compounds References
Rattus norvegicus Serine/threonine-protein kinase pim-3 326 aa 23.4% 282 aa Compounds References

Obtained from network model

Ranking Plot


Putative Drugs List


Compound Raw Global Species
0.0093 0.8828 0.5
0.0036 0.5 0.5
0.0033 1 1
0.0032 0.5 0.5
0.0039 0.5 0.5
0.0039 0.9485 1
0.0007 0.5 0.5
0.0091 1 0.5
0.0011 1 0.5
0.0092 1 0.5
0.0059 1 0.5
0.0037 1 0.5
0.0066 0.3101 0.5
0.0008 0.5 0.5
0.0063 0.7244 1
0.0007 0.5 0.5
0.0023 0.5 0.5
0.0012 0.5 0.5
0.0007 0.5 0.5
0.0027 1 0.5
0.0003 0.5 0.5
0.0016 0.5 0.5
0.0059 1 0.5
0.0061 0.6883 0.6563
0.0016 0.5 0.5
0.0018 0.5 0.5
0.0012 0.5 0.5
0.0063 1 1
0.0033 0.5 0.5
0.0081 0.5 0.5
0.0012 0.5 0.5
0.0069 0.3067 1
0.0029 0.5 0.5
0.0088 0.4477 1
0.0004 0.5 0.5
0.0067 0.5 0.5
0.0059 1 0.5
0.0081 1 0.5
0.0022 0.5 0.5
0.0098 0.3242 0.3676
0.0026 0.5 0.5
0.0064 0.3377 0.5
0.0056 1 0.5
0.0062 0.6935 0.5
0.0042 0.5 0.5
0.0039 0.5 0.5
0.0032 0.5 0.5

Assayability

Assay information

No assay information for this target.

Reagent availability

No reagent availability information for this target.

Bibliographic References

79 literature references were collected for this gene.

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

User comments

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Gene identifier Rv3080c (Mycobacterium tuberculosis), Serine/threonine-protein kinase transcriptional regulatory protein PknK (protein kinase K) (STPK K)
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