Detailed view for Rv3247c

Basic information

TDR Targets ID: 980901
Mycobacterium tuberculosis, Thymidylate kinase Tmk (dTMP kinase) (thymidylic acid kinase) (TMPK)
Source Database / ID:  Tuberculist 

pI: 7.3565 | Length (AA): 214 | MW (Da): 22602 | 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

PF02223  

Gene Ontology

Mouse over links to read term descriptions.
No GO information for this protein.

Metabolic Pathways

Pyrimidine metabolism (KEGG)

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
1 209 4unr (A) 1 209 99.00 0 1 2.03854 -0.98

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_126920)

Species Accession Gene Product
Arabidopsis thaliana AT5G59440   protein ZEU1 (ZEUS1)
Babesia bovis BBOV_III006440   thymidylate kinase, putative
Brugia malayi Bm1_23075   thymidylate kinase
Candida albicans CaO19.1137   Thymidylate kinase
Candida albicans CaO19.8730   Thymidylate kinase
Caenorhabditis elegans CELE_R53.2   Protein R53.2
Cryptosporidium hominis Chro.50490   thymidylate kinase
Cryptosporidium parvum cgd5_3630   thymidylate kinase
Chlamydia trachomatis CT_188   thymidylate kinase
Dictyostelium discoideum DDB_G0290033   dTMP kinase
Drosophila melanogaster Dmel_CG5757   CG5757 gene product from transcript CG5757-RB
Escherichia coli b1098   thymidylate kinase
Echinococcus granulosus EgrG_000756200   thymidylate kinase
Entamoeba histolytica EHI_008040   Thymidylate kinase, putative
Echinococcus multilocularis EmuJ_000756200   thymidylate kinase
Giardia lamblia GL50803_15380   CDC8
Homo sapiens ENSG00000168393   deoxythymidylate kinase (thymidylate kinase)
Leishmania braziliensis LbrM.10.0060   thymidylate kinase-like protein
Leishmania donovani LdBPK_100040.1   thymidylate kinase-like protein
Leishmania infantum LinJ.10.0040   thymidylate kinase-like protein
Leishmania major LmjF.10.0060   thymidylate kinase-like protein
Leishmania mexicana LmxM.10.0060   thymidylate kinase-like protein
Loa Loa (eye worm) LOAG_01297   thymidylate kinase
Mycobacterium leprae ML0772   probable thymidylate kinase Tmk (dTMP KINASE) (THYMIDYLIC ACID KINASE) (TMPK)
Mus musculus ENSMUSG00000026281   deoxythymidylate kinase
Mycobacterium tuberculosis Rv3247c   Thymidylate kinase Tmk (dTMP kinase) (thymidylic acid kinase) (TMPK)
Mycobacterium ulcerans MUL_2583   thymidylate kinase
Neospora caninum NCLIV_053180   Thymidylate kinase, related
Oryza sativa 4344056   Os07g0639900
Onchocerca volvulus OVOC10889   Putative thymidylate kinase
Plasmodium berghei PBANKA_1464200   thymidylate kinase, putative
Plasmodium falciparum PF3D7_1251300   thymidylate kinase
Plasmodium knowlesi PKNH_1471300   thymidylate kinase, putative
Plasmodium vivax PVX_101455   thymidylate kinase, putative
Plasmodium yoelii PY01336   Thymidylate kinase
Saccharomyces cerevisiae YJR057W   bifunctional thymidylate/uridylate kinase
Schistosoma japonicum Sjp_0008250   ko:K00943 dTMP kinase [EC2.7.4.9], putative
Schistosoma japonicum Sjp_0056420   Thymidylate kinase, putative
Schistosoma mansoni Smp_027740   hypothetical protein
Schistosoma mansoni Smp_032810   thymidylate kinase
Schistosoma mansoni Smp_001360   thymidylate kinase
Schmidtea mediterranea mk4.014274.01  
Schmidtea mediterranea mk4.004278.02  
Schmidtea mediterranea mk4.001266.05   Probable thymidylate kinase
Trypanosoma brucei gambiense Tbg972.8.3620   thymidylate kinase, putative
Trypanosoma brucei Tb11.v5.0738   thymidylate kinase, putative
Trypanosoma brucei Tb927.8.3510   thymidylate kinase, putative
Trypanosoma congolense TcIL3000_0_00560   thymidylate kinase, putative
Trypanosoma congolense TcIL3000_8_3770   thymidylate kinase, putative
Trypanosoma cruzi TcCLB.506685.30   thymidylate kinase, putative
Trypanosoma cruzi TcCLB.509663.30   thymidylate kinase, putative
Toxoplasma gondii TGME49_306970   thymidylate kinase
Treponema pallidum TP0354   thymidylate kinase (tmk)
Theileria parva TP02_0319   thymidylate kinase, putative
Trichomonas vaginalis TVAG_134830   thymidylate kinase, putative
Trichomonas vaginalis TVAG_315260   thymidylate kinase, putative
Wolbachia endosymbiont of Brugia malayi Wbm0148   thymidylate kinase

Essentiality

Rv3247c has one or more orthologs with essentiality data
Gene/Ortholog Organism Phenotype Source Study
Tb927.8.3910 Trypanosoma brucei significant loss of fitness in bloodstream forms (3 days) alsford
Tb927.8.3910 Trypanosoma brucei significant loss of fitness in bloodstream forms (6 days) alsford
Tb927.8.3910 Trypanosoma brucei no significant loss or gain of fitness in procyclic forms alsford
Tb927.8.3910 Trypanosoma brucei significant loss of fitness in differentiation of procyclic to bloodstream forms alsford
Tb927.8.3510 Trypanosoma brucei significant loss of fitness in bloodstream forms (3 days) alsford
Tb927.8.3510 Trypanosoma brucei no significant loss or gain of fitness in bloodstream forms (6 days) alsford
Tb927.8.3510 Trypanosoma brucei significant loss of fitness in procyclic forms alsford
Tb927.8.3510 Trypanosoma brucei significant loss of fitness in differentiation of procyclic to bloodstream forms alsford
b1098 Escherichia coli essential goodall
CELE_R53.2 Caenorhabditis elegans embryonic lethal wormbase
CELE_R53.2 Caenorhabditis elegans larval arrest wormbase
YJR057W Saccharomyces cerevisiae inviable yeastgenome
TGME49_306970 Toxoplasma gondii Probably essential sidik
Show/Hide essentiality data references
  • shigen Profiling of E. coli Chromosome (PEC) National Institute of Genetics, Japan
  • yeastgenome Systematic deletion of yeast genes Saccharomyces Genome Database
  • 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
  • nmpdr Genome-scale essentiality datasets from published studies (M. tuberculosis) National Microbial Pathogen Data Resource
  • 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.
  • keio Systematic single-gene knock-out mutants of E. coli K12 The Keio Collection
  • 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
  • blattner Systematic mutagenesis of the E. coli (MG1655) genome J Bacteriol 2004, 186:4921-4930

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

77 chemical compounds are associated with this gene

Predicted associations

By orthology with druggable targets
Species Known druggable target Linked compounds Reference
Plasmodium falciparum thymidylate kinase Compounds References
Homo sapiens deoxythymidylate kinase (thymidylate kinase) 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
0.0668 0.7591 1
0.0516 0.323 1
0.0683 0.5 0.5
0.0445 0.2976 0.5954
0.0073 0.2714 0.5
0.0106404 0.895283 1
0.0294 1 1
0.0219 0.3664 0.5
0.0212 0.817 0.5
0.0292 1 0.5
0.0125 1 0.5
0.0355 0.5 0.5
0.0227 0.3572 0.5
0.0142 0.2501 1
0.0125 1 0.5
0.0087 0.4267 1
0.0087 1 0.5
0.0374 0.3475 1
0.057 1 0.5
0.0422 0.2541 0.4348
0.0296 0.6225 1
0.0207691 1 0.5
0.037 0.5 0.5
0.0687 0.6229 0
0.051 0.4201 1
0.0365 0.3803 0.3788
0.0829 1 0.5
0.0072 0.3984 0.5
0.0296 0.6225 1
0.0291 0.2651 1
0.0293 0.9097 1
0.0253 0.3376 0
0.0291 1 0.5
0.0071 0.3392 0.5
0.0145 1 1
0.0298 0.2743 1
0.0219 0.3406 1
0.0221 0.6512 0.5
0.0087 1 0.5
0.0302 1 0.5
0.0154 0.3913 0.5
0.0071 0.5 0.5
0.0292 1 0.5
0.0306 0.7167 0.5
0.0073 0.3529 0.5
0.0365 0.3803 0.3788
0.0824 1 0.5
0.0372 1 0.5
0.0207691 1 0.5
0.0229 1 1
0.0367 1 1
0.0087 0.8037 0.5
0.0691 1 0.5
0.0122 0.3964 0.5
0.0358 0.5 0.5
0.0693 0.5 0.5
0.0282 1 1
0.0447 1 1
0.0691 1 0.5
0.0221 0.5 0.5
0.0161 0.5 0.5
0.0073 0.2864 0.5
0.0538 0.5 0.5
0.014 0.2676 0.5699
0.0122 0.4015 0.5
0.0141 0.4992 1
0.0154 0.3913 0.5
0.0125 0.5307 0.5
0.0087 1 0.5
0.0154 0.2711 1
0.0687 1 1
0.0155 0.2985 1
0.0673 1 0.5
0.0081 0.4113 1
0.0297203 1 0.5
0.0285 0.5149 0.5
0.0144 0.2623 0.8174
0.0073 0.3529 0.5
0.0155 1 0.5
0.0072 0.2566 0.5
0.0367 1 1
0.014 0.2676 0.5699
0.051 0.4201 1
0.0371 1 0.5
0.0525 1 0.5
0.0449 0.3248 0.2224
0.0365 0.3803 0.3788
0.09 1 0.5
0.0195606 0.448021 0.5
0.0445 0.2976 0.5954
0.0302 0.331 1
0.0283 0.2693 1
0.0087 0.5 0.5
0.0212 0.817 0.5
0.0219 0.3664 0.5
0.0154 0.2711 1
0.0154 0.3913 0.5
0.0285 0.2693 1
0.0087 0.8037 0.5
0.0145 0.4141 1
0.0285 0.5149 0.5
0.0457 0.5658 1
0.0212 0.817 0.5
0.0447 1 0.5
0.0228 1 0.5
0.0154 0.2711 1
0.0122 0.4015 0.5
0.0229 1 1
0.00844282 1 0.5
0.0373 1 0.5
0.0087 0.2715 0.5
0.0227 0.3572 0.5
0.0362 0.7093 1
0.053 1 0.5
0.0087 0.5135 0.5
0.0073 1 0.5
0.1122 0.3644 1
0.0302 0.331 1
0.0311 0.26 0.5
0.0087 0.8037 0.5
0.0365 0.3803 0.3788
0.016 0.2944 1
0.1122 0.3644 1
0.0142 0.266 1
0.0285 0.2693 1
0.0306 0.7167 0.5
0.0291 1 0.5
0.053 1 0.5
0.0824 1 0.5
0.0084 0.2522 1
0.00658401 1 0.5
0.00844282 1 0.5
0.0215 1 0.5
0.036 1 0.5
0.1122 0.3644 1
0.0293 0.9097 1
0.1122 0.3644 1
0.0087 0.4113 1
0.0367 1 1
0.057 1 0.5
0.0516 0.323 1
0.0292 1 1
0.0074 0.5 0.5
0.1122 0.3644 1
0.0365 0.3803 0.3788
0.007 0.7315 1
0.0446 0.5 0.5
0.0323 0.3946 1
0.0154 0.2711 1
0.007 0.5 0.5
0.0369 1 0.5
0.0073 0.3529 0.5
0.0141 0.3343 0.7769
0.0344 0.7508 1

Assayability

Assay information

  • Affinity of the compound towards thymidine monophosphate kinase (TMPKmt) in Mycobacterium tuberculosis ChEMBL
  • Affinity towards thymidine monophosphate kinase (TMPKmt) in Mycobacterium tuberculosis
  • Affinity of the compound towards thymidine monophosphate kinase (TMPKmt) in Mycobacterium tuberculosis using HPLC chromatography test ChEMBL
  • Affinity towards thymidine monophosphate kinase (TMPKmt) in Mycobacterium tuberculosis using HPLC chromatography test
  • Kinetic parameter Vm of thymidine monophosphate kinase (TMPKmt) in Mycobacterium tuberculosis was determined ChEMBL
  • Kinetic parameter Vm of thymidine monophosphate kinase (TMPKmt) in Mycobacterium tuberculosis was determined
  • Kinetic parameter Vm of thymidine monophosphate kinase (TMPKmt) in Mycobacterium tuberculosis was determined ChEMBL
  • Kinetic parameter Vm of thymidine monophosphate kinase (TMPKmt) in Mycobacterium tuberculosis was determined
  • Compound was tested for binding affinity against Mycobacterium tuberculosis thymidine monophosphate kinase ChEMBL
  • Compound was tested for binding affinity against Mycobacterium tuberculosis thymidine monophosphate kinase
  • Enzyme Kinetic constant was determined in the presence of Mycobacterium tuberculosis thymidine monophosphate kinase ChEMBL
  • Enzyme Kinetic constant was determined in the presence of Mycobacterium tuberculosis thymidine monophosphate kinase
  • Inhibitory activity against thymidine monophosphate kinase (TMPK) in Mycobacterium tuberculosis ChEMBL
  • Inhibitory activity against thymidine monophosphate kinase (TMPK) in Mycobacterium tuberculosis
  • Inhibitory activity of the compound against thymidine monophosphate kinase (TMPKmt) in Mycobacterium tuberculosis using HPLC chromatography test ChEMBL
  • Inhibitory activity against thymidine monophosphate kinase (TMPKmt) in Mycobacterium tuberculosis using HPLC chromatography test
  • Binding affinity towards mycobacterium tuberculosis thymidine monophosphate kinase ChEMBL
  • Binding affinity towards mycobacterium tuberculosis thymidine monophosphate kinase
  • Binding affinity towards mycobacterium tuberculosis thymidine monophosphate kinase; NI=No inhibition ChEMBL
  • Binding affinity towards mycobacterium tuberculosis thymidine monophosphate kinase; NI=No inhibition
  • Km for mycobacterium tuberculosis thymidine monophosphate kinase ChEMBL
  • Km for mycobacterium tuberculosis thymidine monophosphate kinase
  • Compound was tested for binding affinity against Mycobacterium tuberculosis thymidine monophosphate kinase ChEMBL
  • Compound was tested for binding affinity against Mycobacterium tuberculosis thymidine monophosphate kinase
  • In Vitro inhibition of Thymidine Monophophatase Kinase of Mycobacterium tuberculosis (TMPKm) ChEMBL
  • In Vitro inhibition of Thymidine Monophosphatase Kinase of Mycobacterium tuberculosis (TMPKm)
  • Affinity of the compound towards thymidine monophosphate kinase (TMPKmt) in Mycobacterium tuberculosis ChEMBL
  • Affinity towards thymidine monophosphate kinase (TMPKmt) in Mycobacterium tuberculosis
  • In Vitro inhibition of Thymidine Monophophatase Kinase of Mycobacterium tuberculosis (TMPKm) ChEMBL
  • In Vitro inhibition of Thymidine Monophosphatase Kinase of Mycobacterium tuberculosis (TMPKm)
  • Inhibition of Mycobacterium tuberculosis TMPK by coupled spectrophotometric assay ChEMBL
  • Inhibition of Mycobacterium tuberculosis TMPK by coupled spectrophotometric assay
  • Inhibition of Mycobacterium tuberculosis TMPK at 1 mM by coupled spectrophotometric assay ChEMBL
  • Inhibition of Mycobacterium tuberculosis TMPK at 1 mM by coupled spectrophotometric assay
  • Inhibition of Mycobacterium tuberculosis TMPK expressed in Escherichia coli by spectrophotometric assay ChEMBL
  • Inhibition of Mycobacterium tuberculosis TMPK expressed in Escherichia coli by spectrophotometric assay
  • Activity of Mycobacterium tuberculosis TMPK ChEMBL
  • Activity of Mycobacterium tuberculosis TMPK
  • ChEMBL
  • Inhibition of Mycobacterium tuberculosis TMPK using dTMP substrate and NADH by pyruvate kinase/lactate dehydrogenase coupling system based spectrophotometric assay
  • ChEMBL
  • Inhibition of Mycobacterium tuberculosis recombinant TMPK
  • ChEMBL
  • Inhibition of Mycobacterium tuberculosis recombinant TMPK upto 2 mM
  • ChEMBL
  • Inhibition of Mycobacterium tuberculosis recombinant TMPK upto 0.2 mM
  • ChEMBL
  • Inhibition of Mycobacterium tuberculosis Thymidine monophosphate kinase by spectrophotometry
  • ChEMBL
  • Inhibition of Mycobacterium tuberculosis Thymidylate kinase
  • ChEMBL
  • Competitive inhibition of Mycobacterium tuberculosis TMPK expressed in Escherichia coli NM554 by coupled spectrophotometric assay
  • ChEMBL
  • Competitive inhibition of Mycobacterium tuberculosis TMPK by Lineweaver-Burk analysis
  • ChEMBL
  • Competitive inhibition of Mycobacterium tuberculosis TMPK at 0.05 mM by Lineweaver-Burk analysis
  • ChEMBL
  • Inhibition of Mycobacterium tuberculosis thymidylate kinase
  • ChEMBL
  • Inhibition of Mycobacterium tuberculosis thymidine monophosphate kinase by HPLC analysis
  • ChEMBL
  • Inhibition of Mycobacterium tuberculosis thymidine monophosphate kinase by enzyme-coupling based spectrophotometric assay
  • ChEMBL
  • Inhibition of Mycobacterium tuberculosis thymidine monophosphate kinase
  • ChEMBL
  • Inhibition of Mycobacterium tuberculosis thymidylate kinase activity by pyruvate kinase-lactate dehydrogenase coupled assay

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

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Gene identifier Rv3247c (Mycobacterium tuberculosis), Thymidylate kinase Tmk (dTMP kinase) (thymidylic acid kinase) (TMPK)
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