Detailed view for ML0321

Basic information

TDR Targets ID: 257091
Mycobacterium leprae, Probable 4-diphosphocytidyl-2C-methyl-D-erythritol synthase IspD (2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase) (MEP
Source Database / ID:  Leproma 

pI: 8.7795 | Length (AA): 241 | MW (Da): 24980 | 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

PF01128   2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase

Gene Ontology

Mouse over links to read term descriptions.
GO:0050518   2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase activity  
GO:0070567   GO:cytidylyltransferase activity  

GO:0003824   catalytic activity  
GO:0008299   isoprenoid biosynthetic process  

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
6 240 3okr (A) 6 230 73.00 0 1 1.6479 -0.1
6 240 3q80 (A) 6 230 68.00 0.000000000087 1 1.6642 -0.13
7 241 2xwl (A) 2 220 60.00 0 1 1.6 -0.26

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:

PDB tag
  • 3OKR:
  • Resolution Method # Atoms # Residues Dep. Date Pub. Date Mod. Date

Expression

No expression data available for this gene

Orthologs

Ortholog group members (OG5_129829)

Species Accession Gene Product
Arabidopsis thaliana AT2G02500   2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase
Babesia bovis BBOV_III003490   conserved hypothetical protein
Chlamydia trachomatis CT_462   2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase
Escherichia coli b2747   4-diphosphocytidyl-2C-methyl-D-erythritol synthase
Homo sapiens 729920   isoprenoid synthase domain containing
Mycobacterium leprae ML0321   Probable 4-diphosphocytidyl-2C-methyl-D-erythritol synthase IspD (2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase) (MEP
Mus musculus ENSMUSG00000043153   isoprenoid synthase domain containing
Mycobacterium tuberculosis Rv3582c   4-diphosphocytidyl-2C-methyl-D-erythritol synthase IspD (MEP cytidylyltransferase) (MCT)
Mycobacterium ulcerans MUL_4158   2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase
Oryza sativa 9266653   Os01g0887000
Theileria parva TP03_0057   2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase, putative

Essentiality

ML0321 has one or more orthologs with essentiality data
Gene/Ortholog Organism Phenotype Source Study
b2747 Escherichia coli essential goodall
Show/Hide essentiality data references
  • 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.
  • shigen Profiling of E. coli Chromosome (PEC) National Institute of Genetics, Japan
  • alsford High-throughput phenotyping using parallel sequencing of RNA interference targets in the African trypanosome Genome Res 2011, 21:915-924
  • 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
  • neb C. elegans RNAi phenotypes Data obtained from Wormbase WS150, curated by K. Chaudary and T. Carlow, New England Biolabs
  • gerdes Experimental determination and system-level analysis of essential genes in E. coli MG1655 Gerdes et al., J Bacteriol. 2003 185:5673-84
  • wormbase C. elegans RNAi experiments WormBase web site, http://www.wormbase.org, release WS170
  • nmpdr Genome-scale essentiality datasets from published studies (M. tuberculosis) National Microbial Pathogen Data Resource
  • blattner Systematic mutagenesis of the E. coli (MG1655) genome J Bacteriol 2004, 186:4921-4930
  • 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.
  • keio Systematic single-gene knock-out mutants of E. coli K12 The Keio Collection

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
Species Known druggable target Linked compounds Reference
Arabidopsis thaliana 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase 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
0.0215 0.9051 0.5
0.0227 0.2797 1
0.0228 0.2785 1
0.0213 0.3085 1
0.0212 0.5274 0.5
0.0216 0.3041 0.5
0.0227 0.2797 1
0.0261 0.6175 0
0.0261 1 0.5
0.0221 0.5362 0.5

Assayability

Assay information

No assay information for this target.

Reagent availability

No reagent availability information for this target.

Bibliographic References

2 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 ML0321 (Mycobacterium leprae), Probable 4-diphosphocytidyl-2C-methyl-D-erythritol synthase IspD (2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase) (MEP
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