CDK13

cyclin dependent kinase 13
Cyclin-dependent kinase 13 (CDK13) is known to phosphorylate the C-terminal domain (CTD) of the largest subunit of RNA polymerase II (RPB1), thereby acting as a key regulator of transcription elongation. CDK13 is required for RNA splicing.


TCGA Data Summary

These figures show a summary of data collected by the cancer genome atlas for CDK13. The mutations heatmaps shows the fraction samples with each type of genetic mutation, while the copy number variation shows the percentage of samples where a deletion or amplication was dectected. Finally, the mRNA expression tab shows the amount of mRNA detected on a log-2 scale for each cancer type. The X-axis cancer type abbreviations are described here. This summary of the cancer genome atlas (TCGA) was collated from firebrowse developed by the Broad Institute. The code used to produce these figures is available through github.


PDB Kinase Domains

Kinase Domain Structure:

  • Title: Crystal structure of human Cdk13/Cyclin K in complex with ADP-aluminum fluoride
  • Resolution: 2

Associated Compounds:

  • ADENOSINE-5'-DIPHOSPHATE
  • ALUMINUM FLUORIDE
  • MAGNESIUM ION
  • PHOSPHOTHREONINE

View This Structure on RCSB PDB

IDG Compound

Compound Name: THZ531

Chemical Name: (R,E)-N-(4-(3-((5-chloro-4-(1H-indol-3-yl)pyrimidin-2-yl)amino)piperidine-1-carbonyl)phenyl)-4-(dimethylamino)but-2-enamide

CHEBI: 143122

Smile String: ClC1=CN=C(N[C@H]2CN(C(C3=CC=C(NC(/C=C/CN(C)C)=O)C=C3)=O)CCC2)N=C1C4=CNC5=C4C=CC=C5

Chemical Formula: C30H32ClN7O2

Molecular Weight: 558.07

cLogP: 1.8925

Source: MedChemExpress


This compound is available through MedChemExpress.

Additional data concerning this compound can be found here.


ReNcell Visualizations

This data stems from the differentiation of neural stem cells into fully functional neurons and glia, which requires precise regulation of diverse molecular pathways over time and space. As part of the Harvard Medical School Library of Integrated Network-based Cellular Signatures (LINCS) Program (NIH grant U54 HL127365, lincs.hms.harvard.edu), we used phospho-proteomics to assess changes during ReN VM cell differentiation. Depicted is the dark kinase of interest (black) and two reference kinases (blue and green) to aid interpretation of the values. More information on this work can be found on Synapse.


Interaction Networks

INDRA (Integrated Network and Dynamical Reasoning Assembler) is an automated model assembly system drawing from natural language processing systems and structured databases. It collects mechanistic and causal assertions, represents them in a standardized form (INDRA Statements), and assembles them into various modeling formalisms including causal graphs and dynamical models. More information on this work can be found on Github. In this particular figure, several interaction-types are depicted; physical complexes (blue), phosphorylation (black), and general up- or downregulation (green and red, respectively). Biomacromolecules are represented as squares, small molecule as circles, and biological processes and diamonds. The thickness of each line reflects a confidence score, with thicker lines higher in confidence.

Affinity Purification - Mass Spectrometry


PRM Peptides

The calibration reverse curve plot with linear robust regression analysis is shown [1]. The observed concentrations of the stable isotopically labeled peptide surrogate was obtained for each peptide using LC-MS in parallel reaction mode with a constant quantity of natural isotope abundance peptide as the internal standard (25 fmol/µL) [2]. The analyte matrix was a tryptic digest of pooled patient derived xenografts (1 µg/µL) that was prepared according to CPTAC-SOP. Each of the three most intense peptide fragment ions is depicted as a different symbol. The measurements from replicate LC-MS analyses are depicted as the same symbol [3] The LOD was determined using a non-parametric method with eight LC-MS analyses without added analyte [4]. The LOQ was generated from the LOD [5]. The plots are dimensioned such that the theoretical line is at a 45° angle to facilitate assessment of peptide recovery and performance. The LOD, LOQ, and regression parameters are summarize in the Table.

  1. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2855883/
  2. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3494192/
  3. https://proteomics.cancer.gov/sites/default/files/assay-characterization-guidance-document.pdf
  4. http://clinchem.aaccjnls.org/content/50/4/732
  5. “Algorithms, Routines and S Functions for Robust Statistics” (CRC Press, Boca Raton, Florida, USA, 1993)

View Peptide Parameters

The calibration reverse curve plot with linear robust regression analysis is shown [1]. The observed concentrations of the stable isotopically labeled peptide surrogate was obtained for each peptide using LC-MS in parallel reaction mode with a constant quantity of natural isotope abundance peptide as the internal standard (25 fmol/µL) [2]. The analyte matrix was a tryptic digest of pooled patient derived xenografts (1 µg/µL) that was prepared according to CPTAC-SOP. Each of the three most intense peptide fragment ions is depicted as a different symbol. The measurements from replicate LC-MS analyses are depicted as the same symbol [3] The LOD was determined using a non-parametric method with eight LC-MS analyses without added analyte [4]. The LOQ was generated from the LOD [5]. The plots are dimensioned such that the theoretical line is at a 45° angle to facilitate assessment of peptide recovery and performance. The LOD, LOQ, and regression parameters are summarize in the Table.

  1. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2855883/
  2. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3494192/
  3. https://proteomics.cancer.gov/sites/default/files/assay-characterization-guidance-document.pdf
  4. http://clinchem.aaccjnls.org/content/50/4/732
  5. “Algorithms, Routines and S Functions for Robust Statistics” (CRC Press, Boca Raton, Florida, USA, 1993)

View Peptide Parameters


Available Assays, Cell Lines and Animal Models
Horizon KO HAP1 Cell Lines
IMPC Mouse KO
NanoBRET Assay
A CDK13 NanoBRET Assay has been developed and validated. NanoLuc®-fused CDK13 is available from Promega by special request. Additional information about this assay is available here.

Kinase Tissue Expression Summary

The expression of kinases varies widely across the human tissues assayed by the GTEx project. To gain a better understanding of the kinase tissue distribution, we've created an application that describes and summarizes the expression of each dark kinase in the context of the rest of the kinome. These visualizations show a snapshot of the data associated with CDK13. The two anatograms show the five organs where CDK13 is most abundant. The graph summarizes the expression of the kinase across all the organ systems.

This data can further explored at our Kinase Expression Data Application.