DDR-TRK-1 A chemical probe for the DDR and TRK kinase

This probe is available from Sigma.


The discoidin domain receptors (DDRs), DDR1 and DDR2, are unique among the receptor tyrosine kinases (RTKs) in being activated by interaction with the extracellular matrix via binding to triple-helical collagen by the receptor extracellular domains.1  DDR1 and DDR2 form constitutive dimers making them unusual among RTKs, which typically dimerize only upon activation.2 DDRs regulate extracellular matrix remodeling, as well as cell adhesion, proliferation and migration.3 DDR kinases are linked to the progression of various human diseases, including fibrotic disorders, atherosclerosis and cancer.3-5  Significantly, they are identified as indicators of poor prognosis in ovarian, breast and lung cancer.6 DDR1 overexpression is associated with increased cell survival and invasion in hepatocellular carcinomas, pituitary adenoma and prostate cancer,7 whereas DDR2 is mutated in squamous cell lung cancers8 and contributes to breast cancer metastasis.9 The promise of DDR kinases as a therapeutic target has been demonstrated by DDR1 knockdown that has been shown to reduce metastatic activity in lung cancer models,10 slow the development of atherosclerosis,5 and impede the development of fibrotic disorders.11

The TRK kinases are represented by three members, TRKA, TRKB, and TRKC, which are selectively expressed in neuronal tissue.  Receptor signaling is initiated by binding of the neurotrophic factors NGF, BDNF, and NTR, respectively.  Subsequent signaling is via the RAS, PLCγ and PI3γ pathways.  The TRKs play a vital role in CNS development and survival. Gene fusions, protein overexpression, and single nucleotide alterations, have been implicated in the pathogenesis of specific cancer types including glioblastoma, papillary thyroid carcinoma, and secretory breast carcinomas, but are rare in most other cancers.12

DDR-TRK-1 is a chemical probe for the DDR and TRK kinases with good in vitro and in vivo potency.
DDR-TRK-1 inhibits colony formation and migration of Panc-1 pancreatic cancer cells.  In cellular and mouse models of lung fibrosis, DDR-TRK-1 inhibits signaling, expression of fibrotic markers and fibrotic features such as hydroxproline expression.  With restricted CNS exposure and therefore no TRK inhibition, the in vivo effects of DDR-TRK-1 can be attributed to DDR1-2 inhibition. DDR-TRK-1N is the negative control compound with very minimal differences in compound structure, and should be used in parallel to DDR-TRK-1. The probe can be complemented by the use of BAY-826, which inhibits the kinases TIE1, TIE2, DDR1 and DDR2, but lacks TRK activity to better understand the target involved in the phenotypic effect.

Work on this probe has been published in J.Med.Chem. 2016 59(12), p 5911-5916, 'Structure-Based Design of Tetrahydroisoquinoline-7-carboxamides as Selective Discoidin Domain Receptor 1 (DDR1) inhibitors'.

Potency Against Target Family

DDR-TRK-1 is a chemical probe for the DDR and TRK kinases (IC50 3-43 nM) with corresponding good cellular potency in NanoBRETTM target engagement assays (IC50 104-448 nM).  DDR-TRK-1 was shown to be selective in an in vitro kinase panel followed by cellular NanoBRETTM assays.


DDR-TRK-1 is selective in KINOMEscan® at 1μM. The closest off target is CDK11 (370 nM), which was however shown to be only poorly inhibited in cells  (~5 µM in NanoBRETTM). The negative control DDR-TRK-1N is entirely clean in KINOMEscan at 1μM.


We recommend that DDR-TRK-1 be used at 5μM concentration in cells. The negative control DDR-TRK-1N should be used at 5μM concentration in cells – it is toxic in HeLa cells above 10μM.

We also recommend the use of selective TRK inhibitors or the TIE-DDR BAY-826 probe in parallel to dissect the biology of DDR1/2 versus TRKA/B/C.

Cellular Activity

In NanoBRETTM assays, DDR-TRK-1 shows a potency of 104nM against DDR1, 175nM against DDR2, 448nM against TRKA and 142nM against TRKB.

In vitro Activity

In an activity assay at RBC (10μM ATP), DDR-TRK-1 shows an IC50 value of 27nM against DDR1, 4.5nM against DDR2, 43nM against TRKA, 3.6nM against TRKB and 2.9nM against TRKC.


Click here to download the DDR-TRK-1 SDF file.
Click here to download the DDR-TRK-1N SDF file.

Physical and chemical properties for DDR-TRK1
Molecular weight492.1885
Molecular formulaC29 H31 F3 N4 O
IUPAC name(3-(4-methyl-1H-imidazol-1-yl)-5-(trifluoro-methyl)-phenylamino)-(5-methyl-3-(pyrimidin-5-yl)-3-aza-bicyclo[4.4.0]deca-1(6),7,9-trien-9-yl)-methanone
No. of chiral centres1
No. of rotatable bonds6
No. of hydrogen bond acceptors5
No. of hydrogen bond donors1
Storage-20 as DMSO stock
DissolutionSoluble in DMSO at least up to 50mM
Physical and chemical properties for DDR-TRK-1N
Molecular weight508.2450
Molecular formulaC26 H23 F3 N6 O
IUPAC name(3-((4-methyl-piperazin-1-yl)-methyl)-5-(trifluoro-methyl)-phenylamino)-(3-phenyl-3-aza-bicyclo[4.4.0]deca-1(6),7,9-trien-9-yl)-methanone
No. of chiral centres0
No. of rotatable bonds7
No. of hydrogen bond acceptors4
No. of hydrogen bond donors1
Storage-20 as DMSO stock
DissolutionSoluble in DMSO at least up to 50mM

DDR-TRK-1; Cc1cn(cn1)c1cc(cc(c1)NC(c1ccc2c(CN(C[C@@H]2C)c2cncnc2)c1)=O)C(F)(F)F
DDR-TRK-1N: CN1CCN(CC1)Cc1cc(cc(c1)NC(c1ccc2[C@@]CN(Cc2c1)c1ccccc1)=O)C(F)(F)F

DDR-TRK-1: InChI=1S/C26H23F3N6O/c1-16-11-34(23-9-30-14-31-10-23)13-19-5-18(3-4-24(16)19)25(36)33-21-6-20(26(27,28)29)7-22(8-21)35-12-17(2)32-15-35/h3-10,12,14-16H,11,13H2,1-2H3,(H,33,36)/t16-/m0/s1
DDR-TRK-1N: InChI=1S/C29H31F3N4O/c1-34-11-13-35(14-12-34)19-21-15-25(29(30,31)32)18-26(16-21)33-28(37)23-8-7-22-9-10-36(20-24(22)17-23)27-5-3-2-4-6-27/h2-8,15-18H,9-14,19-20H2,1H3,(H,33,37)


DDR-TRK-1 PK profile

selectivity profile

A KINOMEscan of DDR-TRK-1 at 1μM revealed very few off-targets:

An activity assay at RBC (10μM ATP) revealed the following within the DDR/TRK family:

Compound IC50 (M):
Kinase:DDR-TRK-1DDR-TRK-1NWindow probe/control 
TRKB3.62E-09 NA 
Dose-response curves for the probe (and where collected, the negative control) are shown below:
in vitro potency
cell based assay data

In a NanoBRETTM cellular target engagement assay DDR1-TRK-1 displayed dose dependant inhibition as follows:

 DDR-TRK-1 (M)DDR-TRK-1N (M)Window

NanoBRET assay
Dose-response experiments were conducted in 96 well format using HEK293T cells expressing NanoLuc fused to the C-terminus of full-length protein kinases for DDR2, TRKA and TRKB or isoform 2 for DDR1, using Promega tracer  as indicated below.

KinaseNluc locationfull-length?Tracer[Tracer], nM (@Tracer)
DDR1CIsoform 2 (Uniprot Q08345-2)485
DDR2Ccanonical (Uniprot Q16832-1)445
TrkACcanonical (Uniprot P04629-1)550
TrkBCcanonical (Uniprot Q16620-1)530

  1. Carafoli F., et al., Crystallographic insight into collagen recognition by discoidin domain receptor 2. Structure 2009, 17 1573–1581.
  2. Noordeen N.A., et al., A transmembrane leucine zipper is required for activation of the dimeric receptor tyrosine kinase DDR1. J Biol Chem 2006, 281, 22744–22751.
  3. Vogel W.F., Abdulhussein R., Ford C.E. Sensing extracellular matrix: an update on discoidin domain receptor function. Cell Signalling2006, 18, 1108–1116.
  4. Valiathan R.R., et al., Discoidin domain receptor tyrosine kinases: new players in cancer progression. Cancer Metastasis Rev2012, 31, 295–321.
  5. Franco C., et al., Discoidin domain receptor 1 (DDR1) deletion decreases atherosclerosis by accelerating matrix accumulation and reducing inflammation in low-density lipoprotein receptor-deficient mice. Circ Res2008, 102, 1202–1211.
  6. Yang S.H., et al., Discoidin domain receptor 1 is associated with poor prognosis of non-small cell lung carcinomas. Oncol Rep2010, 24, 311–319.
  7. Shimada K., et al., Prostate cancer antigen-1 contributes to cell survival and invasion though discoidin receptor 1 in human prostate cancer. Cancer Sci 2008, 99, 39–45.
  8. Hammerman P.S., et al., Mutations in the DDR2 kinase gene identify a novel therapeutic target in squamous cell lung cancer. Cancer Discov2011, 1, 78–89.
  9. Zhang K., et al., The collagen receptor discoidin domain receptor 2 stabilizes SNAIL1 to facilitate breast cancer metastasis. Nat Cell Biol2013, 15, 677–687.
  10. Valencia K., et al., Inhibition of collagen receptor discoidin domain receptor-1 (DDR1) reduces cell survival, homing, and colonization in lung cancer bone metastasis. Clin Cancer Res2012, 18, 969–980.
  11. Guerrot D., et al., Discoidin domain receptor 1 is a major mediator of inflammation and fibrosis in obstructive nephropathy. Am J Pathol2011, 179, 83–91.
  12. Lange, A.; Lo, H.-W., Inhibiting TRK Proteins in Clinical Cancer Therapy. Cancers (Basel) 2018, 10 (4), 105.
pk properties
co-crystal structures

Structures of DDR1 complexes. A. Overall view of DDR1. Structural features are labelled for clarity. N-lobe is coloured orange,  A loop is marked in yellow and C-lobe is coloured wheat. B. D2099 compound electron density (PDB 5FDP). C. D2164 compound electron density (PDB 5FDX). D. Molecular docking of DDR-TRK-1 compound.

synthetic schemes
materials and methods

Inhibition of DDR1, DDR2, TRKA, TRKB and TRKC kinase activity was measured using radiometric assay (Reaction Biology Corporation). Compounds were tested in 10-dose IC50 singlicate mode with a 3-fold serial dilution starting at 1 or 10 μM at [ATP] = 10 µM.

Kinome-wide profiling was performed at DiscoverX using the KINOMEscan assay.