The DDR1 Kinase Domain Bound To SR302

Experimental Data Snapshot

  • Resolution: 2.30 Å
  • R-Value Free: 0.308 
  • R-Value Work: 0.243 
  • R-Value Observed: 0.246 

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Development of a Selective Dual Discoidin Domain Receptor (DDR)/p38 Kinase Chemical Probe.

Rohm, S.Berger, B.T.Schroder, M.Chatterjee, D.Mathea, S.Joerger, A.C.Pinkas, D.M.Bufton, J.C.Tjaden, A.Kovooru, L.Kudolo, M.Pohl, C.Bullock, A.N.Muller, S.Laufer, S.Knapp, S.

(2021) J Med Chem 64: 13451-13474

  • DOI: https://doi.org/10.1021/acs.jmedchem.1c00868
  • Primary Citation of Related Structures:  
    7BCM, 7BDO, 7BDQ, 7BE4, 7BE5, 7BE6

  • PubMed Abstract: 

    Discoidin domain receptors 1 and 2 (DDR1/2) play a central role in fibrotic disorders, such as renal and pulmonary fibrosis, atherosclerosis, and various forms of cancer. Potent and selective inhibitors, so-called chemical probe compounds, have been developed to study DDR1/2 kinase signaling. However, these inhibitors showed undesired activity on other kinases such as the tyrosine protein kinase receptor TIE or tropomyosin receptor kinases, which are related to angiogenesis and neuronal toxicity. In this study, we optimized our recently published p38 mitogen-activated protein kinase inhibitor 7 toward a potent and cell-active dual DDR/p38 chemical probe and developed a structurally related negative control. The structure-guided design approach used provided insights into the P-loop folding process of p38 and how targeting of non-conserved amino acids modulates inhibitor selectivity. The developed and comprehensively characterized DDR/p38 probe, 30 (SR-302), is a valuable tool for studying the role of DDR kinase in normal physiology and in disease development.

  • Organizational Affiliation

    Institute of Pharmaceutical Chemistry, Johann Wolfgang Goethe University, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Epithelial discoidin domain-containing receptor 1
A, B
315Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for Q08345 (Homo sapiens)
Explore Q08345 
Go to UniProtKB:  Q08345
PHAROS:  Q08345
GTEx:  ENSG00000204580 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ08345
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
TBK (Subject of Investigation/LOI)
Query on TBK

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
C32 H42 N6 O5 S
Experimental Data & Validation

Experimental Data

  • Resolution: 2.30 Å
  • R-Value Free: 0.308 
  • R-Value Work: 0.243 
  • R-Value Observed: 0.246 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 56.223α = 90
b = 120.402β = 111.348
c = 62.095γ = 90
Software Package:
Software NamePurpose
xia2data reduction
Aimlessdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2021-03-03
    Type: Initial release
  • Version 1.1: 2022-09-14
    Changes: Database references
  • Version 1.2: 2024-01-31
    Changes: Data collection, Refinement description