7BE6 | pdb_00007be6

Structure of DDR1 receptor tyrosine kinase in complex with inhibitor SR159


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.87 Å
  • R-Value Free: 
    0.230 (Depositor), 0.236 (DCC) 
  • R-Value Work: 
    0.187 (Depositor) 
  • R-Value Observed: 
    0.189 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history

Literature

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 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.

Macromolecule Content 

  • Total Structure Weight: 37.04 kDa 
  • Atom Count: 2,654 
  • Modeled Residue Count: 302 
  • Deposited Residue Count: 315 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Epithelial discoidin domain-containing receptor 1315Homo sapiensMutation(s): 0 
Gene Names: DDR1CAKEDDR1NEPNTRK4PTK3ARTK6TRKE
EC: 2.7.10.1
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
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Reference Sequence

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
TJW
(Subject of Investigation/LOI)

Query on TJW



Download:Ideal Coordinates CCD File
J [auth A]5-amino-N-(4-(((2S)-4-cyclohexyl-1-((1-(methylsulfonyl)piperidin-3-yl)amino)-1-oxobutan-2-yl)carbamoyl)benzyl)-1-phenyl-1H-pyrazole-4-carboxamide
C34 H45 N7 O5 S
GODYJVJUBKYVOU-FIBWVYCGSA-N
SO4

Query on SO4



Download:Ideal Coordinates CCD File
H [auth A]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
PO4

Query on PO4



Download:Ideal Coordinates CCD File
G [auth A]PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
EDO

Query on EDO



Download:Ideal Coordinates CCD File
B [auth A]
C [auth A]
D [auth A]
E [auth A]
F [auth A]
B [auth A],
C [auth A],
D [auth A],
E [auth A],
F [auth A],
I [auth A],
K [auth A]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.87 Å
  • R-Value Free:  0.230 (Depositor), 0.236 (DCC) 
  • R-Value Work:  0.187 (Depositor) 
  • R-Value Observed: 0.189 (Depositor) 
Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 63.023α = 90
b = 131.967β = 90
c = 43.803γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


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