7BDQ

MAPK14 bound with SR300


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.75 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.215 
  • R-Value Observed: 0.218 

wwPDB Validation   3D Report Full Report


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 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.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Mitogen-activated protein kinase 14361Mus musculusMutation(s): 0 
Gene Names: Mapk14Crk1Csbp1Csbp2
EC: 2.7.11.24
UniProt
Find proteins for P47811 (Mus musculus)
Explore P47811 
Go to UniProtKB:  P47811
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP47811
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
TJZ (Subject of Investigation/LOI)
Query on TJZ

Download Ideal Coordinates CCD File 
B [auth A]~{N}-[(2~{S})-4-cyclohexyl-1-[[(3~{R})-1-methylsulfonylpiperidin-3-yl]amino]-1-oxidanylidene-butan-2-yl]-4-[[(1-phenylpyrazolo[3,4-d]pyrimidin-4-yl)amino]methyl]benzamide
C35 H44 N8 O4 S
CULJRLFFBRSDOM-MVSFAKPFSA-N
MES
Query on MES

Download Ideal Coordinates CCD File 
E [auth A]2-(N-MORPHOLINO)-ETHANESULFONIC ACID
C6 H13 N O4 S
SXGZJKUKBWWHRA-UHFFFAOYSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.75 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.215 
  • R-Value Observed: 0.218 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 65.027α = 90
b = 73.041β = 90
c = 74.347γ = 90
Software Package:
Software NamePurpose
Aimlessdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
Aimlessdata reduction
PHASERphasing

Structure Validation

View Full Validation Report



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