1PY5

Crystal Structure of TGF-beta receptor I kinase with inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.292 
  • R-Value Work: 0.258 
  • R-Value Observed: 0.258 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Synthesis and activity of new aryl- and heteroaryl-substituted 5,6-dihydro-4H-pyrrolo[1,2-b]pyrazole inhibitors of the transforming growth factor-beta type I receptor kinase domain.

Sawyer, J.S.Beight, D.W.Britt, K.S.Anderson, B.D.Campbell, R.M.Goodson, T.Herron, D.K.Li, H.Y.McMillen, W.T.Mort, N.Parsons, S.Smith, E.C.Wagner, J.R.Yan, L.Zhang, F.Yingling, J.M.

(2004) Bioorg Med Chem Lett 14: 3581-3584

  • DOI: https://doi.org/10.1016/j.bmcl.2004.04.007
  • Primary Citation of Related Structures:  
    1PY5, 1RW8

  • PubMed Abstract: 

    We have expanded our previously reported series of pyrazole-based inhibitors of the TGF-beta type I receptor kinase domain (TbetaR-I) to now include new 5,6-dihydro-4H-pyrrolo[1,2-b]pyrazole analogues. Limited examination of the SAR of this new series in both enzyme and cell based in vitro assays has revealed selectivity differences with respect to p38 MAP kinase (p38 MAPK) depending on the nature of the 'warhead' group on the dihydropyrrolopyrazole ring. As with our original pyrazole series, phenyl substituents tended to show greater selectivity against p38 MAPK than those comprised of the quinoline-4-yl moiety. We have also achieved co-crystallization and X-ray analysis of compounds 3 and 15, two potent examples of this new series, with the TbetaR-I receptor kinase domain.


  • Organizational Affiliation

    Discovery Chemistry Research and Technology, The Lilly Research Laboratories, Lilly Corporate Center, Indianapolis, IN 46285, USA. jss.dcrt@lilly.com


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
TGF-beta receptor type I326Homo sapiensMutation(s): 0 
Gene Names: TGFBR1
EC: 2.7.1.37
UniProt & NIH Common Fund Data Resources
Find proteins for P36897 (Homo sapiens)
Explore P36897 
Go to UniProtKB:  P36897
GTEx:  ENSG00000106799 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP36897
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PY1
Query on PY1

Download Ideal Coordinates CCD File 
C [auth A]4-(3-PYRIDIN-2-YL-1H-PYRAZOL-4-YL)QUINOLINE
C17 H12 N4
IBCXZJCWDGCXQT-UHFFFAOYSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
B [auth A]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Binding Affinity Annotations 
IDSourceBinding Affinity
PY1 BindingDB:  1PY5 Kd: 5 (nM) from 1 assay(s)
IC50: min: 27, max: 2.70e+4 (nM) from 9 assay(s)
EC50: 40 (nM) from 1 assay(s)
PDBBind:  1PY5 IC50: 51 (nM) from 1 assay(s)
Binding MOAD:  1PY5 IC50: 51 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.292 
  • R-Value Work: 0.258 
  • R-Value Observed: 0.258 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 41.829α = 90
b = 78.111β = 90
c = 90.686γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
SCALEPACKdata scaling
AMoREphasing
CNSrefinement
HKL-2000data reduction

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-07-13
    Type: Initial release
  • Version 1.1: 2008-04-29
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2023-08-16
    Changes: Data collection, Database references, Derived calculations, Refinement description