7RUN

Crystal structure of phosphorylated RET tyrosine kinase domain complexed with a pyrrolo[2,3-d]pyrimidine inhibitor.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.51 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.220 
  • R-Value Observed: 0.222 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Antitarget Selectivity and Tolerability of Novel Pyrrolo[2,3- d ]pyrimidine RET Inhibitors.

Mathison, C.J.N.Yang, Y.Nelson, J.Huang, Z.Jiang, J.Chianelli, D.Rucker, P.V.Roland, J.Xie, Y.F.Epple, R.Bursulaya, B.Lee, C.Gao, M.Y.Shaffer, J.Briones, S.Sarkisova, Y.Galkin, A.Li, L.Li, N.Li, C.Hua, S.Kasibhatla, S.Kinyamu-Akunda, J.Kikkawa, R.Molteni, V.Tellew, J.E.

(2021) ACS Med Chem Lett 12: 1912-1919

  • DOI: https://doi.org/10.1021/acsmedchemlett.1c00450
  • Primary Citation of Related Structures:  
    7RUN

  • PubMed Abstract: 

    The selective inhibition of RET kinase as a treatment for relevant cancer types including lung adenocarcinoma has garnered considerable interest in recent years and prompted a variety of efforts toward the discovery of small-molecule therapeutics. Hits uncovered via the analysis of archival kinase data ultimately led to the identification of a promising pyrrolo[2,3- d ]pyrimidine scaffold. The optimization of this pyrrolo[2,3- d ]pyrimidine core resulted in compound 1 , which demonstrated potent in vitro RET kinase inhibition and robust in vivo efficacy in RET-driven tumor xenografts upon multiday dosing in mice. The administration of 1 was well-tolerated at established efficacious doses (10 and 30 mg/kg, po, qd), and plasma exposure levels indicated a minimal risk of KDR or hERG inhibition in vivo , as evaluated by Miles assay and free plasma concentrations, respectively.


  • Organizational Affiliation

    The Genomics Institute of the Novartis Research Foundation, 10675 John Jay Hopkins Drive, San Diego, California 92121, United States.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Proto-oncogene tyrosine-protein kinase receptor Ret
A, B
334Homo sapiensMutation(s): 0 
Gene Names: RETCDHF12CDHR16PTCRET51
EC: 2.7.10.1
UniProt & NIH Common Fund Data Resources
Find proteins for P07949 (Homo sapiens)
Explore P07949 
Go to UniProtKB:  P07949
PHAROS:  P07949
GTEx:  ENSG00000165731 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP07949
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Modified Residues  2 Unique
IDChains TypeFormula2D DiagramParent
PTR
Query on PTR
A, B
L-PEPTIDE LINKINGC9 H12 N O6 PTYR
SEP
Query on SEP
A, B
L-PEPTIDE LINKINGC3 H8 N O6 PSER
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.51 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.220 
  • R-Value Observed: 0.222 
  • Space Group: P 63
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 98.131α = 90
b = 98.131β = 90
c = 145.381γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
SCALEPACKdata scaling
REFMACphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not fundedUnited States--

Revision History  (Full details and data files)

  • Version 1.0: 2022-01-19
    Type: Initial release
  • Version 1.1: 2023-10-18
    Changes: Data collection, Refinement description
  • Version 1.2: 2023-11-15
    Changes: Data collection