6VHG

Crystal structure of phosphorylated RET tyrosine kinase domain complexed with a pyrazolo[1,5-a]pyrimidine inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.203 
  • R-Value Observed: 0.204 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Efficacy and Tolerability of Pyrazolo[1,5-a]pyrimidine RET Kinase Inhibitors for the Treatment of Lung Adenocarcinoma.

Mathison, C.J.N.Chianelli, D.Rucker, P.V.Nelson, J.Roland, J.Huang, Z.Yang, Y.Jiang, 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.

(2020) ACS Med Chem Lett 11: 558-565

  • DOI: https://doi.org/10.1021/acsmedchemlett.0c00015
  • Primary Citation of Related Structures:  
    6VHG

  • PubMed Abstract: 

    RET (REarranged during Transfection) kinase gain-of-function aberrancies have been identified as potential oncogenic drivers in lung adenocarcinoma, along with several other cancer types, prompting the discovery and assessment of selective inhibitors. Internal mining and analysis of relevant kinase data informed the decision to investigate a pyrazolo[1,5- a ]pyrimidine scaffold, where subsequent optimization led to the identification of compound WF-47-JS03 ( 1 ), a potent RET kinase inhibitor with >500-fold selectivity against KDR (Kinase insert Domain Receptor) in cellular assays. In subsequent mouse in vivo studies, compound 1 demonstrated effective brain penetration and was found to induce strong regression of RET-driven tumor xenografts at a well-tolerated dose (10 mg/kg, po, qd). Higher doses of 1 , however, were poorly tolerated in mice, similar to other pyrazolo[1,5- a ]pyrimidine compounds at or near the efficacious dose, and indicative of the narrow therapeutic windows seen with this scaffold.


  • 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 Ret311Homo 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
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
QX1
Query on QX1

Download Ideal Coordinates CCD File 
B [auth A]3-(3,4-dimethoxyphenyl)-N~5~-(1-methylpiperidin-4-yl)-6-phenylpyrazolo[1,5-a]pyrimidine-5,7-diamine
C26 H30 N6 O2
ZVVQDNWRXSSQDL-UHFFFAOYSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A],
E [auth A],
F [auth A]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
ACT
Query on ACT

Download Ideal Coordinates CCD File 
I [auth A]ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
CL
Query on CL

Download Ideal Coordinates CCD File 
G [auth A],
H [auth A]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
PTR
Query on PTR
A
L-PEPTIDE LINKINGC9 H12 N O6 PTYR
Binding Affinity Annotations 
IDSourceBinding Affinity
QX1 Binding MOAD:  6VHG IC50: 5500 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.203 
  • R-Value Observed: 0.204 
  • Space Group: P 63 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 97.815α = 90
b = 97.815β = 90
c = 143.963γ = 120
Software Package:
Software NamePurpose
BUSTERrefinement
DENZOdata reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-02-26
    Type: Initial release
  • Version 1.1: 2020-04-29
    Changes: Database references
  • Version 1.2: 2023-10-11
    Changes: Data collection, Database references, Refinement description
  • Version 1.3: 2023-11-15
    Changes: Data collection