9Z2S | pdb_00009z2s

Structure of KIT V654A mutant with Compound 11


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 
    0.230 (Depositor), 0.238 (DCC) 
  • R-Value Work: 
    0.166 (Depositor), 0.176 (DCC) 
  • R-Value Observed: 
    0.170 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Design and Synthesis of BLU-654, a Potent and Selective Mutant KIT V654A Inhibitor for the Treatment of Imatinib-Resistant GIST.

Moine, L.Hu, W.Davis, A.Perola, E.Guo, J.Barvian, K.Choi, Y.S.Grassian, A.Kim, J.L.Ahmad, O.K.Dineen, T.A.

(2026) J Med Chem 

  • DOI: https://doi.org/10.1021/acs.jmedchem.5c03554
  • Primary Citation Related Structures: 
    9Z1L, 9Z2S

  • PubMed Abstract: 

    Gastrointestinal stromal tumor (GIST) is the most common type of sarcoma of the gastrointestinal tract, with approximately 5000 new cases annually in the USA. Approximately 80% of GIST cases are driven by activating mutations in KIT in exon 9 or 11. Resistance to present therapies like imatinib often arises from secondary KIT mutations, especially V654A (exon 13), which is the most frequent resistance mutation. Tyrosine kinase inhibitors (TKIs) currently approved for GIST can cause dose-limiting side effects due to off-target inhibition of other kinases. Herein, we report the discovery and optimization of BLU-654 (compound 18 ), a highly potent and kinome-sparing KIT V654A inhibitor. Preclinical efficacy studies demonstrated its prolonged antitumor activity in a KIT V654A cell-derived xenograft mouse model. BLU-654 offers a potent and selective profile suitable for combination therapy for KIT- mutant GIST patients.


  • Organizational Affiliation
    • Blueprint Medicines Corporation, 45 Sidney St., Cambridge, Massachusetts 02139, United States.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Mast/stem cell growth factor receptor359Homo sapiensMutation(s): 1 
Gene Names: KIT
EC: 2.7.10.1
UniProt & NIH Common Fund Data Resources
Find proteins for A0A0U2N547 (Homo sapiens)
Explore A0A0U2N547 
Go to UniProtKB:  A0A0U2N547
GTEx:  ENSG00000157404 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0U2N547
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1CZ3 (Subject of Investigation/LOI)
Query on A1CZ3

Download Ideal Coordinates CCD File 
G [auth A]6-[(6-amino-2-cyclopropylpyrimidin-4-yl)amino]-N-methyl-4-[(propan-2-yl)amino]pyridine-3-carboxamide
C17 H23 N7 O
JZWHUUDQWPHFDT-UHFFFAOYSA-N
DMS
Query on DMS

Download Ideal Coordinates CCD File 
B [auth A],
D [auth A]
DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
EDO
Query on EDO

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free:  0.230 (Depositor), 0.238 (DCC) 
  • R-Value Work:  0.166 (Depositor), 0.176 (DCC) 
  • R-Value Observed: 0.170 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 47.682α = 90
b = 79.906β = 90
c = 92.24γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
DIALSdata reduction
PDB_EXTRACTdata extraction
REFMACphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data

  • Released Date: 2026-03-18 
  • Deposition Author(s): Kim, J.L.

Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2026-03-18
    Type: Initial release
  • Version 1.1: 2026-03-25
    Changes: Database references