8XB1 | pdb_00008xb1

Crystal structure of FLT3 in complex with a Pyrazinamide Macrocycle derivative


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.85 Å
  • R-Value Free: 
    0.287 (Depositor), 0.289 (DCC) 
  • R-Value Work: 
    0.230 (Depositor), 0.236 (DCC) 
  • R-Value Observed: 
    0.236 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


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Literature

Structure-Based Optimization of Pyrazinamide-Containing Macrocyclic Derivatives as Fms-like Tyrosine Kinase 3 (FLT3) Inhibitors to Overcome Clinical Mutations.

Zheng, X.Chen, Z.Guo, M.Liang, H.Song, X.Liu, Y.Liao, Z.Zhang, Y.Guo, J.Zhou, Y.Zhang, Z.M.Tu, Z.Zhang, Y.Chen, Y.Zhang, Z.Lu, X.

(2024) Acs Pharmacol Transl Sci 7: 1485-1506

  • DOI: https://doi.org/10.1021/acsptsci.4c00071
  • Primary Citation of Related Structures:  
    8XB1

  • PubMed Abstract: 

    Secondary mutations in Fms-like tyrosine kinase 3-tyrosine kinase domain (FLT3-TKD) (e.g., D835Y and F691L) have become a major on-target resistance mechanism of FLT3 inhibitors, which present a significant clinical challenge. To date, no effective drugs have been approved to simultaneously overcome clinical resistance caused by these two mutants. Thus, a series of pyrazinamide macrocyclic compounds were first designed and evaluated to overcome the secondary mutations of FLT3. The representative 8v exhibited potent inhibitory activities against FLT3 D835Y and FLT3 D835Y/F691L with IC 50 values of 1.5 and 9.7 nM, respectively. 8v also strongly suppressed the proliferation against Ba/F3 cells transfected with FLT3-ITD, FLT3-ITD-D835Y, FLT3-ITD-F691L, FLT3-ITD-D835Y-F691L, and MV4-11 acute myeloid leukemia (AML) cell lines with IC 50 values of 12.2, 10.5, 24.6, 16.9, and 6.8 nM, respectively. Furthermore, 8v demonstrated ideal anticancer efficacy in a Ba/F3-FLT3-ITD-D835Y xenograft model. The results suggested that 8v can serve as a promising macrocycle-based FLT3 inhibitor for the treatment of AML.


  • Organizational Affiliation
    • State Key Laboratory of Bioactive Molecules and Druggability Assessment, International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Discovery of Chinese Ministry of Education, Guangzhou City Key Laboratory of Precision Chemical Drug Development, School of Pharmacy, Jinan University, #855 Xingye Avenue, Guangzhou 510632, China.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Receptor-type tyrosine-protein kinase FLT3346Homo sapiensMutation(s): 0 
EC: 2.7.10.1
UniProt & NIH Common Fund Data Resources
Find proteins for P36888 (Homo sapiens)
Explore P36888 
Go to UniProtKB:  P36888
PHAROS:  P36888
GTEx:  ENSG00000122025 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP36888
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ZX3 (Subject of Investigation/LOI)
Query on ZX3

Download Ideal Coordinates CCD File 
B [auth A]3^3-ethyl-5^4-morpholino-6,9-dioxa-2,4-diaza-3(2,6)-pyrazina-1(4,1)-piperidina-5(1,3)-benzenacycloundecaphane-3^5-carboxamide
C26 H37 N7 O4
LXUHFRDECMQRJE-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.85 Å
  • R-Value Free:  0.287 (Depositor), 0.289 (DCC) 
  • R-Value Work:  0.230 (Depositor), 0.236 (DCC) 
  • R-Value Observed: 0.236 (Depositor) 
Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 83.127α = 90
b = 83.127β = 90
c = 139.208γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
autoPROCdata reduction
XDSdata scaling
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China--

Revision History  (Full details and data files)

  • Version 1.0: 2024-12-11
    Type: Initial release