8E1X

FGFR2 kinase domain in complex with a Pyrazolo[1,5-a]pyrimidine analog (Compound 29)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.68 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.224 
  • R-Value Observed: 0.226 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history


Literature

Discovery of Potent and Selective Inhibitors of Wild-Type and Gatekeeper Mutant Fibroblast Growth Factor Receptor (FGFR) 2/3.

Shvartsbart, A.Roach, J.J.Witten, M.R.Koblish, H.Harris, J.J.Covington, M.Hess, R.Lin, L.Frascella, M.Truong, L.Leffet, L.Conlen, P.Beshad, E.Klabe, R.Katiyar, K.Kaldon, L.Young-Sciame, R.He, X.Petusky, S.Chen, K.J.Horsey, A.Lei, H.T.Epling, L.B.Deller, M.C.Vechorkin, O.Yao, W.

(2022) J Med Chem 65: 15433-15442

  • DOI: https://doi.org/10.1021/acs.jmedchem.2c01366
  • Primary Citation of Related Structures:  
    8E1X

  • PubMed Abstract: 

    Upregulation of the fibroblast growth factor receptor (FGFR) signaling pathway has been implicated in multiple cancer types, including cholangiocarcinoma and bladder cancer. Consequently, small molecule inhibition of FGFR has emerged as a promising therapy for patients suffering from these diseases. First-generation pan-FGFR inhibitors, while highly effective, suffer from several drawbacks. These include treatment-related hyperphosphatemia and significant loss of potency for the mutant kinases. Herein, we present the discovery and optimization of novel FGFR2/3 inhibitors that largely maintain potency for the common gatekeeper mutants and have excellent selectivity over FGFR1. A combination of meticulous structure-activity relationship (SAR) analysis, structure-based drug design, and medicinal chemistry rationale ultimately led to compound 29 , a potent and selective FGFR2/3 inhibitor with excellent in vitro absorption, distribution, metabolism, excretion (ADME), and pharmacokinetics in rat. A pharmacodynamic study of a closely related compound established that maximum inhibition of downstream ERK phosphorylation could be achieved with no significant effect on serum phosphate levels relative to vehicle.


  • Organizational Affiliation

    Prelude Therapeutics, Wilmington, Delaware 19803, United States.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Fibroblast growth factor receptor 2
A, B
330Homo sapiensMutation(s): 0 
Gene Names: FGFR2BEKKGFRKSAM
EC: 2.7.10.1
UniProt & NIH Common Fund Data Resources
Find proteins for P21802 (Homo sapiens)
Explore P21802 
Go to UniProtKB:  P21802
PHAROS:  P21802
GTEx:  ENSG00000066468 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP21802
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
U9P (Subject of Investigation/LOI)
Query on U9P

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
(5M)-N-methyl-5-{(6M,8S)-5-{[(3S)-oxolan-3-yl]amino}-6-[1-(propan-2-yl)-1H-pyrazol-3-yl]pyrazolo[1,5-a]pyrimidin-3-yl}pyridine-3-carboxamide
C23 H26 N8 O2
XGJBIMKIGAOMPJ-KRWDZBQOSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
PTR
Query on PTR
A, B
L-PEPTIDE LINKINGC9 H12 N O6 PTYR
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.68 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.224 
  • R-Value Observed: 0.226 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 76.515α = 90
b = 77.482β = 90
c = 126.272γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other privateUnited States--

Revision History  (Full details and data files)

  • Version 1.0: 2022-11-23
    Type: Initial release
  • Version 1.1: 2022-12-14
    Changes: Database references
  • Version 1.2: 2023-10-25
    Changes: Data collection, Refinement description
  • Version 1.3: 2023-11-15
    Changes: Data collection
  • Version 1.4: 2024-11-20
    Changes: Structure summary