7KIA

Crystal structure of FGFR2 kinase domain gatekeeper mutant V564F in complex with covalent compound 19


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.22 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.200 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.0 of the entry. See complete history


Literature

Discovery of Aminopyrazole Derivatives as Potent Inhibitors of Wild-Type and Gatekeeper Mutant FGFR2 and 3.

Brawn, R.A.Cook, A.Omoto, K.Ke, J.Karr, C.Colombo, F.Virrankoski, M.Prajapati, S.Reynolds, D.Bolduc, D.M.Nguyen, T.V.Gee, P.Borrelli, D.Caleb, B.Yao, S.Irwin, S.Larsen, N.A.Selvaraj, A.Zhao, X.Ioannidis, S.

(2021) ACS Med Chem Lett 12: 93-98

  • DOI: 10.1021/acsmedchemlett.0c00517
  • Primary Citation of Related Structures:  
    7KIA, 7KIE

  • PubMed Abstract: 
  • Fibroblast growth factor receptors (FGFR) 2 and 3 have been established as drivers of numerous types of cancer with multiple drugs approved or entering late stage clinical trials. A limitation of current inhibitors is vulnerability to gatekeeper resistance mutations ...

    Fibroblast growth factor receptors (FGFR) 2 and 3 have been established as drivers of numerous types of cancer with multiple drugs approved or entering late stage clinical trials. A limitation of current inhibitors is vulnerability to gatekeeper resistance mutations. Using a combination of targeted high-throughput screening and structure-based drug design, we have developed a series of aminopyrazole based FGFR inhibitors that covalently target a cysteine residue on the P-loop of the kinase. The inhibitors show excellent activity against the wild-type and gatekeeper mutant versions of the enzymes. Further optimization using SAR analysis and structure-based drug design led to analogues with improved potency and drug metabolism and pharmacokinetics properties.


    Organizational Affiliation

    H3 Biomedicine, 300 Technology Square, Cambridge, Massachusetts 02139, United States.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Fibroblast growth factor receptor 2A, B308Homo sapiensMutation(s): 1 
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
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
WFD (Subject of Investigation/LOI)
Query on WFD

Download Ideal Coordinates CCD File 
C [auth A], F [auth B]1-[4-(4-{4-(4-methylpiperazin-1-yl)-6-[(3-methyl-1H-pyrazol-5-yl)amino]pyrimidin-2-yl}phenyl)piperidin-1-yl]prop-2-en-1-one
C27 H34 N8 O
GPGFFJPUFNKAFY-UHFFFAOYSA-N
 Ligand Interaction
FLC
Query on FLC

Download Ideal Coordinates CCD File 
D [auth A], G [auth B]CITRATE ANION
C6 H5 O7
KRKNYBCHXYNGOX-UHFFFAOYSA-K
 Ligand Interaction
NA
Query on NA

Download Ideal Coordinates CCD File 
E [auth A], H [auth B]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.22 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.200 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 105.98α = 90
b = 117.3β = 90
c = 63.81γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2021-02-10
    Type: Initial release