8XKP | pdb_00008xkp

Crystal structure of human tyrosine-protein kinase Fes/Fps in complex with compound 17c


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 
    0.234 (Depositor), 0.242 (DCC) 
  • R-Value Work: 
    0.190 (Depositor), 0.214 (DCC) 
  • R-Value Observed: 
    0.192 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history

Literature

Optimization of Novel Pyrido-pyridazinone Derivatives as FER Tyrosine Kinase Inhibitors, Leading to the Potent DS08701581.

Taniguchi, T.Yasumatsu, I.Inagaki, H.Baba, D.Toyota, A.Kaneta, Y.Odagiri, T.Momose, T.Kawai, J.Imaoka, T.Nakayama, K.

(2024) ACS Med Chem Lett 15: 1010-1016

  • DOI: https://doi.org/10.1021/acsmedchemlett.4c00030
  • Primary Citation Related Structures: 
    8XKP

  • PubMed Abstract: 

    Previously, we reported the new pyrido-pyridazinone template as a feline sarcoma-related (FER) tyrosine kinase inhibitor. Representative compound 1 ( DS21360717 ) showed strong enzyme inhibitory activity (IC50 = 0.5 nM), however, its antitumor effect was insufficient, probably due to poor solubility and resultant low bioavailability (BA). In addition, the kinase selectivity was inadequate, which may result in certain safety risks. Here, we focused on derivatization of the unoptimized C-5 position to obtain promising FER inhibitors possessing strong antitumor effects and improved selectivity, referring to their X-ray crystal structure and the docking model with FES proto-oncogene tyrosine kinase as an FER surrogate. While establishing the synthetic route of the pyrido-pyridazinone scaffold, we obtained a desired compound via our derivatization. Our optimized compound 17c (DS08701581 ) showed the highest class cell-free and cell activities in this template, good oral BA, and improved kinase selectivity, resulting in significant tumor growth inhibition in the Ba/F3-FER tumor model without body weight loss.


  • Organizational Affiliation
    • R&D Division, Daiichi Sankyo Co., Ltd., 1-2-58 Hiromachi, Shinagawa-ku, Tokyo 140-8710, Japan.

Macromolecule Content 

  • Total Structure Weight: 43.17 kDa 
  • Atom Count: 3,111 
  • Modeled Residue Count: 372 
  • Deposited Residue Count: 375 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Tyrosine-protein kinase Fes/Fps375Homo sapiensMutation(s): 0 
Gene Names: FESFPS
EC: 2.7.10.2
UniProt & NIH Common Fund Data Resources
Find proteins for P07332 (Homo sapiens)
Explore P07332 
Go to UniProtKB:  P07332
PHAROS:  P07332
GTEx:  ENSG00000182511 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP07332
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1LWS
(Subject of Investigation/LOI)

Query on A1LWS



Download:Ideal Coordinates CCD File
D [auth A]7-[[(1R,2S)-2-azanylcyclohexyl]amino]-5-[[3-[(2S,6R)-2,6-dimethylmorpholin-4-yl]phenyl]amino]-4-oxidanylidene-3H-pyrido[3,4-d]pyridazine-8-carbonitrile
C26 H32 N8 O2
KGWLGIOZFOBIIA-VYXDICFBSA-N
SO4

Query on SO4



Download:Ideal Coordinates CCD File
B [auth A],
C [auth A]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free:  0.234 (Depositor), 0.242 (DCC) 
  • R-Value Work:  0.190 (Depositor), 0.214 (DCC) 
  • R-Value Observed: 0.192 (Depositor) 
Space Group: P 63
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 80.651α = 90
b = 80.651β = 90
c = 131.207γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2025-01-01
    Type: Initial release
  • Version 1.1: 2025-03-19
    Changes: Database references