5TR6

Discovery of TAK-659, an Orally Available Investigational Inhibitor of Spleen Tyrosine Kinase (SYK)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.93 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.193 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Discovery of TAK-659 an orally available investigational inhibitor of Spleen Tyrosine Kinase (SYK).

Lam, B.Arikawa, Y.Cramlett, J.Dong, Q.de Jong, R.Feher, V.Grimshaw, C.E.Farrell, P.J.Hoffman, I.D.Jennings, A.Jones, B.Matuszkiewicz, J.Miura, J.Miyake, H.Natala, S.R.Shi, L.Takahashi, M.Taylor, E.Wyrick, C.Yano, J.Zalevsky, J.Nie, Z.

(2016) Bioorg. Med. Chem. Lett. 26: 5947-5950

  • DOI: 10.1016/j.bmcl.2016.10.087
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Spleen Tyrosine Kinase (SYK) is a non-receptor cytoplasmic tyrosine kinase that is primarily expressed in hematopoietic cells. SYK is a key mediator for a variety of inflammatory cells, including B cells, mast cells, macrophages and neutrophils and t ...

    Spleen Tyrosine Kinase (SYK) is a non-receptor cytoplasmic tyrosine kinase that is primarily expressed in hematopoietic cells. SYK is a key mediator for a variety of inflammatory cells, including B cells, mast cells, macrophages and neutrophils and therefore, an attractive approach for treatment of both inflammatory diseases and oncology indications. Using in house co-crystal structure information, and structure-based drug design, we designed and optimized a novel series of heteroaromatic pyrrolidinone SYK inhibitors resulting in the selection of the development candidate TAK-659. TAK-659 is currently undergoing Phase I clinical trials for advanced solid tumor and lymphoma malignancies, a Phase Ib study in advanced solid tumors in combination with nivolumab, and PhIb/II trials for relapsed/refractory AML.


    Organizational Affiliation

    PolyScientific Consulting Inc., 4624 Aragon Dr, San Diego, CA 92115, USA.,Beryllium Discovery, 3 Preston Ct., Bedford, MA 01730, USA.,Neuropore Therapies, 10835 Road to Cure, Suite 230, San Diego, CA 92121, USA.,Schrödinger, Inc., 5820 Oberlin Drive, Ste. 203, San Diego, CA 92121, USA.,Nektar Therapeutics, 455 Mission Bay Boulevard South, San Francisco, CA 94158, USA.,Takeda California, Inc., 10410 Science Center Drive, San Diego, CA 92121, USA. Electronic address: betty.lam@takeda.com.,FronThera US Pharmaceuticals, 11526 Sorrento Valley Road, Suite D, San Diego, CA 92121, USA.,Takeda Pharmaceutical Company Limited, 26-1, Muraoka-Higashi 2-chome, Fujisawa, Kanagawa 251-8555, Japan.,Takeda California, Inc., 10410 Science Center Drive, San Diego, CA 92121, USA.,Celgene Quanticel Research, 9393 Towne Center Drive, Suite 110, San Diego, CA 92121, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Tyrosine-protein kinase SYK
A
289Homo sapiensMutation(s): 0 
Gene Names: SYK
EC: 2.7.10.2
Find proteins for P43405 (Homo sapiens)
Go to Gene View: SYK
Go to UniProtKB:  P43405
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EDO
Query on EDO

Download SDF File 
Download CCD File 
A
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
7KG
Query on 7KG

Download SDF File 
Download CCD File 
A
6-{[(1R,2S)-2-aminocyclohexyl]amino}-7-fluoro-4-(1-methyl-1H-pyrazol-4-yl)-1,2-dihydro-3H-pyrrolo[3,4-c]pyridin-3-one
C17 H21 F N6 O
MJHOMTRKVMKCNE-NWDGAFQWSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
7KGIC50: 2 - 3.2 nM (100) BINDINGDB
7KGEC50: 9.8 nM (100) BINDINGDB
7KGIC50: 3.2 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.93 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.193 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 39.941α = 90.00
b = 85.283β = 90.00
c = 90.283γ = 90.00
Software Package:
Software NamePurpose
MOLREPphasing
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
HKL-2000data scaling
DENZOdata reduction
HKL-2000data reduction
HKL-2000data collection
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-11-30
    Type: Initial release
  • Version 1.1: 2016-12-14
    Type: Database references
  • Version 1.2: 2017-11-22
    Type: Refinement description