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

Experimental Data Snapshot

  • Resolution: 1.77 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.208 

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Ligand Structure Quality Assessment 

This is version 1.2 of the entry. See complete history


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: https://doi.org/10.1016/j.bmcl.2016.10.087
  • Primary Citation of Related Structures:  
    5TR6, 5TT7

  • 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 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.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Tyrosine-protein kinase SYK289Homo sapiensMutation(s): 0 
Gene Names: SYK
UniProt & NIH Common Fund Data Resources
Find proteins for P43405 (Homo sapiens)
Explore P43405 
Go to UniProtKB:  P43405
PHAROS:  P43405
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP43405
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on 7KF

Download Ideal Coordinates CCD File 
B [auth A]2-{[(1R,2S)-2-aminocyclohexyl]amino}-4-[(3-methylphenyl)amino]-6,7-dihydro-5H-pyrrolo[3,4-d]pyrimidin-5-one
C19 H24 N6 O
Binding Affinity Annotations 
IDSourceBinding Affinity
7KF BindingDB:  5TT7 IC50: 13 (nM) from 1 assay(s)
EC50: 35 (nM) from 1 assay(s)
Binding MOAD:  5TT7 IC50: 13 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 1.77 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.208 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 39.815α = 90
b = 85.204β = 90
c = 88.912γ = 90
Software Package:
Software NamePurpose
HKL-2000data scaling
PDB_EXTRACTdata extraction
HKL-2000data reduction
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

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