6VOV

Crystal structure of Syk in complex with GS-9876


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.217 
  • R-Value Observed: 0.220 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report

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This is version 1.2 of the entry. See complete history


Literature

Discovery of Lanraplenib (GS-9876): A Once-Daily Spleen Tyrosine Kinase Inhibitor for Autoimmune Diseases.

Blomgren, P.Chandrasekhar, J.Di Paolo, J.A.Fung, W.Geng, G.Ip, C.Jones, R.Kropf, J.E.Lansdon, E.B.Lee, S.Lo, J.R.Mitchell, S.A.Murray, B.Pohlmeyer, C.Schmitt, A.Suekawa-Pirrone, K.Wise, S.Xiong, J.M.Xu, J.Yu, H.Zhao, Z.Currie, K.S.

(2020) ACS Med Chem Lett 11: 506-513

  • DOI: https://doi.org/10.1021/acsmedchemlett.9b00621
  • Primary Citation of Related Structures:  
    6VOV

  • PubMed Abstract: 

    Spleen tyrosine kinase (SYK) is a critical regulator of signaling in a variety of immune cell types such as B-cells, monocytes, and macrophages. Accordingly, there have been numerous efforts to identify compounds that selectively inhibit SYK as a means to treat autoimmune and inflammatory diseases. We previously disclosed GS-9973 (entospletinib) as a selective SYK inhibitor that is under clinical evaluation in hematological malignancies. However, a BID dosing regimen and drug interaction with proton pump inhibitors (PPI) prevented development of entospletinib in inflammatory diseases. Herein, we report the discovery of a second-generation SYK inhibitor, GS-9876 (lanraplenib), which has human pharmacokinetic properties suitable for once-daily administration and is devoid of any interactions with PPI. Lanraplenib is currently under clinical evaluation in multiple autoimmune indications.


  • Organizational Affiliation

    Gilead Sciences, 199 E. Blaine Street, Seattle, Washington 98102, United States.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Tyrosine-protein kinase SYK
A, B
281Homo sapiensMutation(s): 0 
Gene Names: SYK
EC: 2.7.10.2
UniProt & NIH Common Fund Data Resources
Find proteins for P43405 (Homo sapiens)
Go to UniProtKB:  P43405
PHAROS:  P43405
GTEx:  ENSG00000165025 
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
R6D (Subject of Investigation/LOI)
Query on R6D

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
6-(6-aminopyrazin-2-yl)-N-{4-[4-(oxetan-3-yl)piperazin-1-yl]phenyl}imidazo[1,2-a]pyrazin-8-amine
C23 H25 N9 O
XCIGZBVOUQVIPI-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
R6D BindingDB:  6VOV IC50: min: 6.2, max: 13.5 (nM) from 2 assay(s)
EC50: min: 24, max: 1305 (nM) from 13 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.217 
  • R-Value Observed: 0.220 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 39.973α = 81.015
b = 42.05β = 90.33
c = 87.613γ = 79.252
Software Package:
Software NamePurpose
PHENIXrefinement
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing

Structure Validation

View Full Validation Report

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-03-11
    Type: Initial release
  • Version 1.1: 2020-04-29
    Changes: Database references
  • Version 1.2: 2023-10-11
    Changes: Data collection, Database references, Refinement description