4L02

Crystal Structure of SphK1 with inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.75 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.208 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structure guided design of a series of sphingosine kinase (SphK) inhibitors.

Gustin, D.J.Li, Y.Brown, M.L.Min, X.Schmitt, M.J.Wanska, M.Wang, X.Connors, R.Johnstone, S.Cardozo, M.Cheng, A.C.Jeffries, S.Franks, B.Li, S.Shen, S.Wong, M.Wesche, H.Xu, G.Carlson, T.J.Plant, M.Morgenstern, K.Rex, K.Schmitt, J.Coxon, A.Walker, N.Kayser, F.Wang, Z.

(2013) Bioorg.Med.Chem.Lett. 23: 4608-4616

  • DOI: 10.1016/j.bmcl.2013.06.030

  • PubMed Abstract: 
  • Sphingosine-1-phosphate (S1P) signaling plays a vital role in mitogenesis, cell migration and angiogenesis. Sphingosine kinases (SphKs) catalyze a key step in sphingomyelin metabolism that leads to the production of S1P. There are two isoforms of Sph ...

    Sphingosine-1-phosphate (S1P) signaling plays a vital role in mitogenesis, cell migration and angiogenesis. Sphingosine kinases (SphKs) catalyze a key step in sphingomyelin metabolism that leads to the production of S1P. There are two isoforms of SphK and observations made with SphK deficient mice show the two isoforms can compensate for each other's loss. Thus, inhibition of both isoforms is likely required to block SphK dependent angiogenesis. A structure based approach was used to design and synthesize a series of SphK inhibitors resulting in the identification of the first potent inhibitors of both isoforms of human SphK. Additionally, to our knowledge, this series of inhibitors contains the only sufficiently potent inhibitors of murine SphK1 with suitable physico-chemical properties to pharmacologically interrogate the role of SphK1 in rodent models and to reproduce the phenotype of SphK1 (-/-) mice.


    Organizational Affiliation

    Department of Chemistry, Amgen Inc., 1120 Veterans Boulevard, South San Francisco, CA 94080, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Sphingosine kinase 1
A, B, C
384Homo sapiensMutation(s): 0 
Gene Names: SPHK1 (SK1, SPHK, SPK)
EC: 2.7.1.91
Find proteins for Q9NYA1 (Homo sapiens)
Go to Gene View: SPHK1
Go to UniProtKB:  Q9NYA1
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
1V2
Query on 1V2

Download SDF File 
Download CCD File 
A, B, C
(2R,4S)-1-[2-(4-{[4-(3,4-dichlorophenyl)-1,3-thiazol-2-yl]amino}phenyl)ethyl]-2-(hydroxymethyl)piperidin-4-ol
C23 H25 Cl2 N3 O2 S
SQJKFWCRPARYPY-MOPGFXCFSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
1V2IC50: 20 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.75 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.208 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 102.575α = 90.00
b = 225.684β = 90.00
c = 106.411γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
REFMACrefinement
SCALAdata scaling
MOSFLMdata reduction
BOSdata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-07-24
    Type: Initial release
  • Version 1.1: 2013-08-28
    Type: Database references