4V24

Sphingosine kinase 1 in complex with PF-543


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.182 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal Structure of Sphingosine Kinase 1 with Pf-543.

Wang, J.Knapp, S.Pyne, N.J.Pyne, S.Elkins, J.M.

(2014) Acs Med.Chem.Lett. 5: 1329

  • DOI: 10.1021/ml5004074

  • PubMed Abstract: 
  • The most potent inhibitor of Sphingosine Kinase 1 (SPHK1) so far identified is PF-543. The crystal structure of SPHK1 in complex with inhibitor PF-543 to 1.8 Å resolution reveals the inhibitor bound in a bent conformation analogous to that expected o ...

    The most potent inhibitor of Sphingosine Kinase 1 (SPHK1) so far identified is PF-543. The crystal structure of SPHK1 in complex with inhibitor PF-543 to 1.8 Å resolution reveals the inhibitor bound in a bent conformation analogous to that expected of a bound sphingosine substrate but with a rotated head group. The structural data presented will aid in the design of SPHK1 and SPHK2 inhibitors with improved properties.


    Organizational Affiliation

    Cell Biology Group, Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde , Glasgow G4 0RE, U.K.,Structural Genomics Consortium, University of Oxford , Old Road Campus Research Building, Old Road Campus, Roosevelt Drive, Oxford OX3 7DQ, U.K.,Structural Genomics Consortium, University of Oxford , Old Road Campus Research Building, Old Road Campus, Roosevelt Drive, Oxford OX3 7DQ, U.K. ; Target Discovery Institute, University of Oxford , NDM Research Building, Old Road Campus, Roosevelt Drive, Oxford OX3 7FZ, U.K.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
SPHINGOSINE KINASE 1
A, B
371Homo 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 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ACT
Query on ACT

Download SDF File 
Download CCD File 
A
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
GYR
Query on GYR

Download SDF File 
Download CCD File 
A, B
{(2R)-1-[4-({3-METHYL-5-[(PHENYLSULFONYL)METHYL]PHENOXY}METHYL)BENZYL]PYRROLIDIN-2-YL}METHANOL
PF-543
C27 H31 N O4 S
NPUXORBZRBIOMQ-RUZDIDTESA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
GYRKi: 4.3 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.182 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 86.570α = 90.00
b = 60.549β = 107.17
c = 89.592γ = 90.00
Software Package:
Software NamePurpose
Aimlessdata scaling
REFMACrefinement
PHASERphasing
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-10-15
    Type: Initial release
  • Version 1.1: 2014-12-31
    Type: Database references
  • Version 1.2: 2018-01-24
    Type: Structure summary