3VZD

Crystal structure of Sphingosine Kinase 1 with inhibitor and ADP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.209 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Molecular basis of sphingosine kinase 1 substrate recognition and catalysis.

Wang, Z.Min, X.Xiao, S.H.Johnstone, S.Romanow, W.Meininger, D.Xu, H.Liu, J.Dai, J.An, S.Thibault, S.Walker, N.

(2013) Structure 21: 798-809

  • DOI: 10.1016/j.str.2013.02.025
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Sphingosine kinase 1 (SphK1) is a lipid kinase that catalyzes the conversion of sphingosine to sphingosine-1-phosphate (S1P), which has been shown to play a role in lymphocyte trafficking, angiogenesis, and response to apoptotic stimuli. As a central ...

    Sphingosine kinase 1 (SphK1) is a lipid kinase that catalyzes the conversion of sphingosine to sphingosine-1-phosphate (S1P), which has been shown to play a role in lymphocyte trafficking, angiogenesis, and response to apoptotic stimuli. As a central enzyme in modulating the S1P levels in cells, SphK1 emerges as an important regulator for diverse cellular functions and a potential target for drug discovery. Here, we present the crystal structures of human SphK1 in the apo form and in complexes with a substrate sphingosine-like lipid, ADP, and an inhibitor at 2.0-2.3 Å resolution. The SphK1 structures reveal a two-domain architecture in which its catalytic site is located in the cleft between the two domains and a hydrophobic lipid-binding pocket is buried in the C-terminal domain. Comparative analysis of these structures with mutagenesis and kinetic studies provides insight into how SphK1 recognizes the lipid substrate and catalyzes ATP-dependent phosphorylation.


    Organizational Affiliation

    Department of Molecular Structure and Characterization, Amgen, Inc., 1120 Veterans Boulevard, South San Francisco, CA 94080, USA. zwang@amgen.com



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Sphingosine kinase 1A, B, C, D, E, F361Homo sapiensMutation(s): 0 
Gene Names: SPHK1SPHKSPKSK1
EC: 2.7.1.91 (PDB Primary Data), 2.3.1 (UniProt)
Find proteins for Q9NYA1 (Homo sapiens)
Explore Q9NYA1 
Go to UniProtKB:  Q9NYA1
NIH Common Fund Data Resources
PHAROS  Q9NYA1
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ADP
Query on ADP

Download CCD File 
C, E
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
 Ligand Interaction
UUL
Query on UUL

Download CCD File 
A, B, C, D, E, F
4-{[4-(4-chlorophenyl)-1,3-thiazol-2-yl]amino}phenol
C15 H11 Cl N2 O S
ZFGXZJKLOFCECI-UHFFFAOYSA-N
 Ligand Interaction
POP
Query on POP

Download CCD File 
B
PYROPHOSPHATE 2-
H2 O7 P2
XPPKVPWEQAFLFU-UHFFFAOYSA-L
 Ligand Interaction
CL
Query on CL

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B, C, E
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
MG
Query on MG

Download CCD File 
B, C, E
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
UULIC50:  35000   nM  BindingDB
UULKi:  500   nM  BindingDB
UULKi:  16000   nM  BindingDB
UULKi:  17000   nM  BindingDB
UULIC50 :  500   nM  PDBBind
UULKi:  12000   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.209 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 102.202α = 90
b = 106.573β = 90
c = 226.02γ = 90
Software Package:
Software NamePurpose
SCALAdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-05-01
    Type: Initial release
  • Version 1.1: 2014-01-29
    Changes: Database references