5EUD

S1P Lyase Bacterial Surrogate bound to N-(1-(4-(3-hydroxyprop-1-yn-1-yl)phenyl)-2-((4-methoxy-2,5-dimethylbenzyl)amino)ethyl)-5-methylisoxazole-3-carboxamide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.24 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.162 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Creation of a S1P Lyase bacterial surrogate for structure-based drug design.

Argiriadi, M.A.Banach, D.Radziejewska, E.Marchie, S.DiMauro, J.Dinges, J.Dominguez, E.Hutchins, C.Judge, R.A.Queeney, K.Wallace, G.Harris, C.M.

(2016) Bioorg.Med.Chem.Lett. 26: 2293-2296

  • DOI: 10.1016/j.bmcl.2016.02.084
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • S1P Lyase (SPL) has been described as a drug target in the treatment of autoimmune diseases. It plays an important role in maintaining intracellular levels of S1P thereby affecting T cell egress from lymphoid tissues. Several groups have already publ ...

    S1P Lyase (SPL) has been described as a drug target in the treatment of autoimmune diseases. It plays an important role in maintaining intracellular levels of S1P thereby affecting T cell egress from lymphoid tissues. Several groups have already published approaches to inhibit S1P Lyase with small molecules, which in turn increase endogenous S1P concentrations resulting in immunosuppression. The use of structural biology has previously aided SPL inhibitor design. Novel construct design is at times necessary to provide a reagent for protein crystallography. Here we present a chimeric bacterial protein scaffold used for protein X-ray structures in the presence of early small molecule inhibitors. Mutations were introduced to the bacterial SPL from Symbiobacterium thermophilum which mimic the human enzyme. As a result, two mutant StSPL crystal structures resolved to 2.8Å and 2.2Å resolutions were solved and provide initial structural hypotheses for an isoxazole chemical series, whose optimization is discussed in the accompanying paper.


    Organizational Affiliation

    AbbVie Bioresearch Center, 100 Research Drive, Worcester, MA 01605, USA.,AbbVie, 1 North Waukegan Road, North Chicago, IL 60064, USA.,AbbVie Bioresearch Center, 381 Plantation Street, Worcester, MA 01605, USA. Electronic address: maria.argiriadi@abbvie.com.,AbbVie Bioresearch Center, 381 Plantation Street, Worcester, MA 01605, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Putative sphingosine-1-phosphate lyase
A, B
514Symbiobacterium thermophilum (strain T / IAM 14863)Mutation(s): 4 
Find proteins for Q67PY4 (Symbiobacterium thermophilum (strain T / IAM 14863))
Go to UniProtKB:  Q67PY4
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

Download SDF File 
Download CCD File 
A, B
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
5S6
Query on 5S6

Download SDF File 
Download CCD File 
A
~{N}-[(1~{S})-2-[(4-methoxy-2,5-dimethyl-phenyl)methylamino]-1-[4-(3-oxidanylprop-1-ynyl)phenyl]ethyl]-5-methyl-1,2-oxazole-3-carboxamide
C26 H29 N3 O4
DNHSLHQHJBUNLI-XMMPIXPASA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
LLP
Query on LLP
A, B
L-PEPTIDE LINKINGC14 H22 N3 O7 PLYS
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
5S6IC50: 150 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.24 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.162 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 83.940α = 90.00
b = 85.126β = 90.00
c = 129.507γ = 90.00
Software Package:
Software NamePurpose
BUSTERrefinement
HKL-2000data reduction
AutoPROCdata scaling
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-03-16
    Type: Initial release
  • Version 1.1: 2016-04-06
    Type: Database references
  • Version 1.2: 2016-04-27
    Type: Database references
  • Version 1.3: 2016-07-20
    Type: Data collection