Crystal structure of human sphingosine-1-phosphate lyase in complex with inhibitor 6-[(2R)-4-(4-benzyl-7-chlorophthalazin-1-yl)-2-methylpiperazin-1-yl]pyridine-3-carbonitrile

Experimental Data Snapshot

  • Resolution: 2.40 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.179 

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This is version 1.3 of the entry. See complete history


Orally Active 7-Substituted (4-Benzylphthalazin-1-yl)-2-methylpiperazin-1-yl]nicotinonitriles as Active-Site Inhibitors of Sphingosine 1-Phosphate Lyase for the Treatment of Multiple Sclerosis.

Weiler, S.Braendlin, N.Beerli, C.Bergsdorf, C.Schubart, A.Srinivas, H.Oberhauser, B.Billich, A.

(2014) J Med Chem 57: 5074-5084

  • DOI: https://doi.org/10.1021/jm500338n
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Sphingosine 1-phosphate (S1P) lyase has recently been implicated as a therapeutic target for the treatment of multiple sclerosis (MS), based on studies in a genetic mouse model. Potent active site directed inhibitors of the enzyme are not known so far. Here we describe the discovery of (4-benzylphthalazin-1-yl)-2-methylpiperazin-1-yl]nicotinonitrile 5 in a high-throughput screen using a biochemical assay, and its further optimization. This class of compounds was found to inhibit catalytic activity of S1PL by binding to the active site of the enzyme, as seen in the cocrystal structure of derivative 31 with the homodimeric human S1P lyase. 31 induces profound reduction of peripheral T cell numbers after oral dosage and confers pronounced protection in a rat model of multiple sclerosis. In conclusion, this novel class of direct S1P lyase inhibitors provides excellent tools to further explore the therapeutic potential of T cell-targeted therapies in multiple sclerosis and other autoimmune and inflammatory diseases.

  • Organizational Affiliation

    Novartis Institutes for BioMedical Research , Basel, CH-4002, Switzerland.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Sphingosine-1-phosphate lyase 1
A, B
511Homo sapiensMutation(s): 0 
Gene Names: KIAA1252SGPL1
UniProt & NIH Common Fund Data Resources
Find proteins for O95470 (Homo sapiens)
Explore O95470 
Go to UniProtKB:  O95470
PHAROS:  O95470
GTEx:  ENSG00000166224 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO95470
Sequence Annotations
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
Query on LLP
A, B
Binding Affinity Annotations 
IDSourceBinding Affinity
30J BindingDB:  4Q6R IC50: 210 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 2.40 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.179 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 127.985α = 90
b = 130.532β = 90
c = 68.224γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
XDSdata reduction
XSCALEdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

  • Released Date: 2014-05-21 
  • Deposition Author(s): Srinivas, H.

Revision History  (Full details and data files)

  • Version 1.0: 2014-05-21
    Type: Initial release
  • Version 1.1: 2014-07-23
    Changes: Database references
  • Version 1.2: 2023-09-20
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.3: 2023-12-06
    Changes: Data collection