4Q6R Lyase Lyase Inhibitor date Apr 23, 2014
title Crystal Structure Of Human Sphingosine-1-Phosphate Lyase In With Inhibitor 6-[(2r)-4-(4-Benzyl-7-Chlorophthalazin-1-Yl) Methylpiperazin-1-Yl]Pyridine-3-Carbonitrile
authors H.Srinivas
compound source
Molecule: Sphingosine-1-Phosphate Lyase 1
Chain: A, B
Synonym: S1pl, Sp-Lyase 1, Spl 1, Hspl, Sphingosine-1-Phosp Aldolase;
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Kiaa1252, Sgpl1
Expression_system: Spodoptera Frugiperda
Expression_system_taxid: 7108
symmetry Space Group: P 21 21 2
R_factor 0.178 R_Free 0.206
length a length b length c angle alpha angle beta angle gamma
127.985 130.532 68.224 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.40 Å
ligand 30J, GOL, LLP, PO4, SIN enzyme Lyase E.C. BRENDA
A, B

Primary referenceOrally Active 7-Substituted (4-Benzyl-phthalazin-1-yl)-2-methyl-piperazin-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, J Med Chem. 2014 May 8. PMID:24809814
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (155 Kb) [Save to disk]
  • Biological Unit Coordinates (4q6r.pdb1.gz) 149 Kb
  • LPC: Ligand-Protein Contacts for 4Q6R
  • CSU: Contacts of Structural Units for 4Q6R
  • Structure Factors (412 Kb)
  • Retrieve 4Q6R in mmCIF format [Save to disk]
  • Re-refined 4q6r structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4Q6R in 3D
  • Proteopedia, because life has more than 2D.
  • On Jmol, a nice Rasmol like molecule viewer. This is good for easiest viewing of basic structure.
  • On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz.
  • Visual 3D analysis of 4Q6R
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Electron Density related parameters from EDS Electron Density Server, at Upsala
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 4Q6R, from MSDmotif at EBI
  • Fold representative 4q6r from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4q6r_A] [4q6r] [4q6r_B]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 4Q6R
  • Community annotation for 4Q6R at PDBWiki (http://pdbwiki.org)

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