4L02 Transferase Transferase Inhibitor date May 30, 2013
title Crystal Structure Of Sphk1 With Inhibitor
authors X.Min, N.Walker, Z.Wang
compound source
Molecule: Sphingosine Kinase 1
Chain: A, B, C
Fragment: Unp Residues 9-364
Synonym: Sk 1, Spk 1
Ec: 2.7.1.91
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Sphingosine Kinase 1, Sphk, Sphk1, Spk
Expression_system: Spodoptera Frugiperda
Expression_system_taxid: 7108
Expression_system_strain: Sf9
Expression_system_vector_type: Pfastbac
symmetry Space Group: C 2 2 21
R_factor 0.208 R_Free 0.255
crystal
cell
length a length b length c angle alpha angle beta angle gamma
102.575 225.684 106.411 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.75 Å
ligand 1V2 enzyme Transferase E.C.2.7.1.91 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, C, B
  • sphinganine kinase activity
  • sphingosine-1-phosphate rece...


  • Primary referenceStructure guided design of a series of sphingosine kinase (SphK) inhibitors., Gustin DJ, Li Y, Brown ML, Min X, Schmitt MJ, Wanska M, Wang X, Connors R, Johnstone S, Cardozo M, Cheng AC, Jeffries S, Franks B, Li S, Shen S, Wong M, Wesche H, Xu G, Carlson TJ, Plant M, Morgenstern K, Rex K, Schmitt J, Coxon A, Walker N, Kayser F, Wang Z, Bioorg Med Chem Lett. 2013 Jun 20. pii: S0960-894X(13)00739-7. doi:, 10.1016/j.bmcl.2013.06.030. PMID:23845219
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (173 Kb) [Save to disk]
  • Biological Unit Coordinates (4l02.pdb1.gz) 59 Kb
  • Biological Unit Coordinates (4l02.pdb2.gz) 57 Kb
  • Biological Unit Coordinates (4l02.pdb3.gz) 57 Kb
  • LPC: Ligand-Protein Contacts for 4L02
  • CSU: Contacts of Structural Units for 4L02
  • Structure Factors (706 Kb)
  • Retrieve 4L02 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4L02 from S2C, [Save to disk]
  • Re-refined 4l02 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4L02 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 4L02
  • 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 4L02, from MSDmotif at EBI
  • Fold representative 4l02 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4l02_B] [4l02_C] [4l02_A] [4l02]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 4L02: [DAGKc ] by SMART
  • Other resources with information on 4L02
  • Community annotation for 4L02 at PDBWiki (http://pdbwiki.org)

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