› 4l02

X-ray diffraction
2.75Å resolution

Crystal Structure of SphK1 with inhibitor

Released:
DOI: 10.2210/pdb4l02/pdb
PDB entry 4l02 coloured by chain, front view.
PDB entry 4l02 coloured by chain, side view.
PDB entry 4l02 coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Structure 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 23 4608-16 (2013)
PMID: 23845219

Function and Biology Details

Reaction catalysed: 
ATP + a sphingoid base = ADP + a sphingoid base 1-phosphate
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-192699 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Sphingosine kinase 1 Chains: A, B, C
Molecule details ›
Chains: A, B, C
Length: 384 amino acids
Theoretical weight: 42.89 KDa
Source organism: Homo sapiens
Expression system: Spodoptera frugiperda
UniProt:
  • Canonical: Q9NYA1 (Residues: 9-364; Coverage: 93%)
Gene names: SK1, SPHK, SPHK1, SPK
Sequence domains: Diacylglycerol kinase catalytic domain
Structure domains:

Ligands and Environments

1 bound ligand:
Ligand 1V2 3 x 1V2
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ALS BEAMLINE 5.0.2
Spacegroup: C2221
Unit cell:
a: 102.575Å b: 225.684Å c: 106.411Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.21 0.208 0.255
Expression system: Spodoptera frugiperda

Quick links

Citations

16 review citations

Targeting of proangiogenic signalling pathways in chronic inflammation.
Tas et al. (2016)
15 more

7 mentions without citation

Sphingolipid biosynthesis in man and microbes.
Harrison et al. (2018)
6 more