4V24 | pdb_00004v24

Sphingosine kinase 1 in complex with PF-543

• PDB DOI: https://doi.org/10.2210/pdb4V24/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2014-10-05 Released: 2014-10-15 
• Deposition Author(s): Elkins, J.M., Wang, J., Sorrell, F., Tallant, C., Wang, D., Shrestha, L., Bountra, C., von Delft, F., Knapp, S., Edwards, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.210 (Depositor), 0.210 (DCC) 
• R-Value Work: 
  0.182 (Depositor) 
• R-Value Observed: 
  0.183 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of Sphingosine Kinase 1 with Pf-543.

Wang, J., Knapp, S., Pyne, N.J., Pyne, S., Elkins, J.M.

(2014) ACS Med Chem Lett 5: 1329

• PubMed: 25516793 
• DOI: https://doi.org/10.1021/ml5004074
• Primary Citation Related Structures: 
  4V24


• PubMed Abstract: 
  

  The most potent inhibitor of Sphingosine Kinase 1 (SPHK1) so far identified is PF-543. The crystal structure of SPHK1 in complex with inhibitor PF-543 to 1.8 Å resolution reveals the inhibitor bound in a bent conformation analogous to that expected of a bound sphingosine substrate but with a rotated head group. The structural data presented will aid in the design of SPHK1 and SPHK2 inhibitors with improved properties.

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Organizational Affiliation: 
• Structural Genomics Consortium, University of Oxford , Old Road Campus Research Building, Old Road Campus, Roosevelt Drive, Oxford OX3 7DQ, U.K.
Structural Genomics Consortium, University of Oxford , Old Road Campus Research Building, Old Road Campus, Roosevelt Drive, Oxford OX3 7DQ, U.K. ; Target Discovery Institute, University of Oxford , NDM Research Building, Old Road Campus, Roosevelt Drive, Oxford OX3 7FZ, U.K.
Cell Biology Group, Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde , Glasgow G4 0RE, U.K.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 83.33 kDa 
• Atom Count: 6,004 
• Modeled Residue Count: 700 
• Deposited Residue Count: 742 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SPHINGOSINE KINASE 1	A, B	371	Homo sapiens	Mutation(s): 0  EC: 2.7.1.91 (PDB Primary Data), 2.3.1 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NYA1 (Homo sapiens) Explore Q9NYA1  Go to UniProtKB:  Q9NYA1
PHAROS:  Q9NYA1 GTEx:  ENSG00000176170

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GYR	C [auth A], E [auth B]	{(2R)-1-[4-({3-METHYL-5-[(PHENYLSULFONYL)METHYL]PHENOXY}METHYL)BENZYL]PYRROLIDIN-2-YL}METHANOL C27 H31 N O4 S NPUXORBZRBIOMQ-RUZDIDTESA-N
ACT	D [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Binding Affinity Annotations
ID	Source	Binding Affinity
GYR	BindingDB:  4V24	Ki: min: 3.6, max: 4.3 (nM) from 3 assay(s)
		Kd: 5 (nM) from 1 assay(s)
		IC50: min: 0.8, max: 387 (nM) from 11 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.210 (Depositor), 0.210 (DCC) 
• R-Value Work:  0.182 (Depositor) 
• R-Value Observed: 0.183 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 86.57	α = 90
b = 60.549	β = 107.17
c = 89.592	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-10-15 
Deposition Author(s): Elkins, J.M., Wang, J., Sorrell, F., Tallant, C., Wang, D., Shrestha, L., Bountra, C., von Delft, F., Knapp, S., Edwards, A.

Revision History  

• Version 1.0: 2014-10-15
  Type: Initial release
  
• Version 1.1: 2014-12-31
  Changes: Database references
• Version 1.2: 2018-01-24
  Changes: Structure summary
• Version 1.3: 2024-01-10
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description