4V2O

Structure of saposin B in complex with chloroquine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.13 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.229 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

The Lysosomal Protein Saposin B Binds Chloroquine.

Huta, B.P.Mehlenbacher, M.R.Nie, Y.Lai, X.Zubieta, C.Bou-Abdallah, F.Doyle, R.P.

(2016) Chemmedchem 11: 277

  • DOI: 10.1002/cmdc.201500494

  • PubMed Abstract: 
  • Chloroquine (CQ) has been widely used in the treatment of malaria since the 1950s, though toxicity and resistance is increasingly limiting its use in the clinic. More recently, CQ is also becoming recognized as an important therapeutic compound for t ...

    Chloroquine (CQ) has been widely used in the treatment of malaria since the 1950s, though toxicity and resistance is increasingly limiting its use in the clinic. More recently, CQ is also becoming recognized as an important therapeutic compound for the treatment of autoimmune disorders and has shown activity as an anticancer agent. However, the full extent of CQ pharmacology in humans is still unclear. Herein, we demonstrate that the lysosomal protein saposin B (sapB), critical for select lipid degradation, binds CQ with implications for both CQ function and toxicity. Using isothermal titration calorimetry (ITC) and fluorescence quenching experiments, CQ was shown to bind to the dimeric form of sapB at both pH 5.5 and pH 7.4 with an average binding affinity of 2.3×10(4)  m(-1). X-ray crystallography confirmed this, and the first complete crystal structure of sapB with a bound small molecule (CQ) is reported. The results suggest that sapB might play a role in mitigating CQ-based toxicity and that sapB might itself be overwhelmed by CQ causing impaired lipid degradation.


    Organizational Affiliation

    Department of Chemistry, Syracuse University, 111 College Place, Syracuse, NY, 13244, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
SAPOSIN-B
A, B, C
82Homo sapiensMutation(s): 0 
Gene Names: PSAP (GLBA, SAP1)
Find proteins for P07602 (Homo sapiens)
Go to Gene View: PSAP
Go to UniProtKB:  P07602
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CLQ
Query on CLQ

Download SDF File 
Download CCD File 
B, C
N4-(7-CHLORO-QUINOLIN-4-YL)-N1,N1-DIETHYL-PENTANE-1,4-DIAMINE
CHLOROQUINE
C18 H26 Cl N3
WHTVZRBIWZFKQO-CQSZACIVSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.13 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.229 
  • Space Group: P 32 2 1
Unit Cell:
Length (Å)Angle (°)
a = 75.299α = 90.00
b = 75.299β = 90.00
c = 94.716γ = 120.00
Software Package:
Software NamePurpose
XSCALEdata scaling
XDSdata reduction
BUSTERrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-12-09
    Type: Initial release
  • Version 1.1: 2016-03-02
    Type: Database references