4U5T

Crystal Structure of VBP Leucine Zipper with Bound Arylstibonic Acid


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.30 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.260 
  • R-Value Observed: 0.262 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

P6981, an arylstibonic acid, is a novel low nanomolar inhibitor of cAMP response element-binding protein binding to DNA.

Zhao, J.Stagno, J.R.Varticovski, L.Nimako, E.Rishi, V.McKinnon, K.Akee, R.Shoemaker, R.H.Ji, X.Vinson, C.

(2012) Mol Pharmacol 82: 814-823

  • DOI: 10.1124/mol.112.080820
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Several basic leucine zipper (B-ZIP) transcription factors have been implicated in cancer, substance abuse, and other pathological conditions. We previously identified arylstibonic acids that bind to B-ZIP proteins and inhibit their interaction with ...

    Several basic leucine zipper (B-ZIP) transcription factors have been implicated in cancer, substance abuse, and other pathological conditions. We previously identified arylstibonic acids that bind to B-ZIP proteins and inhibit their interaction with DNA. In this study, we used electrophoretic mobility shift assay to analyze 46 arylstibonic acids for their activity to disrupt the DNA binding of three B-ZIP [CCAAT/enhancer-binding protein α, cyclic AMP-response element-binding protein (CREB), and vitellogenin gene-binding protein (VBP)] and two basic helix-loop-helix leucine zipper (B-HLH-ZIP) [USF (upstream stimulating factor) and Mitf] proteins. Twenty-five arylstibonic acids showed activity at micromolar concentrations. The most active compound, P6981 [2-(3-stibonophenyl)malonic acid], had half-maximal inhibition at ~5 nM for CREB. Circular dichroism thermal denaturation studies indicated that P6981 binds both the B-ZIP domain and the leucine zipper. The crystal structure of an arylstibonic acid, NSC13778, bound to the VBP leucine zipper identified electrostatic interactions between both the stibonic and carboxylic acid groups of NSC13778 [(E)-3-(3-stibonophenyl)acrylic acid] and arginine side chains of VBP, which is also involved in interhelical salt bridges in the leucine zipper. P6981 induced GFP-B-ZIP chimeric proteins to partially localize to the cytoplasm, demonstrating that it is active in cells. P6981 inhibited the growth of a patient-derived clear cell sarcoma cell line whose oncogenic potential is driven by a chimeric protein EWS-ATF1 (Ewing's sarcoma protein-activating transcription factor 1), which contains the DNA binding domain of ATF1, a B-ZIP protein. NSC13778 inhibited the growth of xenografted clear cell sarcoma, and no toxicity was observed. These experiments suggest that antimony containing arylstibonic acids are promising leads for suppression of DNA binding activities of B-ZIP and B-HLH-ZIP transcription factors.


    Organizational Affiliation

    Laboratory of Metabolism, National Cancer Institute, Bethesda, Maryland 20892, USA.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
VBP leucine zipper
A, B
39Homo sapiensMutation(s): 0 
Gene Names: TEFKIAA1655
Find proteins for Q10587 (Homo sapiens)
Go to UniProtKB:  Q10587
NIH Common Fund Data Resources
PHAROS  Q10587
Protein Feature View
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
3CG
Query on 3CG

Download CCD File 
A
(2Z)-3-{3-[dihydroxy(oxido)-lambda~5~-stibanyl]phenyl}prop-2-enoic acid
C9 H9 O5 Sb
ZTQRMGDLUGQTTF-VSJPESBJSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.30 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.260 
  • R-Value Observed: 0.262 
  • Space Group: P 61
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 68.84α = 90
b = 68.84β = 90
c = 77.23γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
PDB_EXTRACTdata extraction
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 2014-07-25 
  • Released Date: 2014-08-06 
  • Deposition Author(s): Stagno, J.R., Ji, X.

Revision History 

  • Version 1.0: 2014-08-06
    Type: Initial release
  • Version 1.1: 2017-11-22
    Changes: Derived calculations, Other, Refinement description, Source and taxonomy