3BL7

Synthetic Gene Encoded DcpS bound to inhibitor DG156844

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.31 Å
  • R-Value Free: 0.276 
  • R-Value Work: 0.211 
  • R-Value Observed: 0.214 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history. 


Literature

DcpS as a therapeutic target for spinal muscular atrophy.

Singh, J., Salcius, M., Liu, S.W., Staker, B.L., Mishra, R., Thurmond, J., Michaud, G., Mattoon, D.R., Printen, J., Christensen, J., Bjornsson, J.M., Pollok, B.A., Kiledjian, M., Stewart, L., Jarecki, J., Gurney, M.E.

(2008) ACS Chem Biol 3: 711-722

  • DOI: 10.1021/cb800120t
  • Primary Citation of Related Structures:  
    3BL7, 3BL9, 3BLA

  • PubMed Abstract: 

    • Spinal muscular atrophy (SMA) is caused by deletion or mutation of both copies of the SMN1 gene, which produces an essential protein known as SMN. The severity of SMA is modified by variable copy number of a second gene,SMN2, which produces an mRNA that is incorrectly spliced with deletion of the last exon ...

    Spinal muscular atrophy (SMA) is caused by deletion or mutation of both copies of the SMN1 gene, which produces an essential protein known as SMN. The severity of SMA is modified by variable copy number of a second gene,SMN2, which produces an mRNA that is incorrectly spliced with deletion of the last exon. We described previously the discovery of potent C5-substituted quinazolines that increase SMN2 gene expression by 2-fold. Discovery of potent SMN2 promoter inducers relied on a cellular assay without knowledge of the molecular target. Using protein microarray scanning with a radiolabeled C5-substituted quinazoline probe, we identified the scavenger decapping enzyme, DcpS, as a potential binder. We show that the C5-substituted quinazolines potently inhibit DcpS decapping activity and that the potency of inhibition correlates with potency forSMN2 promoter induction. Binding of C5-substituted quinazolines to DcpS holds the enzyme in an open, catalytically incompetent conformation. DcpS is a nuclear shuttling protein that binds and hydrolyzes the m(7)GpppN mRNA cap structure and a modulator of RNA metabolism. Therefore DcpS represents a novel therapeutic target for modulating gene expression by a small molecule.

    Organizational Affiliation: 

    deCODE chemistry, Inc., 2501 Davey Road, Woodridge, Illinois 60517, USA.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Scavenger mRNA-decapping enzyme DcpSA, B301Homo sapiensMutation(s): 0 
Gene Names: DCPS, DCS1, HINT5, HSPC015
EC: 3 (PDB Primary Data), 3.6.1.59 (UniProt)
Find proteins for Q96C86 (Homo sapiens)
Explore Q96C86 
Go to UniProtKB:  Q96C86
NIH Common Fund Data Resources
PHAROS:  Q96C86
GTEx:  ENSG00000110063
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
DD1
Query on DD1
Download Ideal Coordinates CCD File 
 C [auth A]5-{[1-(2-fluorobenzyl)piperidin-4-yl]methoxy}quinazoline-2,4-diamine
C21 H24 F N5 O
GYKIQIOWVKCVBP-UHFFFAOYSA-N		 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
DD1IC50:  0.029999999329447746   nM  BindingDB
DD1IC50:  7.619999885559082   nM  BindingDB
DD1IC50:  7.619999885559082   nM  Binding MOAD
DD1IC50 :  4   nM  PDBBind
DD1EC50:  4   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.31 Å
  • R-Value Free: 0.276 
  • R-Value Work: 0.211 
  • R-Value Observed: 0.214 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 49.257α = 118.81
b = 56.271β = 92.39
c = 60.334γ = 99.99
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-10-21
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance