3BL9

Synthetic Gene Encoded DcpS bound to inhibitor DG157493


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.174 
  • R-Value Observed: 0.176 

wwPDB Validation 3D Report Full Report


This is version 1.2 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
  • Structures With Same Primary Citation

  • 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 t ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Scavenger mRNA-decapping enzyme DcpS
A, B
301Homo sapiensMutation(s): 0 
Gene Names: DCPSDCS1HINT5HSPC015
EC: 3 (PDB Primary Data), 3.6.1.59 (UniProt)
Find proteins for Q96C86 (Homo sapiens)
Go to UniProtKB:  Q96C86
NIH Common Fund Data Resources
PHAROS  Q96C86
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
DD2
Query on DD2

Download CCD File 
A
5-{[1-(2,3-dichlorobenzyl)piperidin-4-yl]methoxy}quinazoline-2,4-diamine
C21 H23 Cl2 N5 O
XVLUVRFYGVJKGJ-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
DD2IC50:  43.939998626708984   nM  BindingDB
DD2EC50:  67   nM  BindingDB
DD2IC50:  43.939998626708984   nM  Binding MOAD
DD2IC50:  0.07999999821186066   nM  BindingDB
DD2IC50:  66   nM  PDBBind
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.174 
  • R-Value Observed: 0.176 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 49.406α = 62.35
b = 56.867β = 77.93
c = 59.504γ = 79.54
Software Package:
Software NamePurpose
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
d*TREKdata scaling
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-10-21
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2017-10-25
    Changes: Refinement description