4NBL

Tailoring Small Molecules for an Allosteric Site on Procaspase-6


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.756 Å
  • R-Value Free: 0.179 
  • R-Value Work: 0.155 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Tailoring small molecules for an allosteric site on procaspase-6.

Murray, J.Giannetti, A.M.Steffek, M.Gibbons, P.Hearn, B.R.Cohen, F.Tam, C.Pozniak, C.Bravo, B.Lewcock, J.Jaishankar, P.Ly, C.Q.Zhao, X.Tang, Y.Chugha, P.Arkin, M.R.Flygare, J.Renslo, A.R.

(2014) Chemmedchem 9: 73-77

  • DOI: 10.1002/cmdc.201300424
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Although they represent attractive therapeutic targets, caspases have so far proven recalcitrant to the development of drugs targeting the active site. Allosteric modulation of caspase activity is an alternate strategy that potentially avoids the nee ...

    Although they represent attractive therapeutic targets, caspases have so far proven recalcitrant to the development of drugs targeting the active site. Allosteric modulation of caspase activity is an alternate strategy that potentially avoids the need for anionic and electrophilic functionality present in most active-site inhibitors. Caspase-6 has been implicated in neurodegenerative disease, including Huntington's and Alzheimer's diseases. Herein we describe a fragment-based lead discovery effort focused on caspase-6 in its active and zymogen forms. Fragments were identified for procaspase-6 using surface plasmon resonance methods and subsequently shown by X-ray crystallography to bind a putative allosteric site at the dimer interface. A fragment-merging strategy was employed to produce nanomolar-affinity ligands that contact residues in the L2 loop at the dimer interface, significantly stabilizing procaspase-6. Because rearrangement of the L2 loop is required for caspase-6 activation, our results suggest a strategy for the allosteric control of caspase activation with drug-like small molecules.


    Organizational Affiliation

    Departments of Structural Biology, Biochemical Pharmacology, Neuroscience, and Discovery Chemistry, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080 (USA). murray.jeremy@gene.com.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Caspase-6
A, B
282Homo sapiensMutation(s): 1 
Gene Names: CASP6 (MCH2)
EC: 3.4.22.59
Find proteins for P55212 (Homo sapiens)
Go to Gene View: CASP6
Go to UniProtKB:  P55212
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

Download SDF File 
Download CCD File 
A, B
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
2J6
Query on 2J6

Download SDF File 
Download CCD File 
A
5-fluoro-2-({[3-(pyrimidin-2-yl)pyridin-2-yl]amino}methyl)phenol
C16 H13 F N4 O
YTVDOVJPKJLMHL-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
2J6Kd: 470 nM (99) BINDINGDB
2J6Kd: 470 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.756 Å
  • R-Value Free: 0.179 
  • R-Value Work: 0.155 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 115.784α = 90.00
b = 115.784β = 90.00
c = 79.544γ = 90.00
Software Package:
Software NamePurpose
CBASSdata collection
PHENIXrefinement
PHASERphasing
SCALAdata scaling
PDB_EXTRACTdata extraction
XSCALEdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-01-01
    Type: Initial release
  • Version 1.1: 2014-01-22
    Type: Database references