1RWO

Crystal structure of human caspase-1 in complex with 4-oxo-3-{6-[4-(quinoxalin-2-ylamino)-benzoylamino]-2-thiophen-2-yl-hexanoylamino}-pentanoic acid

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.200 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history. 


Literature

Structural analysis of caspase-1 inhibitors derived from Tethering.

O'Brien, T., Fahr, B.T., Sopko, M.M., Lam, J.W., Waal, N.D., Raimundo, B.C., Purkey, H.E., Pham, P., Romanowski, M.J.

(2005) Acta Crystallogr Sect F Struct Biol Cryst Commun 61: 451-458

  • DOI: 10.1107/S1744309105010109
  • Primary Citation of Related Structures:  
    1RWM, 1RWK, 1RWP, 1RWO, 1RWN

  • PubMed Abstract: 

    • Caspase-1 is a key endopeptidase responsible for the post-translational processing of the IL-1beta and IL-18 cytokines and small-molecule inhibitors that modulate the activity of this enzyme are predicted to be important therapeutic treatments for many i ...

    Caspase-1 is a key endopeptidase responsible for the post-translational processing of the IL-1beta and IL-18 cytokines and small-molecule inhibitors that modulate the activity of this enzyme are predicted to be important therapeutic treatments for many inflammatory diseases. A fragment-assembly approach, accompanied by structural analysis, was employed to generate caspase-1 inhibitors. With the aid of Tethering with extenders (small molecules that bind to the active-site cysteine and contain a free thiol), two novel fragments that bound to the active site and made a disulfide bond with the extender were identified by mass spectrometry. Direct linking of each fragment to the extender generated submicromolar reversible inhibitors that significantly reduced secretion of IL-1beta but not IL-6 from human peripheral blood mononuclear cells. Thus, Tethering with extenders facilitated rapid identification and synthesis of caspase-1 inhibitors with cell-based activity and subsequent structural analyses provided insights into the enzyme's ability to accommodate different inhibitor-binding modes in the active site.

    Organizational Affiliation: 

    Department of Biology, Sunesis Pharmaceuticals Inc., USA.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Interleukin-1 beta convertase A178Homo sapiensMutation(s): 0 
Gene Names: CASP1, IL1BC, IL1BCE
EC: 3.4.22.36
Find proteins for P29466 (Homo sapiens)
Explore P29466 
Go to UniProtKB:  P29466
NIH Common Fund Data Resources
PHAROS:  P29466
GTEx:  ENSG00000137752
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Interleukin-1 beta convertase B88Homo sapiensMutation(s): 0 
Gene Names: CASP1, IL1BC, IL1BCE
EC: 3.4.22.36
Find proteins for P29466 (Homo sapiens)
Explore P29466 
Go to UniProtKB:  P29466
NIH Common Fund Data Resources
PHAROS:  P29466
GTEx:  ENSG00000137752
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BTH
Query on BTH
Download Ideal Coordinates CCD File 
A
4-OXO-3-{6-[4-(QUINOXALIN-2-YLAMINO)-BENZOYLAMINO]-2-THIOPHEN-2-YL-HEXANOYLAMINO}-PENTANOIC ACID
C30 H31 N5 O5 S
FDQYFIJPZTYCIY-RDGATRHJSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.200 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 63.184α = 90
b = 63.184β = 90
c = 160.931γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
d*TREKdata scaling
AMoREphasing

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-12-28
    Type: Initial release
  • Version 1.1: 2008-04-29
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance