1RWX

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.214 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Tethering identifies fragment that yields potent inhibitors of human caspase-1.

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

(2006) Bioorg.Med.Chem.Lett. 16: 559-562

  • DOI: 10.1016/j.bmcl.2005.10.048
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Disulfide Tethering was applied to the active site of human caspase-1, resulting in the discovery of a novel, tricyclic molecular fragment that selectively binds in S4. This fragment was developed into a class of potent inhibitors of human caspase-1. ...

    Disulfide Tethering was applied to the active site of human caspase-1, resulting in the discovery of a novel, tricyclic molecular fragment that selectively binds in S4. This fragment was developed into a class of potent inhibitors of human caspase-1. Several key analogues determined the optimal distance of the tricycle from the catalytic residues, the relative importance of various features of the tricycle, and the importance of the linker.


    Organizational Affiliation

    Department of Chemistry, Sunesis Pharmaceuticals, 341 Oyster Point Boulevard, South San Francisco, CA 94080, USA. bfahr@sunesis.com




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Interleukin-1 beta convertase
A
178Homo sapiensMutation(s): 0 
Gene Names: CASP1 (IL1BC, IL1BCE)
EC: 3.4.22.36
Find proteins for P29466 (Homo sapiens)
Go to Gene View: CASP1
Go to UniProtKB:  P29466
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Interleukin-1 beta convertase
B
88Homo sapiensMutation(s): 0 
Gene Names: CASP1 (IL1BC, IL1BCE)
EC: 3.4.22.36
Find proteins for P29466 (Homo sapiens)
Go to Gene View: CASP1
Go to UniProtKB:  P29466
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
YBH
Query on YBH

Download SDF File 
Download CCD File 
A
4-OXO-3-{6-[4-(QUINOXALIN-2-YLOXY)-BENZOYLAMINO]-2-THIOPHEN-2-YL-HEXANOYLAMINO}-BUTYRIC ACID
C29 H28 N4 O6 S
DJLHSAXTGGXZPX-UNMCSNQZSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
YBHKi: 43 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.214 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 63.371α = 90.00
b = 63.371β = 90.00
c = 162.399γ = 90.00
Software Package:
Software NamePurpose
AMoREphasing
REFMACrefinement
CrystalCleardata reduction
d*TREKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-12-28
    Type: Initial release
  • Version 1.1: 2007-10-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Version format compliance