1RWW

Crystal structure of human caspase-1 in complex with 4-oxo-3-[(6-{[4-(quinoxalin-2-ylamino)-benzoylamino]-methyl}-pyridine-3-carbonyl)-amino]-butyric acid

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.193 

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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: https://doi.org/10.1016/j.bmcl.2005.10.048
  • Primary Citation of Related Structures:  
    1RWW, 1RWX

  • 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. 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 ...

    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
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Interleukin-1 beta convertaseA178Homo sapiensMutation(s): 0 
Gene Names: CASP1, IL1BC, IL1BCE
EC: 3.4.22.36
UniProt & NIH Common Fund Data Resources
Find proteins for P29466 (Homo sapiens)
Explore P29466 
Go to UniProtKB:  P29466
PHAROS:  P29466
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP29466
Protein Feature View
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  • Reference Sequence
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(by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Interleukin-1 beta convertaseB88Homo sapiensMutation(s): 0 
Gene Names: CASP1, IL1BC, IL1BCE
EC: 3.4.22.36
UniProt & NIH Common Fund Data Resources
Find proteins for P29466 (Homo sapiens)
Explore P29466 
Go to UniProtKB:  P29466
PHAROS:  P29466
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP29466
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
OQB
Query on OQB
Download Ideal Coordinates CCD File 
C [auth A]4-OXO-3-[(6-{[4-(QUINOXALIN-2-YLAMINO)-BENZOYLAMINO]-METHYL}-PYRIDINE-3-CARBONYL)-AMINO]-BUTYRIC ACID
C26 H22 N6 O5
GOTFAMYWTAZALY-FQEVSTJZSA-N		 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
OQB BindingDB:  1RWW Ki: 5 (nM) from 1 assay(s)
IC50: 5 (nM) from 1 assay(s)
PDBBind:  1RWW Ki: 5 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.193 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 62.962α = 90
b = 62.962β = 90
c = 161.401γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
d*TREKdata scaling
AMoREphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

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