3NS7

Succinic Acid Amides as P2-P3 Replacements for Inhibitors of Interleukin-1beta Converting Enzyme (ICE or Caspase 1)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Work: 0.188 
  • R-Value Observed: 0.214 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history. 


Literature

Succinic acid amides as P2-P3 replacements for inhibitors of interleukin-1beta converting enzyme (ICE or caspase 1).

Galatsis, P., Caprathe, B., Gilmore, J., Thomas, A., Linn, K., Sheehan, S., Harter, W., Kostlan, C., Lunney, E., Stankovic, C., Rubin, J., Brady, K., Allen, H., Talanian, R.

(2010) Bioorg Med Chem Lett 20: 5184-5190

  • DOI: https://doi.org/10.1016/j.bmcl.2010.07.004
  • Primary Citation of Related Structures:  
    3NS7

  • PubMed Abstract: 

    Succinic acid amides have been found to be effective P2-P3 scaffold replacements for peptidic ICE inhibitors. Heteroarylalkyl fragments occupying the P4 position provided access to compounds with nM affinities. Utilization of an acylal prodrug moiety was required to overcome biopharmaceutical issues which led to the identification of 17f, a potential clinical candidate.

    • Organizational Affiliation: 

    Pfizer Global R&D, Ann Arbor, MI 48105, USA. paul.galatsis@pfizer.com


Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Caspase-1162Homo 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
GTEx:  ENSG00000137752 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP29466
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Caspase-188Homo 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
GTEx:  ENSG00000137752 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP29466
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
3NS
Query on 3NS
Download Ideal Coordinates CCD File 
C [auth B](3S)-4-hydroxy-3-{[(2S)-4-{[2-(2-methyl-1H-benzimidazol-1-yl)ethyl]amino}-2-(1-methylethyl)-4-oxobutanoyl]amino}butanoic acid
C21 H30 N4 O5
LAXUUUDZAVTGRW-HOTGVXAUSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
3NS PDBBind:  3NS7 Ki: 4.68 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Work: 0.188 
  • R-Value Observed: 0.214 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 63.95α = 90
b = 63.95β = 90
c = 158.55γ = 90
Software Package:
Software NamePurpose
CrystalCleardata collection
X-PLORmodel building
X-PLORrefinement
XDSdata reduction
MAR345data collection
X-PLORphasing

Structure Validation

View Full Validation Report



View more in-depth experimental data
Entry History 

Deposition Data

  • Released Date: 2011-08-17 
    • Deposition Author(s): Galatsis, P.

Revision History  (Full details and data files)

  • Version 1.0: 2011-08-17
    Type: Initial release
  • Version 1.1: 2012-12-12
    Changes: Other
  • Version 1.2: 2017-11-08
    Changes: Advisory, Refinement description
  • Version 1.3: 2023-12-27
    Changes: Advisory, Data collection, Database references, Derived calculations