1BMQ

CRYSTAL STRUCTURE OF THE COMPLEX OF INTERLEUKIN-1BETA CONVERTING ENZYME (ICE) WITH A PEPTIDE BASED INHIBITOR, (3S )-N-METHANESULFONYL-3-({1-[N-(2-NAPHTOYL)-L-VALYL]-L-PROLYL }AMINO)-4-OXOBUTANAMIDE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.317 
  • R-Value Work: 0.233 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Peptide based interleukin-1 beta converting enzyme (ICE) inhibitors: synthesis, structure activity relationships and crystallographic study of the ICE-inhibitor complex.

Okamoto, Y.Anan, H.Nakai, E.Morihira, K.Yonetoku, Y.Kurihara, H.Sakashita, H.Terai, Y.Takeuchi, M.Shibanuma, T.Isomura, Y.

(1999) Chem.Pharm.Bull. 47: 11-21


  • PubMed Abstract: 
  • Based on the X-ray structure of the complex of Ac-Tyr-Val-Ala-Asp-H (L-709049) and interleukin-1 beta converting enzyme (ICE), we synthesized compounds which were derived from 2-NapCO-Val-Pro-Asp-CH2OPh (1) to obtain a potent inhibitor in the cell as ...

    Based on the X-ray structure of the complex of Ac-Tyr-Val-Ala-Asp-H (L-709049) and interleukin-1 beta converting enzyme (ICE), we synthesized compounds which were derived from 2-NapCO-Val-Pro-Asp-CH2OPh (1) to obtain a potent inhibitor in the cell assay. Among these compounds, (3S)-N-methanesulfonyl-3-[[1-[N-(2-naphthoyl)-L-valyl]-L-prolyl]amino]- 4-oxobutanamide (27c) showed high potency not only in the enzyme assay but also cell assay with IC50 values of 38 nM and 0.23 microM, respectively. Compound 27c, with a c log P value of 1.76, had a more hydrophilic character compared with 1. Compound 27c also dose dependently inhibited LPS-primed ATP-induced IL-1 beta release in mice. The crystal structure of the complex of compound 27c and ICE revealed that compound 27c had further interactions with ICE in the naphthoyl group at the P4 position and in the methyl group of the methanesulfonamidecarbonyl group at the P1 position, compared with L-709049. To our knowledge, compound 27c is the first example that shows a strong inhibitory activity without the carboxyl group at the P1 position.


    Organizational Affiliation

    Institute for Drug Discovery Research, Yamanouchi Pharmaceutical Co. Ltd., Ibaraki, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PROTEIN (INTERLEUKIN-1 BETA CONVERTASE)
A
167Homo 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
PROTEIN (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
MNO
Query on MNO

Download SDF File 
Download CCD File 
A
(3S)-N-METHANESULFONYL-3-({1-[N-(2-NAPHTOYL)-L-VALYL]-L-PROLYL}AMINO)-4-OXOBUTANAMIDE
C26 H32 N4 O7 S
IGFYXXJBAZZOHF-FUDKSRODSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
MNOIC50: 38 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.317 
  • R-Value Work: 0.233 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 64.700α = 90.00
b = 64.700β = 90.00
c = 161.400γ = 90.00
Software Package:
Software NamePurpose
PROCESSdata reduction
PROCESSdata scaling
X-PLORphasing
X-PLORrefinement
X-PLORmodel building

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1998-07-29
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance