Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Hetero 4-mer - A2B2 

Biological assembly 2 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 29.61 kDa 
• Atom Count: 2070 
• Residue Count: 255 
• Unique protein chains: 2

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

• DOI: 10.2210/pdb1BMQ/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 1998-07-24 Released: 1998-07-29 
• Deposition Author(s): Okamoto, Y., Anan, H., Nakai, E., Morihira, K., Yonetoku, Y., Kurihara, H., Katayama, N., Sakashita, H., Terai, Y., Takeuchi, M., Shibanuma, T., Isomura, Y.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.317 
• R-Value Work: 0.233 
• R-Value Observed: 0.233 

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 (Tokyo) 47: 11-21

• PubMed: 9987822 
• DOI: 10.1248/cpb.47.11
• Primary Citation of Related Structures:  
  1BMQ


• 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 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.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTEIN (INTERLEUKIN-1 BETA CONVERTASE)	A	167	Homo sapiens	Mutation(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

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTEIN (INTERLEUKIN-1 BETA CONVERTASE)	B	88	Homo sapiens	Mutation(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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MNO	A	(3S)-N-METHANESULFONYL-3-({1-[N-(2-NAPHTOYL)-L-VALYL]-L-PROLYL}AMINO)-4-OXOBUTANAMIDE C26 H32 N4 O7 S IGFYXXJBAZZOHF-FUDKSRODSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
MNO	IC50 :  38   nM  PDBBind

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.317 
• R-Value Work: 0.233 
• R-Value Observed: 0.233 
• Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 64.7	α = 90
b = 64.7	β = 90
c = 161.4	γ = 90

Software Package:

Software Name	Purpose
X-PLOR	model building
X-PLOR	refinement
PROCESS	data reduction
PROCESS	data scaling
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 1998-07-24 
• Released Date: 1998-07-29 
Deposition Author(s): Okamoto, Y., Anan, H., Nakai, E., Morihira, K., Yonetoku, Y., Kurihara, H., Katayama, N., Sakashita, H., Terai, Y., Takeuchi, M., Shibanuma, T., Isomura, Y.

Revision History 

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