1FZZ | pdb_00001fzz

THE CRYSTAL STRUCTURE OF THE COMPLEX OF NON-PEPTIDIC INHIBITOR ONO-6818 AND PORCINE PANCREATIC ELASTASE.

• PDB DOI: https://doi.org/10.2210/pdb1FZZ/pdb

• Classification: HYDROLASE
• Organism(s): Sus scrofa
• Mutation(s): No 


• Deposited: 2000-10-04 Released: 2001-10-04 
• Deposition Author(s): Odagaki, Y., Ohmoto, K., Matsuoka, S., Hamanaka, N., Nakai, H., Toda, M., Katsuya, Y.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.86 Å
• R-Value Free: 
  0.238 (Depositor) 
• R-Value Work: 
  0.198 (Depositor) 

Literature

The crystal structure of the complex of non-peptidic inhibitor of human neutrophil elastase ONO-6818 and porcine pancreatic elastase.

Odagaki, Y., Ohmoto, K., Matsuoka, S., Hamanaka, N., Nakai, H., Toda, M., Katsuya, Y.

(2001) Bioorg Med Chem 9: 647-651

• PubMed: 11310599 
• DOI: https://doi.org/10.1016/s0968-0896(00)00277-7
• Primary Citation Related Structures: 
  1FZZ


• PubMed Abstract: 
  

  The crystal structure of a new inhibitor of human neutrophil elastase (HNE), N-[2-[5-(tert-butyl)-1,3,4-oxadiazol-2-yl]-(IRS)-1-(methylethyl)-2-oxoethyl]-2-(5-amino-6-oxo-2-phenyl-6H-pyrimidin-1-ly)acetamide (ONO-6818, 1) complexed to porcine pancreatic elastase (PPE) has been determined at 1.86 A resolution. Analytical results provided evidence of a 1:1 complex in which the electrophilic ketone of 1 covalently bound to O gamma of Ser195 at the active site of PPE. The role of the unique electron-withdrawing ketone of 1 has been elucidated.

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Organizational Affiliation: 
• Minase Research Institute, Ono Pharmaceutical Co., Ltd. Mishima-Gun, Osaka, Japan. [e-mail]

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 26.38 kDa 
• Atom Count: 1,919 
• Modeled Residue Count: 240 
• Deposited Residue Count: 240 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ELASTASE 1	A	240	Sus scrofa	Mutation(s): 0  EC: 3.4.21.36
UniProt
Find proteins for P00772 (Sus scrofa) Explore P00772  Go to UniProtKB:  P00772

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
681	B [auth A]	2-(5-AMINO-6-OXO-2-PHENYL-6H-PYRIMIDIN-1-YL)-N-[2-(5-TERT-BUTYL-1,3,4-OXADIAZOL-2-YL)-1-(METHYLETHYL)-2-HYDROXYETHYL]ACETAMIDE C23 H30 N6 O4 HMPQTEPEMQZWQH-ROUUACIJSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.86 Å
• R-Value Free:  0.238 (Depositor) 
• R-Value Work:  0.198 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.038	α = 90
b = 58.5	β = 90
c = 75.643	γ = 90

Software Package:

Software Name	Purpose
X-PLOR	model building
X-PLOR	refinement
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2001-10-04 
Deposition Author(s): Odagaki, Y., Ohmoto, K., Matsuoka, S., Hamanaka, N., Nakai, H., Toda, M., Katsuya, Y.

Revision History  

• Version 1.0: 2001-10-04
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-10-04
  Changes: Refinement description
• Version 1.4: 2024-12-25
  Changes: Advisory, Data collection, Database references, Derived calculations, Structure summary