9SI4 | pdb_00009si4

Structure of human neutrophil elastase in complex with a 5,8-dihydro[1,2,4]triazolo[4,3-a]pyrimidin-3(2H)-one inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.14 Å
  • R-Value Free: 
    0.155 (Depositor), 0.159 (DCC) 
  • R-Value Work: 
    0.134 (Depositor), 0.140 (DCC) 
  • R-Value Observed: 
    0.135 (Depositor) 

Starting Model: experimental
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Literature

Design, Synthesis, and Biological Evaluation of the Novel Neutrophil Elastase Inhibitor CHF-6333 for the Inhaled Treatment of Bronchiectasis.

Armani, E.Rizzi, A.Miglietta, D.Bassanetti, I.Amadei, F.Brogin, G.Capaldi, C.Rancati, F.Carnini, C.Xanxo Fernandez, S.Civelli, M.Puccini, P.Bellini, M.Jennings, A.Heald, R.A.Alcaraz, L.Sutton, J.M.Finch, H.Fitzgerald, M.Fox, C.Villetti, G.

(2025) J Med Chem 68: 24869-24889

  • DOI: https://doi.org/10.1021/acs.jmedchem.5c02638
  • Primary Citation of Related Structures:  
    9SI4

  • PubMed Abstract: 

    The inhibitors of neutrophil elastase (NE) have long attracted interest for the treatment of respiratory diseases. We report the breakthrough of a new potent, selective NE inhibitor with a 24 h duration of action: CHF-6333, is currently undergoing clinical studies for the inhaled treatment of bronchiectasis (BE). The story of the discovery project to identify novel small molecules that inhibit extracellular elastase in the lung with prolonged activity is described. Medicinal chemistry investigation, supported by docking studies, led to N-quaternary compounds with an in vitro profile suitable for inhalatory administration. Compound 15 emerged from in vivo pharmacokinetic and pharmacodynamic studies, also showing safety and no off-target effects in vitro . Salt screening of different counterions, in conjunction with in vivo local irritancy testing, aided in the selection of compound 15 -xinafoate (CHF-6333). Efficacy in a lung injury model and no findings in non-GLP toxicity studies promoted CHF-6333 as a clinical candidate.


  • Organizational Affiliation
    • Chiesi Farmaceutici S.p.A, Centro Ricerche, 43122 Parma, Italy.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Neutrophil elastase218Homo sapiensMutation(s): 0 
EC: 3.4.21.37
UniProt & NIH Common Fund Data Resources
Find proteins for P08246 (Homo sapiens)
Explore P08246 
Go to UniProtKB:  P08246
PHAROS:  P08246
GTEx:  ENSG00000197561 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP08246
Glycosylation
Glycosylation Sites: 2Go to GlyGen: P08246-1
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranoseB [auth F]2N-Glycosylation
Glycosylation Resources
GlyTouCan:  G86851RC
GlyCosmos:  G86851RC
GlyGen:  G86851RC
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1JN2 (Subject of Investigation/LOI)
Query on A1JN2

Download Ideal Coordinates CCD File 
G [auth A]methyl (5~{R})-5-[4-cyano-2-[2-(trimethyl-$l^{4}-azanyl)ethyl]phenyl]-7-methyl-3-oxidanylidene-8-[3-(trifluoromethyl)phenyl]-2,5-dihydro-[1,2,4]triazolo[4,3-a]pyrimidine-6-carboxylate
C27 H28 F3 N6 O3
IHTRPSMRGYWUIM-HSZRJFAPSA-O
NAG
Query on NAG

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A],
F [auth A]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
FUC
Query on FUC

Download Ideal Coordinates CCD File 
E [auth A]alpha-L-fucopyranose
C6 H12 O5
SHZGCJCMOBCMKK-SXUWKVJYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.14 Å
  • R-Value Free:  0.155 (Depositor), 0.159 (DCC) 
  • R-Value Work:  0.134 (Depositor), 0.140 (DCC) 
  • R-Value Observed: 0.135 (Depositor) 
Space Group: P 63
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 73.16α = 90
b = 73.16β = 90
c = 70.15γ = 120
Software Package:
Software NamePurpose
PDB-REDOrefinement
PHASERphasing
xia2data scaling
Cootmodel building
autoPROCdata reduction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2025-12-10
    Type: Initial release
  • Version 1.1: 2025-12-24
    Changes: Database references