5A09

Crystal Structure of human neutrophil elastase in complex with a dihydropyrimidone inhibitor

• PDB DOI: https://doi.org/10.2210/pdb5A09/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Mutation(s): No 


• Deposited: 2015-04-17 Released: 2015-08-19 
• Deposition Author(s): vonNussbaum, F., Li, V.M.-J., Allerheiligen, S., Anlauf, S., Baerfacker, L., Bechem, M., Delbeck, M., Fitzgerald, M.F., Gerisch, M., Gielen-Haertwig, H., Haning, H., Karthaus, D., Lang, D., Lustig, K., Meibom, D., Mittendorf, J., Rosentreter, U., Schaefer, M., Schaefer, S., Schamberger, J., Telan, L.A., Tersteegen, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.81 Å
• R-Value Free: 0.239 
• R-Value Work: 0.182 
• R-Value Observed: 0.185 

Starting Model: experimental

Literature

Freezing the Bioactive Conformation to Boost Potency: The Identification of BAY 85-8501, a Selective and Potent Inhibitor of Human Neutrophil Elastase for Pulmonary Diseases.

von Nussbaum, F., Li, V.M., Allerheiligen, S., Anlauf, S., Barfacker, L., Bechem, M., Delbeck, M., Fitzgerald, M.F., Gerisch, M., Gielen-Haertwig, H., Haning, H., Karthaus, D., Lang, D., Lustig, K., Meibom, D., Mittendorf, J., Rosentreter, U., Schafer, M., Schafer, S., Schamberger, J., Telan, L.A., Tersteegen, A.

(2015) ChemMedChem 10: 1163-1173

• PubMed: 26083237 
• DOI: https://doi.org/10.1002/cmdc.201500131
• Primary Citation of Related Structures:  
  5A09, 5A0A, 5A0B, 5A0C


• PubMed Abstract: 
  

  Human neutrophil elastase (HNE) is a key protease for matrix degradation. High HNE activity is observed in inflammatory diseases. Accordingly, HNE is a potential target for the treatment of pulmonary diseases such as chronic obstructive pulmonary disease (COPD), acute lung injury (ALI), acute respiratory distress syndrome (ARDS), bronchiectasis (BE), and pulmonary hypertension (PH). HNE inhibitors should reestablish the protease-anti-protease balance. By means of medicinal chemistry a novel dihydropyrimidinone lead-structure class was identified. Further chemical optimization yielded orally active compounds with favorable pharmacokinetics such as the chemical probe BAY-678. While maintaining outstanding target selectivity, picomolar potency was achieved by locking the bioactive conformation of these inhibitors with a strategically positioned methyl sulfone substituent. An induced-fit binding mode allowed tight interactions with the S2 and S1 pockets of HNE. BAY 85-8501 ((4S)-4-[4-cyano-2-(methylsulfonyl)phenyl]-3,6-dimethyl-2-oxo-1-[3-(trifluoromethyl)phenyl]-1,2,3,4-tetrahydropyrimidine-5-carbonitrile) was shown to be efficacious in a rodent animal model related to ALI. BAY 85-8501 is currently being tested in clinical studies for the treatment of pulmonary diseases.

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Organizational Affiliation: 

Medicinal Chemistry Berlin, Bayer HealthCare AG, 13353 Berlin (Germany). [e-mail].

Biological Assembly 1  

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

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

Macromolecule Content

• Total Structure Weight: 24.73 kDa 
• Atom Count: 1,910 
• Modelled Residue Count: 218 
• Deposited Residue Count: 218 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NEUTROPHIL ELASTASE	A	218	Homo sapiens	Mutation(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
Glycosylation
Glycosylation Sites: 2		Go to GlyGen: P08246-1

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose	B, C	2		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G86851RC GlyCosmos:  G86851RC GlyGen:  G86851RC

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
JJD	E [auth A]	2-[(4R)-4-(4-cyanophenyl)-5-ethanoyl-6-methyl-2-oxidanylidene-1-[3-(trifluoromethyl)phenyl]-4H-pyrimidin-3-yl]ethanoic acid C23 H18 F3 N3 O4 RRKQYMJDNSVFCG-OAQYLSRUSA-N
NAG	D [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
JJD	BindingDB:  5A09	IC50: 3.5 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.81 Å
• R-Value Free: 0.239 
• R-Value Work: 0.182 
• R-Value Observed: 0.185 
• Space Group: P 6₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 72.77	α = 90
b = 72.77	β = 90
c = 69.626	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-08-19 
Deposition Author(s): vonNussbaum, F., Li, V.M.-J., Allerheiligen, S., Anlauf, S., Baerfacker, L., Bechem, M., Delbeck, M., Fitzgerald, M.F., Gerisch, M., Gielen-Haertwig, H., Haning, H., Karthaus, D., Lang, D., Lustig, K., Meibom, D., Mittendorf, J., Rosentreter, U., Schaefer, M., Schaefer, S., Schamberger, J., Telan, L.A., Tersteegen, A.

Revision History  

• Version 1.0: 2015-08-19
  Type: Initial release
  
• Version 1.1: 2017-03-22
  Changes: Database references
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Other, Structure summary
• Version 2.1: 2021-04-28
  Changes: Data collection, Structure summary
• Version 2.2: 2024-01-10
  Changes: Data collection, Database references, Refinement description
• Version 2.3: 2024-10-16
  Changes: Structure summary