5A0B

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.23 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.173 
  • R-Value Observed: 0.175 

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Ligand Structure Quality Assessment 


This is version 2.1 of the entry. See complete history


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

  • 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.


  • Organizational Affiliation

    Medicinal Chemistry Berlin, Bayer HealthCare AG, 13353 Berlin (Germany). [email protected].


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-glucopyranose
B, C
2N-Glycosylation
Glycosylation Resources
GlyTouCan:  G86851RC
GlyCosmos:  G86851RC
GlyGen:  G86851RC
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
JJX
Query on JJX

Download Ideal Coordinates CCD File 
E [auth A](4R)-4-(4-cyanophenyl)-6-methyl-2-oxidanylidene-3-[2-oxidanylidene-2-(4-propan-2-ylpiperazin-1-yl)ethyl]-1-[3-(trifluoromethyl)phenyl]-4H-pyrimidine-5-carbonitrile
C29 H29 F3 N6 O2
MJSBQGLWAKMDDF-HHHXNRCGSA-N
NAG
Query on NAG

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

Download Ideal Coordinates CCD File 
F [auth A]DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.23 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.173 
  • R-Value Observed: 0.175 
  • Space Group: P 63 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 77.459α = 90
b = 77.459β = 90
c = 149.625γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2015-08-19
    Type: Initial release
  • Version 1.1: 2017-03-22
    Changes: Database references
  • Version 1.2: 2017-06-28
    Changes: Data collection
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Other, Structure summary
  • Version 2.1: 2024-11-06
    Changes: Data collection, Database references, Structure summary