5A0C

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.163 
  • R-Value Observed: 0.166 

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Ligand Structure Quality Assessment 


This is version 3.0 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: 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) ...

    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

    Lead Discovery Wuppertal, Bayer HealthCare AG, 42096 Wuppertal (Germany).



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
NEUTROPHIL ELASTASEA, B218Homo sapiensMutation(s): 0 
Gene Names: ELANEELA2
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
Protein Feature View
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranoseC, E 3N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G21290RB
GlyCosmos:  G21290RB
GlyGen:  G21290RB
Entity ID: 3
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranoseD, F 2N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G86851RC
GlyCosmos:  G86851RC
GlyGen:  G86851RC
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
JJV
Query on JJV

Download Ideal Coordinates CCD File 
G [auth A],
J [auth B]
(6S)-6-(4-cyano-2-methylsulfonyl-phenyl)-4-methyl-2-oxidanylidene-3-[3-(trifluoromethyl)phenyl]-1,6-dihydropyrimidine-5-carbonitrile
C21 H15 F3 N4 O3 S
WQASVWJQEKONLG-LJQANCHMSA-N
 Ligand Interaction
XPE
Query on XPE

Download Ideal Coordinates CCD File 
I [auth A]3,6,9,12,15,18,21,24,27-NONAOXANONACOSANE-1,29-DIOL
C20 H42 O11
DTPCFIHYWYONMD-UHFFFAOYSA-N
 Ligand Interaction
MES
Query on MES

Download Ideal Coordinates CCD File 
H [auth A],
K [auth B]
2-(N-MORPHOLINO)-ETHANESULFONIC ACID
C6 H13 N O4 S
SXGZJKUKBWWHRA-UHFFFAOYSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
JJV BindingDB:  5A0C IC50: 0.3 (nM) from 1 assay(s)
Binding MOAD:  5A0C IC50: 0.54 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.163 
  • R-Value Observed: 0.166 
  • Space Group: P 32
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 71.517α = 90
b = 71.517β = 90
c = 97.4γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
SAINTdata reduction
SADABSdata scaling
MOLREPphasing

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: 2017-07-05
    Changes: Data collection
  • Version 2.0: 2019-01-23
    Changes: Advisory, Atomic model, Data collection
  • Version 3.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Other, Structure summary