5A8Z

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.192 

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Ligand Structure Quality Assessment 


This is version 2.0 of the entry. See complete history


Literature

Potent and Selective Human Neutrophil Elastase Inhibitors with Novel Equatorial Ring Topology: in vivo Efficacy of the Polar Pyrimidopyridazine BAY-8040 in a Pulmonary Arterial Hypertension Rat Model.

von Nussbaum, F.Li, V.M.Meibom, D.Anlauf, S.Bechem, M.Delbeck, M.Gerisch, M.Harrenga, A.Karthaus, D.Lang, D.Lustig, K.Mittendorf, J.Schafer, M.Schafer, S.Schamberger, J.

(2016) ChemMedChem 11: 199-206

  • DOI: 10.1002/cmdc.201500269
  • Primary Citation of Related Structures:  
    5A8X, 5A8Y, 5A8Z

  • PubMed Abstract: 
  • Human neutrophil elastase (HNE) is a key driver of inflammation in many cardiopulmonary and systemic inflammatory and autoimmune conditions. Overshooting high HNE activity is the consequence of a disrupted protease-antiprotease balance. Accordingly, there has been an intensive search for potent and selective HNE inhibitors with suitable pharmacokinetics that would allowing oral administration in patients ...

    Human neutrophil elastase (HNE) is a key driver of inflammation in many cardiopulmonary and systemic inflammatory and autoimmune conditions. Overshooting high HNE activity is the consequence of a disrupted protease-antiprotease balance. Accordingly, there has been an intensive search for potent and selective HNE inhibitors with suitable pharmacokinetics that would allowing oral administration in patients. Based on the chemical probe BAY-678 and the clinical candidate BAY 85-8501 we explored further ring topologies along the equator of the parent pyrimidinone lead series. Novel ring systems were annulated in the east, yielding imidazolo-, triazolo-, and tetrazolopyrimidines in order to ensure additional inhibitor-HNE contacts beyond the S1 and the S2 pocket of HNE. The western annulation of pyridazines led to the polar pyrimidopyridazine BAY-8040, which combines excellent potency and selectivity with a promising pharmacokinetic profile. In vivo efficacy with regard to decreasing cardiac remodeling and amelioration of cardiac function was shown in a monocrotaline-induced rat model for pulmonary arterial hypertension. This demonstrated in vivo proof of concept in animals.


    Organizational Affiliation

    Medicinal Chemistry Wuppertal, Bayer HealthCare AG, 42096, Wuppertal, Germany.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Neutrophil elastaseA218Homo 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

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Entity ID: 2
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranoseB, C 2N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G86851RC
GlyCosmos:  G86851RC
GlyGen:  G86851RC
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
IUL
Query on IUL

Download Ideal Coordinates CCD File 
E [auth A]4-[(4R)-7-methyl-2,5-bis(oxidanylidene)-1-[3-(trifluoromethyl)phenyl]-3,4,6,8-tetrahydropyrimido[4,5-d]pyridazin-4-yl]benzenecarbonitrile
C21 H16 F3 N5 O2
UPNMBPLODWPJQQ-GOSISDBHSA-N
 Ligand Interaction
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
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
IUL Binding MOAD:  5A8Z IC50: 28 (nM) from 1 assay(s)
BindingDB:  5A8Z IC50: 28 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.192 
  • Space Group: P 63
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 73.119α = 90
b = 73.119β = 90
c = 70.162γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

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Ligand Structure Quality Assessment 



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-08-03
    Type: Initial release
  • Version 1.1: 2017-06-28
    Changes: Data collection
  • Version 1.2: 2018-12-12
    Changes: Advisory, Data collection, Database references, Source and taxonomy, Structure summary
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Other, Structure summary