5A8Y

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.161 

wwPDB Validation 3D Report Full Report


This is version 1.2 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

  • DOI: 10.1002/cmdc.201500269
  • Primary Citation of Related Structures:  

  • 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, ...

    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

    DMPK Wuppertal, Bayer HealthCare AG, 42096, Wuppertal, Germany.,Medicinal Chemistry Wuppertal, Bayer HealthCare AG, 42096, Wuppertal, Germany. daniel.meibom@bayer.com.,Department of Cardiology Research Wuppertal, Bayer HealthCare AG, 42096, Wuppertal, Germany.,Medicinal Chemistry Wuppertal, Bayer HealthCare AG, 42096, Wuppertal, Germany.,Medicinal Chemistry Berlin, Bayer HealthCare AG, 13353, Berlin, Germany. franz.nussbaum@bayer.com.,Lead Discovery, Structural Biology Berlin, Bayer HealthCare AG, 13353, Berlin, Germany.,Lead Discovery Wuppertal, Bayer HealthCare AG, 42096, Wuppertal, Germany. volkhart.li@bayer.com.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
NEUTROPHIL ELASTASE
A
218Homo sapiensMutation(s): 0 
Gene Names: ELANE (ELA2)
EC: 3.4.21.37
Find proteins for P08246 (Homo sapiens)
Go to Gene View: ELANE
Go to UniProtKB:  P08246
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
VBM
Query on VBM

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Download CCD File 
A
METHYL {(7R)-6-CYANO-7-(4-CYANOPHENYL)-5-METHYL-4-[3-(TRIFLUOROMETHYL)PHENYL]-4,7-DIHYDRO[1,2,4]TRIAZOLO[1,5-A]PYRIMIDIN-2-YL}CARBAMATE
C23 H16 F3 N7 O2
CBMCUAQNNUOHFF-LJQANCHMSA-N
 Ligand Interaction
MLI
Query on MLI

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Download CCD File 
A
MALONATE ION
C3 H2 O4
OFOBLEOULBTSOW-UHFFFAOYSA-L
 Ligand Interaction
FUC
Query on FUC

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Download CCD File 
A
ALPHA-L-FUCOSE
C6 H12 O5
SHZGCJCMOBCMKK-SXUWKVJYSA-N
 Ligand Interaction
NAG
Query on NAG

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Download CCD File 
A
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
MES
Query on MES

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Download CCD File 
A
2-(N-MORPHOLINO)-ETHANESULFONIC ACID
C6 H13 N O4 S
SXGZJKUKBWWHRA-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
VBMIC50: 0.17 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.161 
  • Space Group: P 63
Unit Cell:
Length (Å)Angle (°)
a = 73.025α = 90.00
b = 73.025β = 90.00
c = 69.842γ = 120.00
Software Package:
Software NamePurpose
REFMACrefinement
SADABSdata scaling
SAINTdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-08-03
    Type: Initial release
  • Version 1.1: 2016-09-21
    Type: Atomic model, Derived calculations, Non-polymer description, Other
  • Version 1.2: 2018-04-04
    Type: Data collection