Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

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

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

Macromolecule Content

• Total Structure Weight: 25.03 kDa 
• Atom Count: 1945 
• Modelled Residue Count: 216 
• Deposited Residue Count: 218 
• Unique protein chains: 1

5A8Y

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

• PDB DOI: 10.2210/pdb5A8Y/pdb

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


• Deposited: 2015-07-17 Released: 2016-08-03 
• Deposition Author(s): vonNussbaum, F., Li, V.M., Meibom, D., Anlauf, S., Bechem, M., Delbeck, M., Gerisch, M., Harrenga, A., Karthaus, D., Lang, D., Lustig, K., Mittendorf, J., Schaefer, M., Schaefer, S., Schamberger, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.221 
• R-Value Work: 0.161 
• R-Value Observed: 0.164 

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

• PubMed: 26333652 
• 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. 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.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NEUTROPHIL ELASTASE	A	218	Homo sapiens	Mutation(s): 0  Gene Names: ELANE, ELA2 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

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose	B	3		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G21290RB GlyCosmos:  G21290RB GlyGen:  G21290RB

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

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
VBM	D [auth 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
MES	E [auth A]	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C6 H13 N O4 S SXGZJKUKBWWHRA-UHFFFAOYSA-N
MLI	F [auth A]	MALONATE ION C3 H2 O4 OFOBLEOULBTSOW-UHFFFAOYSA-L

Binding Affinity Annotations
ID	Source	Binding Affinity
VBM	Binding MOAD:  5A8Y	IC50: 0.17 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.221 
• R-Value Work: 0.161 
• R-Value Observed: 0.164 
• Space Group: P 6₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 73.025	α = 90
b = 73.025	β = 90
c = 69.842	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
SAINT	data reduction
SADABS	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2015-07-17 
• Released Date: 2016-08-03 
Deposition Author(s): vonNussbaum, F., Li, V.M., Meibom, D., Anlauf, S., Bechem, M., Delbeck, M., Gerisch, M., Harrenga, A., Karthaus, D., Lang, D., Lustig, K., Mittendorf, J., Schaefer, M., Schaefer, S., Schamberger, J.

Revision History  

• Version 1.0: 2016-08-03
  Type: Initial release
  
• Version 1.1: 2016-09-21
  Changes: Atomic model, Derived calculations, Non-polymer description, Other
• Version 1.2: 2018-04-04
  Changes: Data collection
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Other, Structure summary