Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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

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

Macromolecule Content

• Total Structure Weight: 24939.63 
• Atom Count: 1712 
• Residue Count: 218 
• Unique protein chains: 1

5A0B

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

• DOI: 10.2210/pdb5A0B/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens


• Deposited: 2015-04-17 Released: 2015-08-19 
• Deposition Author(s): vonNussbaum, F., Li, V.M.-J., Allerheiligen, S., Anlauf, S., Baerfacker, 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., Schaefer, M., Schaefer, S., Schamberger, J., Telan, L.A., Tersteegen, A.

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Experimental Data Snapshot

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

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

• PubMed: 26083237 
• DOI: 10.1002/cmdc.201500131
• Primary Citation of Related Structures:  
  5A0C, 5A0A, 5A09


• 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.

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Organizational Affiliation: 

Medicinal Chemistry Wuppertal, Bayer HealthCare AG, 42096 Wuppertal (Germany).,Department of Cardiology Research Wuppertal, Bayer HealthCare AG, 42096 Wuppertal (Germany).,COPD Research, Bayer Healthcare AG, Slough SL2 4LY, Berkshire (UK).,Lead Discovery, Structural Biology Berlin, Bayer HealthCare AG, 13353 Berlin (Germany).,Lead Discovery Wuppertal, Bayer HealthCare AG, 42096 Wuppertal (Germany). [e-mail].,DMPK Wuppertal, Bayer HealthCare AG, 42096 Wuppertal (Germany).,Lead Discovery Wuppertal, Bayer HealthCare AG, 42096 Wuppertal (Germany).,Medicinal Chemistry Berlin, Bayer HealthCare AG, 13353 Berlin (Germany). [e-mail].

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
NEUTROPHIL ELASTASE	A	218	Homo sapiens	Mutation(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 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
JJX	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
FUC	A	ALPHA-L-FUCOSE C6 H12 O5 SHZGCJCMOBCMKK-SXUWKVJYSA-N
DMS	A	DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N
NAG	A	N-ACETYL-D-GLUCOSAMINE C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
JJX	IC50: 5 nM BINDINGMOAD

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.23 Å
• R-Value Free: 0.218 
• R-Value Work: 0.173 
• Space Group: P 6₃ 2 2

Unit Cell:

Length (Å)	Angle (°)
a = 77.459	α = 90.00
b = 77.459	β = 90.00
c = 149.625	γ = 120.00

Software Package:

Software Name	Purpose
PHASER	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2015-04-17 
• Released Date: 2015-08-19 
• Deposition Author(s): vonNussbaum, F., Li, V.M.-J., Allerheiligen, S., Anlauf, S., Baerfacker, 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., Schaefer, M., Schaefer, S., Schamberger, J., Telan, L.A., Tersteegen, A.

Revision History 

• Version 1.0: 2015-08-19
  Type: Initial release
• Version 1.1: 2017-03-22
  Type: Database references
• Version 1.2: 2017-06-28
  Type: Data collection