	235,183 Structures from the PDB
	1,068,577 Computed Structure Models (CSM)

5A0C|pdb_00005a0c

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

PDB DOI: https://doi.org/10.2210/pdb5A0C/pdb

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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free:
0.213 (Depositor), 0.219 (DCC)
R-Value Work:
0.163 (Depositor), 0.172 (DCC)
R-Value Observed:
0.166 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 3.1 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

PubMed: 26083237 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/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). 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

Medicinal Chemistry Berlin, Bayer HealthCare AG, 13353 Berlin (Germany). franz.nussbaum@bayer.com.

Macromolecule Content

Total Structure Weight: 50.28 kDa
Atom Count: 3,848
Modelled Residue Count: 436
Deposited Residue Count: 436
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NEUTROPHIL ELASTASE	A,B	218	Homo sapiens	Mutation(s): 0 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 Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P08246
Glycosylation
Glycosylation Sites: 2	Glycosylation Focus chain A Focus chain B	Go to GlyGen: P08246-1
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose	C, E	3		N-Glycosylation	Interactions Focus chain C Focus chain E Interactions & Density Focus chain C Focus chain E
Glycosylation Resources
GlyTouCan: G21290RB GlyCosmos: G21290RB GlyGen: G21290RB

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose	D, F	2		N-Glycosylation	Interactions Focus chain D Focus chain F Interactions & Density Focus chain D Focus chain F
Glycosylation Resources
GlyTouCan: G86851RC GlyCosmos: G86851RC GlyGen: G86851RC

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
JJV Query on JJV Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain J [auth B] MOL2 format, chain G [auth A] MOL2 format, chain J [auth B] mmCIF format, chain G [auth A] mmCIF format, chain J [auth B]	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		Interactions Focus chain G [auth A] Focus chain J [auth B] Interactions & Density Focus chain G [auth A] Focus chain J [auth B]
XPE Query on XPE Download Ideal Coordinates CCD File SDF format, chain I [auth A] MOL2 format, chain I [auth A] mmCIF format, chain I [auth A]	I [auth A]	3,6,9,12,15,18,21,24,27-NONAOXANONACOSANE-1,29-DIOL C₂₀ H₄₂ O₁₁ DTPCFIHYWYONMD-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Interactions & Density Focus chain I [auth A]
MES Query on MES Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain K [auth B] MOL2 format, chain H [auth A] MOL2 format, chain K [auth B] mmCIF format, chain H [auth A] mmCIF format, chain K [auth B]	H [auth A], K [auth B]	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C₆ H₁₃ N O₄ S SXGZJKUKBWWHRA-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain K [auth B] Interactions & Density Focus chain H [auth A] Focus chain K [auth B]

Binding Affinity Annotations
ID	Source	Binding Affinity
JJV	BindingDB: 5A0C	IC50: 0.3 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.213 (Depositor), 0.219 (DCC)
R-Value Work: 0.163 (Depositor), 0.172 (DCC)
R-Value Observed: 0.166 (Depositor)

Space Group: P 3₂

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.517	α = 90
b = 71.517	β = 90
c = 97.4	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
SAINT	data reduction
SADABS	data scaling
MOLREP	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2015-08-19

Deposition Author(s):

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
Version 3.1: 2024-11-13
Changes: Data collection, Database references, Structure summary