5A8Y: Human neutrophil elastase

Crystal Structure of human neutrophil elastase in complex with a dihydropyrimidone inhibitor. Determined by X-ray diffraction at 1.9 Å resolution. Released 3 Aug 2016.

Method: X-ray diffraction
Resolution: 1.9 Å
Organism: HOMO SAPIENS
Chains: 1
Atoms: 1,945
Mol. weight: 25.03 kDa
Ligands: MLI, VBM
Released: 3 Aug 2016

Explore 5A8Y in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5A8Y contains 6 α-helices and 23 β-strands across 1 chain. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 6 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	17	1	1
β-strand	20-21	2	2
α-helix	22-23	2
β-strand	30-35	6	3
β-strand	39-48	10	3
β-strand	51-54	4	3
α-helix	56-59	4
α-helix	63A-63C	3
β-strand	65-68	4	3
β-strand	72	1	4
β-strand	81-90	10	3
β-strand	95	1	5
β-strand	100	1	5
β-strand	104-108	5	3
β-strand	115	1	6
β-strand	118	1	6
β-strand	135-140	6	2
β-strand	143	1	7
β-strand	151	1	7
β-strand	154	1	4
β-strand	156-163	8	2
β-strand	181-184	4	2
β-strand	189	1	1
β-strand	198-201	4	2
β-strand	208-215	8	2
α-helix	225	1
β-strand	226-230	5	2
α-helix	231-234	4
α-helix	235-242	8

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Neutrophil elastase	A	protein	218	HOMO SAPIENS	P08246 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>5A8Y_1 NEUTROPHIL ELASTASE (chains A)
IVGGRRARPHAWPFMVSLQLRGGHFCGATLIAPNFVMSAAHCVANVNVRAVRVVLGAHNL
SRREPTRQVFAVQRIFENGYDPVNLLNDIVILQLNGSATINANVQVAQLPAQGRRLGNGV
QCLAMGWGLLGRNRGIASVLQELNVTVVTSLCRRSNVCTLVRGRQAGVCFGDSGSPLVCN
GLIHGIASFVRGGCASGLYPDAFAPVAQFVNWIDSIIQ

Ligands and cofactors

ID	Name	Formula	Copies
MLI	Malonate ion	C3 H2 O4	1
VBM	Methyl {(7R)-6-cyano-7-(4-cyanophenyl)-5-methyl-4-[3-(trifluoromethyl)phenyl]-4…	C23 H16 F3 N7 O2	1

Water and common crystallization additives (MES) are not listed.

Primary citation

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. et al. ChemMedChem (2016) 11:199. DOI 10.1002/CMDC.201500269 · PubMed

Other PDB entries of the same protein (UniProt P08246 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9SI4 1.14 Å, Structure of human neutrophil elastase in complex with a…
8VK5 1.56 Å, Human Sputum Leucocyte Elastase (uncomplexed)
5ABW 1.6 Å, Neutrophil elastase inhibitors for the treatment of (cardio)pulmonary diseases
4WVP 1.63 Å, Crystal structure of an activity-based probe HNE complex
2Z7F 1.7 Å, Crystal structure of the complex of human neutrophil elastase with 1/2SLPI
9ASS 1.75 Å, Crystal Structure of Neutrophil Elastase Inhibited by Eap4 from S. aureus
5A0A 1.78 Å, Crystal Structure of human neutrophil elastase in complex with a dihydropyrimidone…
1PPF 1.8 Å, X-ray crystal structure of the complex of human leukocyte elastase (pmn elastase) and…
2RG3 1.8 Å, Covalent complex structure of elastase
8G25 1.8 Å, Crystal Structure of Cathepsin-G and Neutrophil Elastase Inhibited by S. aureus EapH2 at…
5A09 1.81 Å, Crystal Structure of human neutrophil elastase in complex with a dihydropyrimidone…
8G24 1.82 Å, Crystal Structure of Cathepsin-G and Neutrophil Elastase Inhibited by S. aureus EapH2 at…

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