5A8Y

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

PDB DOI: https://doi.org/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.

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

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.0 of the entry. See complete history.

Macromolecule Content

Total Structure Weight: 25.03 kDa
Atom Count: 1,945
Modelled Residue Count: 216
Deposited Residue Count: 218
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	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
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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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	B	3		N-Glycosylation	Interactions Focus chain B Interactions & Density Focus chain B
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	C	2		N-Glycosylation	Interactions Focus chain C Interactions & Density Focus chain C
Glycosylation Resources
GlyTouCan: G86851RC GlyCosmos: G86851RC GlyGen: G86851RC

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
VBM Query on VBM Download Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A]	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		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
MES Query on MES Download Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A]	E [auth A]	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C₆ H₁₃ N O₄ S SXGZJKUKBWWHRA-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]
MLI Query on MLI Download Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A]	F [auth A]	MALONATE ION C₃ H₂ O₄ OFOBLEOULBTSOW-UHFFFAOYSA-L		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]

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

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2016-08-03

Deposition Author(s):

Revision History (Full details and data files)

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