6E69 | pdb_00006e69

Ortho-substituted phenyl sulfonyl fluoride and fluorosulfate as potent elastase inhibitory fragments

PDB DOI: https://doi.org/10.2210/pdb6E69/pdb

Classification: HYDROLASE/HYDROLASE INHIBITOR
Organism(s): Homo sapiens
Mutation(s): No

Deposited: 2018-07-24 Released: 2019-07-24
Deposition Author(s): Wolan, D.W., Woehl, J.L., Kitamura, S.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.33 Å
R-Value Free:
0.241 (Depositor), 0.229 (DCC)
R-Value Work:
0.193 (Depositor)
R-Value Observed:
0.195 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.3 of the entry. See complete history.

Literature

SuFEx-enabled, agnostic discovery of covalent inhibitors of human neutrophil elastase.

Zheng, Q., Woehl, J.L., Kitamura, S., Santos-Martins, D., Smedley, C.J., Li, G., Forli, S., Moses, J.E., Wolan, D.W., Sharpless, K.B.

(2019) Proc Natl Acad Sci U S A 116: 18808-18814

PubMed: 31484779 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1073/pnas.1909972116
Primary Citation Related Structures:
6E69

PubMed Abstract:
Sulfur fluoride exchange (SuFEx) has emerged as the new generation of click chemistry. We report here a SuFEx-enabled, agnostic approach for the discovery and optimization of covalent inhibitors of human neutrophil elastase (hNE). Evaluation of our ever-growing collection of SuFExable compounds toward various biological assays unexpectedly revealed a selective and covalent hNE inhibitor: benzene-1,2-disulfonyl fluoride. Synthetic derivatization of the initial hit led to a more potent agent, 2-(fluorosulfonyl)phenyl fluorosulfate with IC ₅₀ 0.24 μM and greater than 833-fold selectivity over the homologous neutrophil serine protease, cathepsin G. The optimized, yet simple benzenoid probe only modified active hNE and not its denatured form.

Organizational Affiliation

Department of Chemistry, The Scripps Research Institute, La Jolla, CA 92037.

Macromolecule Content

Total Structure Weight: 98.01 kDa
Atom Count: 6,978
Modeled Residue Count: 869
Deposited Residue Count: 872
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Neutrophil elastase	A, B, C, D	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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P08246
Glycosylation
Glycosylation Sites: 2	Glycosylation Focus chain A Focus chain B Focus chain C Focus chain D	Go to GlyGen: P08246-1
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	F, H, K	2		N-Glycosylation	Interactions Focus chain F Focus chain H Focus chain K Interactions & Density Focus chain F Focus chain H Focus chain K
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HVP Query on HVP Download:Ideal Coordinates CCD File SDF format, chain P [auth D] SDF format, chain O [auth C] SDF format, chain M [auth B] SDF format, chain L [auth A] MOL2 format, chain P [auth D] MOL2 format, chain O [auth C] MOL2 format, chain M [auth B] MOL2 format, chain L [auth A] mmCIF format, chain P [auth D] mmCIF format, chain O [auth C] mmCIF format, chain M [auth B] mmCIF format, chain L [auth A]	L [auth A], M [auth B], O [auth C], P [auth D]	2-(fluorosulfonyl)benzene-1-sulfonic acid C₆ H₅ F O₅ S₂ AFQCDYWSMCQAJJ-UHFFFAOYSA-N		Interactions Focus chain L [auth A] Focus chain M [auth B] Focus chain O [auth C] Focus chain P [auth D] Interactions & Density Focus chain L [auth A] Focus chain M [auth B] Focus chain O [auth C] Focus chain P [auth D]
NAG Query on NAG Download:Ideal Coordinates CCD File SDF format, chain N [auth C] MOL2 format, chain N [auth C] mmCIF format, chain N [auth C]	N [auth C]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain N [auth C] Interactions & Density Focus chain N [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.33 Å
R-Value Free: 0.241 (Depositor), 0.229 (DCC)
R-Value Work: 0.193 (Depositor)
R-Value Observed: 0.195 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 69.47	α = 90
b = 124.59	β = 90
c = 126.704	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction
HKL-2000	data reduction

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2019-07-24

Deposition Author(s):

Wolan, D.W.

Woehl, J.L.

Kitamura, S.

Revision History (Full details and data files)

Version 1.0: 2019-07-24
Type: Initial release
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
Version 2.1: 2020-08-05
Changes: Database references, Derived calculations, Structure summary
Version 2.2: 2023-10-11
Changes: Data collection, Database references, Refinement description
Version 2.3: 2024-10-16
Changes: Structure summary