8AVA | pdb_00008ava

Leukotriene A4 hydrolase in complex with 4-(4-benzylphenyl)-oxazol-2-amine

PDB DOI: https://doi.org/10.2210/pdb8AVA/pdb

Classification: IMMUNE SYSTEM
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2022-08-26 Released: 2023-05-03
Deposition Author(s): Teder, T., Haeggstrom, J.Z.
Funding Organization(s): Swedish Research Council, Estonian Research Council

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.35 Å
R-Value Free:
0.169 (Depositor), 0.177 (DCC)
R-Value Work:
0.146 (Depositor), 0.155 (DCC)
R-Value Observed:
0.147 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Modulation of the 5-Lipoxygenase Pathway by Chalcogen-Containing Inhibitors of Leukotriene A 4 Hydrolase.

Teder, T., Konig, S., Singh, R., Samuelsson, B., Werz, O., Garscha, U., Haeggstrom, J.Z.

(2023) Int J Mol Sci 24

PubMed: 37108702 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.3390/ijms24087539
Primary Citation Related Structures:
8AVA, 8AWH

PubMed Abstract:
The 5-lipoxygenase (5-LOX) pathway gives rise to bioactive inflammatory lipid mediators, such as leukotrienes (LTs). 5-LOX carries out the oxygenation of arachidonic acid to the 5-hydroperoxy derivative and then to the leukotriene A ₄ epoxide which is converted to a chemotactic leukotriene B ₄ (LTB ₄) by leukotriene A ₄ hydrolase (LTA ₄H). In addition, LTA ₄H possesses aminopeptidase activity to cleave the N-terminal proline of a pro-inflammatory tripeptide, prolyl-glycyl-proline (PGP). Based on the structural characteristics of LTA ₄H, it is possible to selectively inhibit the epoxide hydrolase activity while sparing the inactivating, peptidolytic, cleavage of PGP. In the current study, chalcogen-containing compounds, 4-(4-benzylphenyl) thiazol-2-amine (ARM1) and its selenazole (TTSe) and oxazole (TTO) derivatives were characterized regarding their inhibitory and binding properties. All three compounds selectively inhibit the epoxide hydrolase activity of LTA ₄H at low micromolar concentrations, while sparing the aminopeptidase activity. These inhibitors also block the 5-LOX activity in leukocytes and have distinct inhibition constants with recombinant 5-LOX. Furthermore, high-resolution structures of LTA ₄H with inhibitors were determined and potential binding sites to 5-LOX were proposed. In conclusion, we present chalcogen-containing inhibitors which differentially target essential steps in the biosynthetic route for LTB ₄ and can potentially be used as modulators of inflammatory response by the 5-LOX pathway.

Organizational Affiliation

Division of Physiological Chemistry II, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 17177 Stockholm, Sweden.

Macromolecule Content

Total Structure Weight: 71.76 kDa
Atom Count: 5,783
Modeled Residue Count: 607
Deposited Residue Count: 617
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Leukotriene A-4 hydrolase	A	617	Homo sapiens	Mutation(s): 0 Gene Names: LTA4H, LTA4 EC: 3.3.2.6 (PDB Primary Data), 3.4.11.4 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for P09960 (Homo sapiens) Explore P09960 Go to UniProtKB: P09960
PHAROS: P09960 GTEx: ENSG00000111144
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P09960
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
OVO (Subject of Investigation/LOI) Query on OVO Download:Ideal Coordinates CCD File SDF format, chain L [auth A] MOL2 format, chain L [auth A] mmCIF format, chain L [auth A]	L [auth A]	4-[4-(phenylmethyl)phenyl]-1,3-oxazol-2-amine C₁₆ H₁₄ N₂ O FZDQKNHCMWUWBD-UHFFFAOYSA-N		Interactions Focus chain L [auth A] Interactions & Density Focus chain L [auth A]
YB Query on YB Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain E [auth A] SDF format, chain D [auth A] SDF format, chain C [auth A] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A]	C [auth A], D [auth A], E [auth A], F [auth A]	YTTERBIUM (III) ION Yb AWSFICBXMUKWSK-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain O [auth A] SDF format, chain N [auth A] MOL2 format, chain O [auth A] MOL2 format, chain N [auth A] mmCIF format, chain O [auth A] mmCIF format, chain N [auth A]	N [auth A], O [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain N [auth A] Focus chain O [auth A] Interactions & Density Focus chain N [auth A] Focus chain O [auth A]
IMD Query on IMD Download:Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain K [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A]	J [auth A], K [auth A]	IMIDAZOLE C₃ H₅ N₂ RAXXELZNTBOGNW-UHFFFAOYSA-O		Interactions Focus chain J [auth A] Focus chain K [auth A] Interactions & Density Focus chain J [auth A] Focus chain K [auth A]
ZN (Subject of Investigation/LOI) Query on ZN Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
ACT Query on ACT Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain M [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain M [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain M [auth A]	G [auth A], H [auth A], I [auth A], M [auth A]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain M [auth A] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain M [auth A]