8AWH | pdb_00008awh

Leukotriene A4 hydrolase in complex with 4-(4-Benzylphenyl)-selenazol-2-amine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.42 Å
  • R-Value Free: 
    0.187 (Depositor), 0.190 (DCC) 
  • R-Value Work: 
    0.156 (Depositor), 0.160 (DCC) 
  • R-Value Observed: 
    0.158 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted OD6Click on this verticalbar to view details

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

  • DOI: https://doi.org/10.3390/ijms24087539
  • Primary Citation of 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 4 H). In addition, LTA 4 H 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 4 H, 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 4 H 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 4 H 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.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Leukotriene A-4 hydrolase617Homo sapiensMutation(s): 0 
Gene Names: LTA4HLTA4
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 Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP09960
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
OD6 (Subject of Investigation/LOI)
Query on OD6

Download Ideal Coordinates CCD File 
K [auth A]4-[4-(phenylmethyl)phenyl]-1,3-selenazol-2-amine
C16 H14 N2 Se
TVNNGQGXOFXDAF-UHFFFAOYSA-N
YB
Query on YB

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A],
E [auth A]
YTTERBIUM (III) ION
Yb
AWSFICBXMUKWSK-UHFFFAOYSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
M [auth A],
N [auth A]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
IMD
Query on IMD

Download Ideal Coordinates CCD File 
I [auth A],
J [auth A]
IMIDAZOLE
C3 H5 N2
RAXXELZNTBOGNW-UHFFFAOYSA-O
ZN (Subject of Investigation/LOI)
Query on ZN

Download Ideal Coordinates CCD File 
B [auth A]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
ACT
Query on ACT

Download Ideal Coordinates CCD File 
F [auth A],
G [auth A],
H [auth A],
L [auth A]
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.42 Å
  • R-Value Free:  0.187 (Depositor), 0.190 (DCC) 
  • R-Value Work:  0.156 (Depositor), 0.160 (DCC) 
  • R-Value Observed: 0.158 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 77.022α = 90
b = 87.519β = 90
c = 99.007γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
PHASERphasing
PDB_EXTRACTdata extraction
STARANISOdata scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted OD6Click on this verticalbar to view details

Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Swedish Research CouncilSweden2018-02818
Estonian Research CouncilEstoniaPUTJD1046

Revision History  (Full details and data files)

  • Version 1.0: 2023-05-03
    Type: Initial release
  • Version 1.1: 2023-05-10
    Changes: Database references
  • Version 1.2: 2024-02-07
    Changes: Data collection, Refinement description