Structure of human Leukotriene A4 hydrolase in complex with inhibitor dimethyl(2- (4-phenoxyphenoxy)ethyl)amine

Experimental Data Snapshot

  • Resolution: 1.86 Å
  • R-Value Free: 0.189 
  • R-Value Work: 0.170 
  • R-Value Observed: 0.171 

Starting Model: experimental
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This is version 1.3 of the entry. See complete history


Peng: A Neural Gas-Based Approach for Pharmacophore Elucidation. Method Design, Validation and Virtual Screening for Novel Ligands of Lta4H.

Moser, D.Wittmann, S.K.Kramer, J.Blocher, R.Achenbach, J.Pogoryelov, D.Proschak, E.

(2015) J Chem Inf Model 55: 284

  • DOI: https://doi.org/10.1021/ci500618u
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    The pharmacophore concept is commonly employed in virtual screening for hit identification. A pharmacophore is generally defined as the three-dimensional arrangement of the structural and physicochemical features of a compound responsible for its affinity to a pharmacological target. Given a number of active ligands binding to a particular target in the same manner, it can reasonably be assumed that they have some shared features, a common pharmacophore. We present a growing neural gas (GNG)-based approach for the extraction of the relevant features which we called PENG (pharmacophore elucidation by neural gas). Results of retrospective validation indicate an acceptable quality of the generated models. Additionally a prospective virtual screening for leukotriene A4 hydrolase (LTA4H) inhibitors was performed. LTA4H is a bifunctional zinc metalloprotease which displays both epoxide hydrolase and aminopeptidase activity. We could show that the PENG approach is able to predict the binding mode of the ligand by X-ray crystallography. Furthermore, we identified a novel chemotype of LTA4H inhibitors.

  • Organizational Affiliation

    Institute of Pharmaceutical Chemistry, Goethe University , 60438 Frankfurt, Germany.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
LEUKOTRIENE A-4 HYDROLASE608Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P09960 (Homo sapiens)
Explore P09960 
Go to UniProtKB:  P09960
GTEx:  ENSG00000111144 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP09960
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on DP8

Download Ideal Coordinates CCD File 
B [auth A]N,N-dimethyl-2-(4-phenoxyphenoxy)ethanamine
C16 H19 N O2
Query on YB

Download Ideal Coordinates CCD File 
D [auth A],
E [auth A],
F [auth A],
G [auth A]
Query on IMD

Download Ideal Coordinates CCD File 
H [auth A],
I [auth A]
C3 H5 N2
Query on ZN

Download Ideal Coordinates CCD File 
C [auth A]ZINC ION
Binding Affinity Annotations 
IDSourceBinding Affinity
DP8 BindingDB:  5AEN Ki: 160 (nM) from 1 assay(s)
Kd: min: 60, max: 270 (nM) from 2 assay(s)
IC50: 60 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 1.86 Å
  • R-Value Free: 0.189 
  • R-Value Work: 0.170 
  • R-Value Observed: 0.171 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 76.996α = 90
b = 86.953β = 90
c = 98.223γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XDSdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-02-11
    Type: Initial release
  • Version 1.1: 2015-03-11
    Changes: Database references
  • Version 1.2: 2019-02-27
    Changes: Data collection, Experimental preparation, Other
  • Version 1.3: 2024-01-10
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description