Leukotriene A4 hydrolase in complex with resveratrol

Experimental Data Snapshot

  • Resolution: 2.33 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.181 

Starting Model: experimental
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Ligand Structure Quality Assessment 

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Discovery of leukotriene A4 hydrolase inhibitors using metabolomics biased fragment crystallography.

Davies, D.R.Mamat, B.Magnusson, O.T.Christensen, J.Haraldsson, M.H.Mishra, R.Pease, B.Hansen, E.Singh, J.Zembower, D.Kim, H.Kiselyov, A.S.Burgin, A.B.Gurney, M.E.Stewart, L.J.

(2009) J Med Chem 52: 4694-4715

  • DOI: https://doi.org/10.1021/jm900259h
  • Primary Citation of Related Structures:  
    3FTS, 3FTU, 3FTV, 3FTW, 3FTX, 3FTY, 3FU0, 3FU3, 3FU5, 3FU6, 3FUD, 3FUE, 3FUF, 3FUH, 3FUI, 3FUJ, 3FUK, 3FUM, 3FUN

  • PubMed Abstract: 

    We describe a novel fragment library termed fragments of life (FOL) for structure-based drug discovery. The FOL library includes natural small molecules of life, derivatives thereof, and biaryl protein architecture mimetics. The choice of fragments facilitates the interrogation of protein active sites, allosteric binding sites, and protein-protein interaction surfaces for fragment binding. We screened the FOL library against leukotriene A4 hydrolase (LTA4H) by X-ray crystallography. A diverse set of fragments including derivatives of resveratrol, nicotinamide, and indole were identified as efficient ligands for LTA4H. These fragments were elaborated in a small number of synthetic cycles into potent inhibitors of LTA4H representing multiple novel chemotypes for modulating leukotriene biosynthesis. Analysis of the fragment-bound structures also showed that the fragments comprehensively recapitulated key chemical features and binding modes of several reported LTA4H inhibitors.

  • Organizational Affiliation

    deCODE biostructures, Inc., 7869 NE Day Road West, Bainbridge Island, Washington 98110, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Leukotriene A-4 hydrolase611Homo sapiensMutation(s): 0 
Gene Names: LTA4HLTA4
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
Binding Affinity Annotations 
IDSourceBinding Affinity
STL PDBBind:  3FTS IC50: 2.12e+5 (nM) from 1 assay(s)
BindingDB:  3FTS IC50: min: 2.12e+5, max: 3.66e+5 (nM) from 2 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 2.33 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.181 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 78.028α = 90
b = 87.18β = 90
c = 98.75γ = 90
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

  • Released Date: 2009-07-28 
  • Deposition Author(s): Davies, D.R.

Revision History  (Full details and data files)

  • Version 1.0: 2009-07-28
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2017-11-01
    Changes: Refinement description
  • Version 1.3: 2023-09-06
    Changes: Data collection, Database references, Derived calculations, Refinement description