3FUF

Leukotriene A4 hydrolase in complex with fragment 5-fluoroindole and bestatin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.189 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

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: 10.1021/jm900259h
  • Primary Citation of Related Structures:  
    3FTY, 3FU3, 3FTS, 3FU5, 3FTU, 3FU6, 3FTV, 3FTW, 3FTX, 3FU0

  • 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 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.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Leukotriene A-4 hydrolase A611Homo sapiensMutation(s): 0 
Gene Names: LTA4HLTA4
EC: 3.3.2.6 (PDB Primary Data), 3.4.11.4 (UniProt)
Find proteins for P09960 (Homo sapiens)
Explore P09960 
Go to UniProtKB:  P09960
NIH Common Fund Data Resources
PHAROS:  P09960
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BES
Query on BES

Download Ideal Coordinates CCD File 
A
2-(3-AMINO-2-HYDROXY-4-PHENYL-BUTYRYLAMINO)-4-METHYL-PENTANOIC ACID
C16 H24 N2 O4
VGGGPCQERPFHOB-RDBSUJKOSA-N
 Ligand Interaction
YB
Query on YB

Download Ideal Coordinates CCD File 
A
YTTERBIUM (III) ION
Yb
AWSFICBXMUKWSK-UHFFFAOYSA-N
 Ligand Interaction
14O
Query on 14O

Download Ideal Coordinates CCD File 
A
5-fluoro-1H-indole
C8 H6 F N
ODFFPRGJZRXNHZ-UHFFFAOYSA-N
 Ligand Interaction
IMD
Query on IMD

Download Ideal Coordinates CCD File 
A
IMIDAZOLE
C3 H5 N2
RAXXELZNTBOGNW-UHFFFAOYSA-O
 Ligand Interaction
ZN
Query on ZN

Download Ideal Coordinates CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
BESIC50:  300   nM  BindingDB
BESIC50:  20000   nM  BindingDB
BESIC50:  18010   nM  BindingDB
BESIC50:  4000   nM  BindingDB
BESIC50:  4200   nM  BindingDB
BESKd:  2050   nM  BindingDB
BESKi:  320   nM  BindingDB
14OIC50:  1000000   nM  BindingDB
BESIC50:  10100   nM  BindingDB
14OIC50 :  2000000   nM  PDBBind
BESIC50:  500   nM  BindingDB
BESKd:  4630   nM  BindingDB
14OIC50:  2000000   nM  BindingDB
BESKd:  5150   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.189 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 78.497α = 90
b = 87.075β = 90
c = 99.573γ = 90
Software Package:
Software NamePurpose
ADSCdata collection
MOLREPphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 2009-01-14 
  • 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