3FUL

Leukotriene A4 hydrolase in complex with pyridin-4-yl[4-(2-pyrrolidin-1-ylethoxy)phenyl]methanone


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.39 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.186 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Discovery of 4-[(2S)-2-{[4-(4-chlorophenoxy)phenoxy]methyl}-1-pyrrolidinyl]butanoic acid (DG-051) as a novel leukotriene A4 hydrolase inhibitor of leukotriene B4 biosynthesis.

Sandanayaka, V.Mamat, B.Mishra, R.K.Winger, J.Krohn, M.Zhou, L.M.Keyvan, M.Enache, L.Sullins, D.Onua, E.Zhang, J.Halldorsdottir, G.Sigthorsdottir, H.Thorlaksdottir, A.Sigthorsson, G.Thorsteinnsdottir, M.Davies, D.R.Stewart, L.J.Zembower, D.E.Andresson, T.Kiselyov, A.S.Singh, J.Gurney, M.E.

(2010) J Med Chem 53: 573-585

  • DOI: 10.1021/jm900838g
  • Primary Citation of Related Structures:  
    3FTZ, 3FUL, 3FHE, 3FH5, 3FH7, 3FH8

  • PubMed Abstract: 
  • Both in-house human genetic and literature data have converged on the identification of leukotriene 4 hydrolase (LTA(4)H) as a key target for the treatment of cardiovascular disease. We combined fragment-based crystallography screening with an iterative ...

    Both in-house human genetic and literature data have converged on the identification of leukotriene 4 hydrolase (LTA(4)H) as a key target for the treatment of cardiovascular disease. We combined fragment-based crystallography screening with an iterative medicinal chemistry effort to optimize inhibitors of LTA(4)H. Ligand efficiency was followed throughout our structure-activity studies. As applied within the context of LTA(4)H inhibitor design, the chemistry team was able to design a potent compound 20 (DG-051) (K(d) = 26 nM) with high aqueous solubility (>30 mg/mL) and high oral bioavailability (>80% across species) that is currently undergoing clinical evaluation for the treatment of myocardial infarction and stroke. The structural biology-chemistry interaction described in this paper provides a sound alternative to conventional screening techniques. This is the first example of a gene-to-clinic paradigm enabled by a fragment-based drug discovery effort.


    Organizational Affiliation

    Medicinal Chemistry, deCODE Chemistry, Inc., 2501 Davey Road, Woodridge, Illinois 60517, 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 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
52D
Query on 52D

Download Ideal Coordinates CCD File 
A
pyridin-4-yl[4-(2-pyrrolidin-1-ylethoxy)phenyl]methanone
C18 H20 N2 O2
AFGONOGEOHNVPG-UHFFFAOYSA-N
 Ligand Interaction
YB
Query on YB

Download Ideal Coordinates CCD File 
A
YTTERBIUM (III) ION
Yb
AWSFICBXMUKWSK-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 %)
52DIC50:  199000   nM  BindingDB
52DIC50:  199000   nM  Binding MOAD
52DIC50 :  199000   nM  PDBBind
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.39 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.186 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 78.337α = 90
b = 87.083β = 90
c = 99.766γ = 90
Software Package:
Software NamePurpose
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: 2010-01-05 
  • Deposition Author(s): Davies, D.R.

Revision History 

  • Version 1.0: 2010-01-05
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2017-11-01
    Changes: Refinement description