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 

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:  

  • 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 iterat ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Leukotriene A-4 hydrolase
A
611Homo sapiensMutation(s): 0 
Gene Names: LTA4H (LTA4)
EC: 3.3.2.6
Find proteins for P09960 (Homo sapiens)
Go to Gene View: LTA4H
Go to UniProtKB:  P09960
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
YB
Query on YB

Download SDF File 
Download CCD File 
A
YTTERBIUM (III) ION
Yb
AWSFICBXMUKWSK-UHFFFAOYSA-N
 Ligand Interaction
52D
Query on 52D

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

Download SDF File 
Download CCD File 
A
IMIDAZOLE
C3 H5 N2
RAXXELZNTBOGNW-UHFFFAOYSA-O
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
52DIC50: 199000 nM (100) BINDINGDB
52DIC50: 199000 nM BINDINGMOAD
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 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 78.337α = 90.00
b = 87.083β = 90.00
c = 99.766γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data scaling
MOLREPphasing
HKL-2000data reduction
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



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
    Type: Version format compliance
  • Version 1.2: 2017-11-01
    Type: Refinement description