3CHO

Crystal structure of leukotriene a4 hydrolase in complex with 2-amino-N-[4-(phenylmethoxy)phenyl]-acetamide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.188 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Synthesis of glutamic acid analogs as potent inhibitors of leukotriene A4 hydrolase.

Kirkland, T.A.Adler, M.Bauman, J.G.Chen, M.Haeggstrom, J.Z.King, B.Kochanny, M.J.Liang, A.M.Mendoza, L.Phillips, G.B.Thunnissen, M.Trinh, L.Whitlow, M.Ye, B.Ye, H.Parkinson, J.Guilford, W.J.

(2008) Bioorg Med Chem 16: 4963-4983

  • DOI: 10.1016/j.bmc.2008.03.042
  • Primary Citation of Related Structures:  
    3CHP, 3CHQ, 3CHR, 3CHS, 3CHO

  • PubMed Abstract: 
  • Leukotriene B(4) (LTB(4)) is a potent pro-inflammatory mediator that has been implicated in the pathogenesis of multiple diseases, including psoriasis, inflammatory bowel disease, multiple sclerosis and asthma. As a method to decrease the level of LTB(4) and possibly identify novel treatments, inhibitors of the LTB(4) biosynthetic enzyme, leukotriene A(4) hydrolase (LTA(4)-h), have been explored ...

    Leukotriene B(4) (LTB(4)) is a potent pro-inflammatory mediator that has been implicated in the pathogenesis of multiple diseases, including psoriasis, inflammatory bowel disease, multiple sclerosis and asthma. As a method to decrease the level of LTB(4) and possibly identify novel treatments, inhibitors of the LTB(4) biosynthetic enzyme, leukotriene A(4) hydrolase (LTA(4)-h), have been explored. Here we describe the discovery of a potent inhibitor of LTA(4)-h, arylamide of glutamic acid 4f, starting from the corresponding glycinamide 2. Analogs of 4f are then described, focusing on compounds that are both active and stable in whole blood. This effort culminated in the identification of amino alcohol 12a and amino ester 6b which meet these criteria.


    Related Citations: 
    • Crystal Structure of Human Leukotriene A4 Hydrolase, a Bifunctional Enzyme in Inflammation
      Thunnissen, M.M.G.M., Nordlund, P.N., Haeggstrom, J.Z.
      (2001) Nat Struct Biol 8: 131
    • Crystal structures of LEUKOTRIENE A4 HYDROLASE in complex with captopril and two competitive tight-binding inhibitors.
      Thunnissen, M.M.G.M., Anderson, B., Samuelsson, B., Wong, C.-H., Haeggstrom, J.Z.
      (2002) FASEB J 16: 1648
    • Leukotriene A4 Hydrolase: Selective Abrogation of Leukotriene B4 Formation by Mutation of Aspartic Acid 375.
      Rudberg, P.C., Tholander, F., Thunnissen, M.M., Samuelsson, B., Haeggstrom, J.Z.
      (2002) Proc Natl Acad Sci U S A 99: 4215
    • Leukotriene A4 Hydrolase: Identification of a Common Carboxylate Recognition Site for the Epoxide Hydrolase and Aminopeptidase Substrates
      Rudberg, P.C., Tholander, F.O.T., Andberg, M., Thunnissen, M.M.G.M., Haeggstrom, J.Z.
      (2004) J Biol Chem 279: 27376

    Organizational Affiliation

    Department of Medicinal Chemistry, Berlex Biosciences, 2600 Hilltop Drive, Richmond, CA 94804, United States. Thomas.kirkland@promega.com



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Leukotriene A-4 hydrolase A610Homo 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
4BG
Query on 4BG

Download Ideal Coordinates CCD File 
A
N-[4-(benzyloxy)phenyl]glycinamide
C15 H16 N2 O2
YJPUATSIKWOSST-UHFFFAOYSA-N
 Ligand Interaction
YB
Query on YB

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

Download Ideal Coordinates CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
ACT
Query on ACT

Download Ideal Coordinates CCD File 
A
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
4BGIC50:  135   nM  BindingDB
4BGIC50:  280   nM  Binding MOAD
4BGIC50:  280   nM  BindingDB
4BGIC50 :  280   nM  PDBBind
4BGIC50:  300   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.188 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 78.312α = 90
b = 87.124β = 90
c = 99.364γ = 90
Software Package:
Software NamePurpose
CNXrefinement
MOSFLMdata reduction
SCALAdata scaling
CNXphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-04-22
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2018-03-07
    Changes: Data collection
  • Version 1.3: 2019-11-20
    Changes: Derived calculations