3K83

Crystal Structure Analysis of a Biphenyl/Oxazole/Carboxypyridine alpha-ketoheterocycle Inhibitor Bound to a Humanized Variant of Fatty Acid Amide Hydrolase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.144 
  • R-Value Observed: 0.147 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

X-ray crystallographic analysis of alpha-ketoheterocycle inhibitors bound to a humanized variant of fatty acid amide hydrolase.

Mileni, M.Garfunkle, J.Ezzili, C.Kimball, F.S.Cravatt, B.F.Stevens, R.C.Boger, D.L.

(2010) J Med Chem 53: 230-240

  • DOI: 10.1021/jm9012196
  • Primary Citation of Related Structures:  
    3K83, 3K84, 3K7F

  • PubMed Abstract: 
  • Three cocrystal X-ray structures of the alpha-ketoheterocycle inhibitors 3-5 bound to a humanized variant of fatty acid amide hydrolase (FAAH) are disclosed and comparatively discussed alongside those of 1 (OL-135) and its isomer 2. These five X-ray structures systematically probe each of the three active site regions key to substrate or inhibitor binding: (1) the conformationally mobile acyl chain-binding pocket and membrane access channel responsible for fatty acid amide substrate and inhibitor acyl chain binding, (2) the atypical active site catalytic residues and surrounding oxyanion hole that covalently binds the core of the alpha-ketoheterocycle inhibitors captured as deprotonated hemiketals mimicking the tetrahedral intermediate of the enzyme-catalyzed reaction, and (3) the cytosolic port and its uniquely important imbedded ordered water molecules and a newly identified anion binding site ...

    Three cocrystal X-ray structures of the alpha-ketoheterocycle inhibitors 3-5 bound to a humanized variant of fatty acid amide hydrolase (FAAH) are disclosed and comparatively discussed alongside those of 1 (OL-135) and its isomer 2. These five X-ray structures systematically probe each of the three active site regions key to substrate or inhibitor binding: (1) the conformationally mobile acyl chain-binding pocket and membrane access channel responsible for fatty acid amide substrate and inhibitor acyl chain binding, (2) the atypical active site catalytic residues and surrounding oxyanion hole that covalently binds the core of the alpha-ketoheterocycle inhibitors captured as deprotonated hemiketals mimicking the tetrahedral intermediate of the enzyme-catalyzed reaction, and (3) the cytosolic port and its uniquely important imbedded ordered water molecules and a newly identified anion binding site. The detailed analysis of their key active site interactions and their implications on the interpretation of the available structure-activity relationships are discussed providing important insights for future design.


    Organizational Affiliation

    Department of Chemistry, The Skaggs Institute for Chemical Biology,The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Fatty-acid amide hydrolase 1 AB573Rattus norvegicusMutation(s): 6 
Gene Names: Faahfaah-1Faah1
EC: 3.5.1 (PDB Primary Data), 3.5.1.99 (UniProt), 3.1.1 (UniProt)
Find proteins for P97612 (Rattus norvegicus)
Explore P97612 
Go to UniProtKB:  P97612
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
F27
Query on F27

Download Ideal Coordinates CCD File 
A, B
6-[2-(3-biphenyl-4-ylpropanoyl)-1,3-oxazol-5-yl]pyridine-2-carboxylic acid
C24 H18 N2 O4
VGYASWDHSIVABN-UHFFFAOYSA-N
 Ligand Interaction
1DO
Query on 1DO

Download Ideal Coordinates CCD File 
B
1-DODECANOL
C12 H26 O
LQZZUXJYWNFBMV-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download Ideal Coordinates CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
F27Ki:  22   nM  BindingDB
F27Ki :  22   nM  PDBBind
F27IC50:  6   nM  BindingDB
F27Ki:  22   nM  BindingDB
F27Ki:  22   nM  Binding MOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.144 
  • R-Value Observed: 0.147 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 103.404α = 90
b = 103.404β = 90
c = 254.439γ = 120
Software Package:
Software NamePurpose
HKL-2000data collection
PHASERphasing
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-12-01
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance