Crystal Structure Analysis of a Phenhexyl/Oxazole/Carboxypyridine alpha-Ketoheterocycle Inhibitor Bound to a Humanized Variant of Fatty Acid Amide Hydrolase'

Experimental Data Snapshot

  • Resolution: 1.95 Å
  • R-Value Free: 0.188 
  • R-Value Work: 0.154 
  • R-Value Observed: 0.156 

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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: https://doi.org/10.1021/jm9012196
  • Primary Citation of Related Structures:  
    3K7F, 3K83, 3K84

  • 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. 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.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Fatty-acid amide hydrolase 1
A, B
573Rattus norvegicusMutation(s): 6 
Gene Names: Faahfaah-1Faah1
EC: 3.5.1
Find proteins for P97612 (Rattus norvegicus)
Explore P97612 
Go to UniProtKB:  P97612
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP97612
Sequence Annotations
  • Reference Sequence
Small Molecules
Binding Affinity Annotations 
IDSourceBinding Affinity
F2C PDBBind:  3K7F Ki: 20 (nM) from 1 assay(s)
BindingDB:  3K7F Ki: min: 10.4, max: 26 (nM) from 3 assay(s)
IC50: 100 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 1.95 Å
  • R-Value Free: 0.188 
  • R-Value Work: 0.154 
  • R-Value Observed: 0.156 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 103.87α = 90
b = 103.87β = 90
c = 255.41γ = 120
Software Package:
Software NamePurpose
XDSdata scaling
XDSdata reduction
XSCALEdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

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
  • Version 1.2: 2021-10-13
    Changes: Database references, Derived calculations
  • Version 1.3: 2023-09-06
    Changes: Data collection, Refinement description