3PPM

Crystal Structure of a Noncovalently Bound alpha-Ketoheterocycle Inhibitor (Phenhexyl/Oxadiazole/Pyridine) to a Humanized Variant of Fatty Acid Amide Hydrolase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.78 Å
  • R-Value Free: 0.176 
  • R-Value Work: 0.151 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Fluoride-mediated capture of a noncovalent bound state of a reversible covalent enzyme inhibitor: X-ray crystallographic analysis of an exceptionally potent alpha-ketoheterocycle inhibitor of fatty acid amide hydrolase.

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

(2011) J.Am.Chem.Soc. 133: 4092-4100

  • DOI: 10.1021/ja110877y
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Two cocrystal X-ray structures of the exceptionally potent α-ketoheterocycle inhibitor 1 (K(i) = 290 pM) bound to a humanized variant of rat fatty acid amide hydrolase (FAAH) are disclosed, representing noncovalently and covalently bound states of th ...

    Two cocrystal X-ray structures of the exceptionally potent α-ketoheterocycle inhibitor 1 (K(i) = 290 pM) bound to a humanized variant of rat fatty acid amide hydrolase (FAAH) are disclosed, representing noncovalently and covalently bound states of the same inhibitor with the enzyme. Key to securing the structure of the noncovalently bound state of the inhibitor was the inclusion of fluoride ion in the crystallization conditions that is proposed to bind the oxyanion hole precluding inhibitor covalent adduct formation with stabilization of the tetrahedral hemiketal. This permitted the opportunity to detect important noncovalent interactions stabilizing the binding of the inhibitor within the FAAH active site independent of the covalent reaction. Remarkably, noncovalently bound 1 in the presence of fluoride appears to capture the active site in the same "in action" state with the three catalytic residues Ser241-Ser217-Lys142 occupying essentially identical positions observed in the covalently bound structure of 1, suggesting that this technique of introducing fluoride may have important applications in structural studies beyond inhibiting substrate or inhibitor oxyanion hole binding. Key insights to emerge from the studies include the observations that noncovalently bound 1 binds in its ketone (not gem diol) form, that the terminal phenyl group in the acyl side chain of the inhibitor serves as the key anchoring interaction overriding the intricate polar interactions in the cytosolic port, and that the role of the central activating heterocycle is dominated by its intrinsic electron-withdrawing properties. These two structures are also briefly compared with five X-ray structures of α-ketoheterocycle-based inhibitors bound to FAAH recently disclosed.


    Organizational Affiliation

    Department of Chemistry, Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Fatty-acid amide hydrolase 1
A, B
573Rattus norvegicusMutation(s): 6 
Gene Names: Faah (Faah1)
EC: 3.5.1.99
Find proteins for P97612 (Rattus norvegicus)
Go to UniProtKB:  P97612
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
F
Query on F

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A, B
FLUORIDE ION
F
KRHYYFGTRYWZRS-UHFFFAOYSA-M
 Ligand Interaction
CL
Query on CL

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A, B
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
JG1
Query on JG1

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Download CCD File 
A, B
7-phenyl-1-[5-(pyridin-2-yl)-1,3,4-oxadiazol-2-yl]heptan-1-one
C20 H21 N3 O2
BYQFWIOGPFHXFV-UHFFFAOYSA-N
 Ligand Interaction
1DO
Query on 1DO

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B
1-DODECANOL
C12 H26 O
LQZZUXJYWNFBMV-UHFFFAOYSA-N
 Ligand Interaction
PEG
Query on PEG

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A, B
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
JG1Ki: 0.3 - 290 nM (90) BINDINGDB
JG1Ki: 0.29 nM BINDINGMOAD
JG1Ki: 0.29 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.78 Å
  • R-Value Free: 0.176 
  • R-Value Work: 0.151 
  • Space Group: P 32 2 1
Unit Cell:
Length (Å)Angle (°)
a = 103.692α = 90.00
b = 103.692β = 90.00
c = 254.705γ = 120.00
Software Package:
Software NamePurpose
PHENIXrefinement
PHASERphasing
HKL-2000data reduction
HKL-2000data scaling
HKL-2000data collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-11-09
    Type: Initial release