4FM5

X-ray structure of des-methylflurbiprofen bound to murine COX-2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.81 Å
  • R-Value Free: 0.290 
  • R-Value Work: 0.240 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Substrate-Selective Inhibition of Cyclooxygenase-2: Development and Evaluation of Achiral Profen Probes.

Windsor, M.A.Hermanson, D.J.Kingsley, P.J.Xu, S.Crews, B.C.Ho, W.Keenan, C.M.Banerjee, S.Sharkey, K.A.Marnett, L.J.

(2012) ACS Med Chem Lett 3: 759-763

  • DOI: 10.1021/ml3001616

  • PubMed Abstract: 
  • Cyclooxygenase-2 (COX-2) oxygenates arachidonic acid and the endocannabinoids 2-arachidonoylglycerol (2-AG) and arachidonoylethanolamide (AEA). We recently reported that (R)-profens selectively inhibit endocannabinoid oxygenation but not arachidonic ...

    Cyclooxygenase-2 (COX-2) oxygenates arachidonic acid and the endocannabinoids 2-arachidonoylglycerol (2-AG) and arachidonoylethanolamide (AEA). We recently reported that (R)-profens selectively inhibit endocannabinoid oxygenation but not arachidonic acid oxygenation. In this work, we synthesized achiral derivatives of five profen scaffolds and evaluated them for substrate-selective inhibition using in vitro and cellular assays. The size of the substituents dictated the inhibitory strength of the analogs, with smaller substituents enabling greater potency but less selectivity. Inhibitors based on the flurbiprofen scaffold possessed the greatest potency and selectivity, with desmethylflurbiprofen (3a) exhibiting an IC(50) of 0.11 μM for inhibition of 2-AG oxygenation. The crystal structure of desmethylflurbiprofen complexed to mCOX-2 demonstrated a similar binding mode to other profens. Desmethylflurbiprofen exhibited a half-life in mice comparable to that of ibuprofen. The data presented suggest that achiral profens can act as lead molecules toward in vivo probes of substrate-selective COX-2 inhibition.


    Organizational Affiliation

    A.B. Hancock Jr. Memorial Laboratory for Cancer Research, Departments of Biochemistry, Chemistry, and Pharmacology, Vanderbilt Institute of Chemical Biology, Center in Molecular Toxicology, and Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine , Nashville, Tennessee, United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Prostaglandin G/H synthase 2
A, B, C, D
604Mus musculusMutation(s): 0 
Gene Names: Ptgs2 (Cox-2, Cox2, Pghs-b, Tis10)
EC: 1.14.99.1
Find proteins for Q05769 (Mus musculus)
Go to UniProtKB:  Q05769
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
DF0
Query on DF0

Download SDF File 
Download CCD File 
A, B, C, D
(2-fluorobiphenyl-4-yl)acetic acid
Des-methylflurbiprofen
C14 H11 F O2
ZLLZRKQQNGBXRD-UHFFFAOYSA-N
 Ligand Interaction
HEM
Query on HEM

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Download CCD File 
A, B, C, D
PROTOPORPHYRIN IX CONTAINING FE
HEME
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
NAG
Query on NAG

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Download CCD File 
A, B, C, D
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
BOG
Query on BOG

Download SDF File 
Download CCD File 
A, B, C, D
B-OCTYLGLUCOSIDE
C14 H28 O6
HEGSGKPQLMEBJL-RKQHYHRCSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
DF0IC50: 110 - 600 nM (100) BINDINGDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.81 Å
  • R-Value Free: 0.290 
  • R-Value Work: 0.240 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 181.632α = 90.00
b = 135.696β = 90.00
c = 125.150γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
PHASERphasing
HKL-2000data collection
SCALAdata scaling
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-08-29
    Type: Initial release
  • Version 1.1: 2012-12-19
    Type: Database references