3RR3 | pdb_00003rr3

Structure of (R)-flurbiprofen bound to mCOX-2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.84 Å
  • R-Value Free: 
    0.244 (Depositor), 0.236 (DCC) 
  • R-Value Work: 
    0.197 (Depositor), 0.191 (DCC) 
  • R-Value Observed: 
    0.199 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 3RR3

Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history

Literature

(R)-Profens are substrate-selective inhibitors of endocannabinoid oxygenation by COX-2.

Duggan, K.C.Hermanson, D.J.Musee, J.Prusakiewicz, J.J.Scheib, J.L.Carter, B.D.Banerjee, S.Oates, J.A.Marnett, L.J.

(2011) Nat Chem Biol 7: 803-809

  • DOI: https://doi.org/10.1038/nchembio.663
  • Primary Citation Related Structures: 
    3Q7D, 3RR3

  • PubMed Abstract: 

    Cyclooxygenase-2 (COX-2) catalyzes the oxygenation of arachidonic acid and the endocannabinoids 2-arachidonoylglycerol and arachidonoylethanolamide. Evaluation of a series of COX-2 inhibitors revealed that many weak competitive inhibitors of arachidonic acid oxygenation are potent inhibitors of endocannabinoid oxygenation. (R) enantiomers of ibuprofen, naproxen and flurbiprofen, which are considered to be inactive as COX-2 inhibitors, are potent 'substrate-selective inhibitors' of endocannabinoid oxygenation. Crystal structures of the COX-2–(R)-naproxen and COX-2–(R)-flurbiprofen complexes verified this unexpected binding and defined the orientation of the (R) enantiomers relative to (S) enantiomers. (R)-Profens selectively inhibited endocannabinoid oxygenation by lipopolysaccharide-stimulated dorsal root ganglion (DRG) cells. Substrate-selective inhibition provides new tools for investigating the role of COX-2 in endocannabinoid oxygenation and a possible explanation for the ability of (R)-profens to maintain endocannabinoid tone in models of neuropathic pain.


  • Organizational Affiliation
    • Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee, USA.

Macromolecule Content 

  • Total Structure Weight: 266.09 kDa 
  • Atom Count: 18,725 
  • Modeled Residue Count: 2,208 
  • Deposited Residue Count: 2,240 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Prostaglandin G/H synthase 2
A, B, C, D
560Mus musculusMutation(s): 0 
Gene Names: Ptgs2Cox-2Cox2Pghs-bTis10
EC: 1.14.99.1
UniProt
Find proteins for Q05769 (Mus musculus)
Explore Q05769 
Go to UniProtKB:  Q05769
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ05769
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
HEM

Query on HEM



Download:Ideal Coordinates CCD File
FA [auth D],
H [auth A],
P [auth B],
X [auth C]
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
BOG

Query on BOG



Download:Ideal Coordinates CCD File
GA [auth D]
J [auth A]
K [auth A]
R [auth B]
Y [auth C]
GA [auth D],
J [auth A],
K [auth A],
R [auth B],
Y [auth C],
Z [auth C]
octyl beta-D-glucopyranoside
C14 H28 O6
HEGSGKPQLMEBJL-RKQHYHRCSA-N
FLR

Query on FLR



Download:Ideal Coordinates CCD File
DA [auth D],
I [auth A],
Q [auth B],
W [auth C]
(2R)-2-(3-fluoro-4-phenyl-phenyl)propanoic acid
C15 H13 F O2
SYTBZMRGLBWNTM-SNVBAGLBSA-N
NAG

Query on NAG



Download:Ideal Coordinates CCD File
AA [auth C]
BA [auth D]
CA [auth D]
E [auth A]
EA [auth D]
AA [auth C],
BA [auth D],
CA [auth D],
E [auth A],
EA [auth D],
F [auth A],
G [auth A],
HA [auth D],
L [auth A],
M [auth B],
N [auth B],
O [auth B],
S [auth B],
T [auth C],
U [auth C],
V [auth C]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.84 Å
  • R-Value Free:  0.244 (Depositor), 0.236 (DCC) 
  • R-Value Work:  0.197 (Depositor), 0.191 (DCC) 
  • R-Value Observed: 0.199 (Depositor) 
Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 180.615α = 90
b = 134.549β = 90
c = 122.775γ = 90
Software Package:
Software NamePurpose
ADSCdata collection
PHENIXmodel building
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-11-09
    Type: Initial release
  • Version 1.1: 2012-03-21
    Changes: Database references
  • Version 1.2: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary
  • Version 1.3: 2024-10-09
    Changes: Data collection, Database references, Structure summary