3Q7D | pdb_00003q7d

Structure of (R)-naproxen bound to mCOX-2.

• PDB DOI: https://doi.org/10.2210/pdb3Q7D/pdb

• Classification: OXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR
• Organism(s): Mus musculus
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2011-01-04 Released: 2011-11-09 
• Deposition Author(s): Duggan, K.C., Hermanson, D.J., Musee, J., Prusakiewicz, J.J., Scheib, J., Carter, B.D., Banerjee, S., Marnett, L.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 
  0.233 (Depositor), 0.233 (DCC) 
• R-Value Work: 
  0.177 (Depositor), 0.178 (DCC) 
• R-Value Observed: 
  0.180 (Depositor) 

Starting Model: experimental

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

• PubMed: 22053353 
• 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.

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

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 139.66 kDa 
• Atom Count: 9,880 
• Modeled Residue Count: 1,104 
• Deposited Residue Count: 1,174 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Prostaglandin G/H synthase 2	A, B	587	Mus musculus	Mutation(s): 0  Gene Names: Ptgs2, Cox-2, Cox2, Pghs-b, Tis10 EC: 1.14.99.1
UniProt
Find proteins for Q05769 (Mus musculus) Explore Q05769  Go to UniProtKB:  Q05769

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HEM	F [auth A], P [auth B]	PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L
BOG	H [auth A], I [auth A], J [auth A], R [auth B], S [auth B]	octyl beta-D-glucopyranoside C14 H28 O6 HEGSGKPQLMEBJL-RKQHYHRCSA-N
NPX	G [auth A], Q [auth B]	(2R)-2-(6-methoxynaphthalen-2-yl)propanoic acid C14 H14 O3 CMWTZPSULFXXJA-SECBINFHSA-N
NAG	C [auth A], D [auth A], E [auth A], K [auth A], M [auth B], N [auth B], O [auth B], T [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
CL	L [auth A], U [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Binding Affinity Annotations
ID	Source	Binding Affinity
NPX	BindingDB:  3Q7D	IC50: min: 900, max: 2.50e+4 (nM) from 2 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free:  0.233 (Depositor), 0.233 (DCC) 
• R-Value Work:  0.177 (Depositor), 0.178 (DCC) 
• R-Value Observed: 0.180 (Depositor) 

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 122.735	α = 90
b = 133.028	β = 90
c = 181.039	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-11-09 
Deposition Author(s): Duggan, K.C., Hermanson, D.J., Musee, J., Prusakiewicz, J.J., Scheib, J., Carter, B.D., Banerjee, S., Marnett, L.J.

Revision History  

• Version 1.0: 2011-11-09
  Type: Initial release
  
• Version 1.1: 2012-03-28
  Changes: Database references
• Version 1.2: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Structure summary
• Version 1.3: 2023-09-13
  Changes: Data collection, Database references, Refinement description, Structure summary
• Version 1.4: 2024-11-20
  Changes: Structure summary