Crystal structure of Celecoxib bound to S121P murine COX-2 mutant

Experimental Data Snapshot

  • Resolution: 2.82 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.191 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report

Ligand Structure Quality Assessment 

This is version 2.1 of the entry. See complete history


Fatty Acid Binding to the Allosteric Subunit of Cyclooxygenase-2 Relieves a Tonic Inhibition of the Catalytic Subunit.

Dong, L.Yuan, C.Orlando, B.J.Malkowski, M.G.Smith, W.L.

(2016) J Biol Chem 291: 25641-25655

  • DOI: https://doi.org/10.1074/jbc.M116.757310
  • Primary Citation of Related Structures:  
    5JVY, 5JVZ, 5JW1

  • PubMed Abstract: 

    Prostaglandin endoperoxide H synthase-2 (PGHS-2), also called cyclooxygenase-2 (COX-2), converts arachidonic acid to PGH 2 PGHS-2 is a conformational heterodimer composed of allosteric (E allo ) and catalytic (E cat ) subunits. Fatty acids (FAs) bind to Arg-120 of E allo increasing to different degrees, depending on the FA, the V max of its E cat partner. We report here that movement of helical residues 120-122 and loop residues 123-129 of E allo underlies the allosteric effects of FAs and allosteric COX-2 inhibitors, including naproxen and flurbiprofen. An S121P substitution in both PGHS-2 monomers yields a variant (S121P/S121P PGHS-2) that has 1.7-1.8 times the V max of native PGHS-2 and is relatively insensitive to activation by FAs or inhibition by allosteric inhibitors. The S121P substitution in E allo is primarily responsible for these effects. In X-ray crystal structures, the Cα atoms of helical residues 119-122 of S121P/S121P PGHS-2 are displaced from their normal positions. Additionally, the S121P/S121P PGHS-2 variants in which Pro-127 and Ser-541 are replaced by cysteines spontaneously forms Cys-127 to Cys-541 cross-links between monomers. This is unlike the corresponding native PGHS-2 variant and suggests that S121P substitutions also unhinge the loop involving residues 123-129. We conclude the following: (a) the region involving residues 120-129 of unoccupied E allo tonically inhibits E cat ; (b) binding of an activating FA (e.g. arachidonic, palmitic, or oleic acid) to E allo or an S121P substitution in E allo repositions this region to increase E cat activity; and (c) allosteric COX inhibitors act by preventing FA binding to E allo and additionally by relocating E allo residues to inhibit E cat .

  • Organizational Affiliation

    From the Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, Michigan 48109 and.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Prostaglandin G/H synthase 2
A, B
552Mus musculusMutation(s): 1 
Gene Names: Ptgs2Cox-2Cox2Pghs-bTis10
Find proteins for Q05769 (Mus musculus)
Explore Q05769 
Go to UniProtKB:  Q05769
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ05769
Glycosylation Sites: 3Go to GlyGen: Q05769-1
Sequence Annotations
  • Reference Sequence


Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
C, D
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on COH

Download Ideal Coordinates CCD File 
E [auth A],
J [auth B]
C34 H32 Co N4 O4
Query on CEL

Download Ideal Coordinates CCD File 
F [auth A],
K [auth B]
C17 H14 F3 N3 O2 S
Query on BOG

Download Ideal Coordinates CCD File 
G [auth A]octyl beta-D-glucopyranoside
C14 H28 O6
Query on NAG

Download Ideal Coordinates CCD File 
H [auth A],
I [auth A],
L [auth B],
M [auth B]
C8 H15 N O6
Binding Affinity Annotations 
IDSourceBinding Affinity
CEL BindingDB:  5JW1 Ki: min: 340, max: 960 (nM) from 5 assay(s)
Kd: 789.09 (nM) from 1 assay(s)
IC50: min: 0.07, max: 700 (nM) from 106 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 2.82 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.191 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 120.362α = 90
b = 132.198β = 90
c = 180.392γ = 90
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-10-26
    Type: Initial release
  • Version 1.1: 2019-09-11
    Changes: Data collection, Database references, Derived calculations
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Structure summary
  • Version 2.1: 2023-09-27
    Changes: Data collection, Database references, Refinement description, Structure summary