1PXX

CRYSTAL STRUCTURE OF DICLOFENAC BOUND TO THE CYCLOOXYGENASE ACTIVE SITE OF COX-2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.302 
  • R-Value Work: 0.254 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

A Novel Mechanism of Cyclooxygenase-2 Inhibition Involving Interactions with Ser-530 and Tyr-385.

Rowlinson, S.W.Kiefer, J.R.Prusakiewicz, J.J.Pawlitz, J.L.Kozak, K.R.Kalgutkar, A.S.Stallings, W.C.Kurumbail, R.G.Marnett, L.J.

(2003) J.Biol.Chem. 278: 45763-45769

  • DOI: 10.1074/jbc.M305481200

  • PubMed Abstract: 
  • A variety of drugs inhibit the conversion of arachidonic acid to prostaglandin G2 by the cyclooxygenase (COX) activity of prostaglandin endoperoxide synthases. Several modes of inhibitor binding in the COX active site have been described including io ...

    A variety of drugs inhibit the conversion of arachidonic acid to prostaglandin G2 by the cyclooxygenase (COX) activity of prostaglandin endoperoxide synthases. Several modes of inhibitor binding in the COX active site have been described including ion pairing of carboxylic acid containing inhibitors with Arg-120 of COX-1 and COX-2 and insertion of arylsulfonamides and sulfones into the COX-2 side pocket. Recent crystallographic evidence suggests that Tyr-385 and Ser-530 chelate polar or negatively charged groups in arachidonic acid and aspirin. We tested the generality of this binding mode by analyzing the action of a series of COX inhibitors against site-directed mutants of COX-2 bearing changes in Arg-120, Tyr-355, Tyr-348, and Ser-530. Interestingly, diclofenac inhibition was unaffected by the mutation of Arg-120 to alanine but was dramatically attenuated by the S530A mutation. Determination of the crystal structure of a complex of diclofenac with murine COX-2 demonstrates that diclofenac binds to COX-2 in an inverted conformation with its carboxylate group hydrogen-bonded to Tyr-385 and Ser-530. This finding represents the first experimental demonstration that the carboxylate group of an acidic non-steroidal anti-inflammatory drug can bind to a COX enzyme in an orientation that precludes the formation of a salt bridge with Arg-120. Mutagenesis experiments suggest Ser-530 is also important in time-dependent inhibition by nimesulide and piroxicam.


    Related Citations: 
    • Structural Basis for Selective Inhibition of cyclooxygenase-2 by Anti-Inflammatory Agents
      Kurumbail, R.G.,Stevens, A.M.,Gierse, J.K.,McDonald, J.J.,Stegeman, R.A.,Pak, J.Y.,Gildehaus, D.,Miyashiro, J.M.,Penning, T.D.,Seibert, K.,Isakson, P.C.,Stallings, W.C.
      (1996) Nature 384: 644
    • Structural insights into the stereochemistry of the cyclooxygenase reaction
      Kiefer, J.R.,Pawlitz, J.L.,Moreland, K.T.,Stegeman, R.A.,Hood, W.F.,Gierse, J.K.,Stevens, A.M.,Goodwin, D.C.,Rowlinson, S.W.,Marnett, L.J.,Stallings, W.C.,Kurumbail, R.G.
      (2000) Nature 45: 97


    Organizational Affiliation

    Department of Biochemistry, Vanderbilt Institute of Chemical Biology, Center in Molecular Toxicology, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, Tennessee 37232-0146, USA.




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
HEM
Query on HEM

Download SDF File 
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

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

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Download CCD File 
A, B, C, D
2-[2,6-DICHLOROPHENYL)AMINO]BENZENEACETIC ACID
DICLOFENAC
C14 H11 Cl2 N O2
DCOPUUMXTXDBNB-UHFFFAOYSA-N
 Ligand Interaction
BOG
Query on BOG

Download SDF File 
Download CCD File 
A, D
B-OCTYLGLUCOSIDE
C14 H28 O6
HEGSGKPQLMEBJL-RKQHYHRCSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
DIFIC50: 5 - 23620 nM (87) BINDINGDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.302 
  • R-Value Work: 0.254 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 181.145α = 90.00
b = 135.090β = 90.00
c = 124.165γ = 90.00
Software Package:
Software NamePurpose
X-PLORphasing
X-PLORrefinement
HKL-2000data reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-09-09
    Type: Initial release
  • Version 1.1: 2007-10-16
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Version format compliance