1PXX

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.302 
  • R-Value Work: 0.254 

wwPDB Validation   3D Report Full Report


This is version 2.0 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
  • Primary Citation of Related Structures:  
    1PXX

  • 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 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 ...

    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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Prostaglandin G/H synthase 2A, B, C, D604Mus musculusMutation(s): 0 
Gene Names: PTGS2 OR COX2 OR COX-2 OR TIS10 OR PGHS-BPtgs2Cox-2Cox2Pghs-bTis10
EC: 1.14.99.1
UniProt
Find proteins for Q05769 (Mus musculus)
Explore Q05769 
Go to UniProtKB:  Q05769
Protein Feature View
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseE, F, G, H3N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G47362BJ
GlyCosmos:  G47362BJ
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HEM
Query on HEM

Download Ideal Coordinates CCD File 
L [auth A], P [auth B], T [auth C], Y [auth D]PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
DIF
Query on DIF

Download Ideal Coordinates CCD File 
M [auth A], Q [auth B], U [auth C], Z [auth D]2-[2,6-DICHLOROPHENYL)AMINO]BENZENEACETIC ACID
C14 H11 Cl2 N O2
DCOPUUMXTXDBNB-UHFFFAOYSA-N
 Ligand Interaction
BOG
Query on BOG

Download Ideal Coordinates CCD File 
K [auth A], X [auth D]octyl beta-D-glucopyranoside
C14 H28 O6
HEGSGKPQLMEBJL-RKQHYHRCSA-N
 Ligand Interaction
NAG
Query on NAG

Download Ideal Coordinates CCD File 
I [auth A], J [auth A], N [auth B], O [auth B], R [auth C], S [auth C], V [auth D], W [auth D]2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
DIFIC50:  28   nM  BindingDB
DIFIC50:  77   nM  BindingDB
DIFIC50:  26   nM  BindingDB
DIFIC50:  500   nM  BindingDB
DIFIC50:  5   nM  BindingDB
DIFIC50:  20   nM  BindingDB
DIFIC50:  23620   nM  BindingDB
DIFIC50:  4200   nM  BindingDB
DIFIC50:  16900   nM  BindingDB
DIFIC50:  70   nM  BindingDB
DIFIC50:  60   nM  BindingDB
DIFIC50:  15000   nM  BindingDB
DIFIC50:  30   nM  BindingDB
DIFIC50:  50   nM  BindingDB
DIFIC50:  2700   nM  BindingDB
DIFIC50:  10   nM  BindingDB
DIFIC50:  630   nM  BindingDB
DIFIC50:  2940   nM  BindingDB
DIFIC50:  100   nM  BindingDB
DIFIC50:  22   nM  BindingDB
Biologically Interesting Molecules (External Reference) 1 Unique
Entity ID: 2
IDChainsNameType/Class2D Diagram3D Interactions
PRD_900017
Query on PRD_900017
E, F, G, Htriacetyl-beta-chitotrioseOligosaccharide /  Inhibitor Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 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
b = 135.09β = 90
c = 124.165γ = 90
Software Package:
Software NamePurpose
X-PLORrefinement
HKL-2000data reduction
SCALEPACKdata scaling
X-PLORphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2003-09-09
    Type: Initial release
  • Version 1.1: 2007-10-16
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary