4COX

CYCLOOXYGENASE-2 (PROSTAGLANDIN SYNTHASE-2) COMPLEXED WITH A NON-SELECTIVE INHIBITOR, INDOMETHACIN


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.309 
  • R-Value Work: 0.219 
  • R-Value Observed: 0.219 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

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: 644-648

  • DOI: 10.1038/384644a0
  • Primary Citation of Related Structures:  
    4COX, 3PGH, 6COX, 5COX, 1CX2

  • PubMed Abstract: 
  • Prostaglandins and glucocorticoids are potent mediators of inflammation. Non-steroidal anti-inflammatory drugs (NSAIDs) exert their effects by inhibition of prostaglandin production. The pharmacological target of NSAIDs is cyclooxygenase (COX, also known as PGH synthase), which catalyses the first committed step in arachidonic-acid metabolism ...

    Prostaglandins and glucocorticoids are potent mediators of inflammation. Non-steroidal anti-inflammatory drugs (NSAIDs) exert their effects by inhibition of prostaglandin production. The pharmacological target of NSAIDs is cyclooxygenase (COX, also known as PGH synthase), which catalyses the first committed step in arachidonic-acid metabolism. Two isoforms of the membrane protein COX are known: COX-1, which is constitutively expressed in most tissues, is responsible for the physiological production of prostaglandins; and COX-2, which is induced by cytokines, mitogens and endotoxins in inflammatory cells, is responsible for the elevated production of prostaglandins during inflammation. The structure of ovine COX-1 complexed with several NSAIDs has been determined. Here we report the structures of unliganded murine COX-2 and complexes with flurbiprofen, indomethacin and SC-558, a selective COX-2 inhibitor, determined at 3.0 to 2.5 A resolution. These structures explain the structural basis for the selective inhibition of COX-2, and demonstrate some of the conformational changes associated with time-dependent inhibition.


    Related Citations: 
    • Erratum. 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.
      (1997) Nature 385: 555

    Organizational Affiliation

    G.D. Searle, St Louis, Missouri 63198, USA. rgkuru@punchiri.monsanto.com



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
CYCLOOXYGENASE-2A, B, C, D587Mus 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
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HEM
Query on HEM

Download Ideal Coordinates CCD File 
H [auth A], M [auth B], R [auth C], W [auth D]PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
IMN
Query on IMN

Download Ideal Coordinates CCD File 
I [auth A], N [auth B], S [auth C], X [auth D]INDOMETHACIN
C19 H16 Cl N O4
CGIGDMFJXJATDK-UHFFFAOYSA-N
 Ligand Interaction
NAG
Query on NAG

Download Ideal Coordinates CCD File 
E [auth A] , F [auth A] , G [auth A] , J [auth B] , K [auth B] , L [auth B] , O [auth C] , P [auth C] , 
E [auth A],  F [auth A],  G [auth A],  J [auth B],  K [auth B],  L [auth B],  O [auth C],  P [auth C],  Q [auth C],  T [auth D],  U [auth D],  V [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 %)
IMNIC50:  40   nM  BindingDB
IMNIC50:  4000   nM  BindingDB
IMNIC50:  36   nM  BindingDB
IMNIC50:  100   nM  BindingDB
IMNIC50:  0.47999998927116394   nM  BindingDB
IMNIC50:  48   nM  BindingDB
IMNIC50:  49   nM  BindingDB
IMNIC50:  9   nM  BindingDB
IMNIC50:  900   nM  BindingDB
IMNIC50:  4000   nM  BindingDB
IMNIC50:  26   nM  BindingDB
IMNIC50:  30   nM  BindingDB
IMNIC50:  537   nM  BindingDB
IMNIC50:  558   nM  BindingDB
IMNIC50:  750   nM  BindingDB
IMNIC50:  2.5999999046325684   nM  BindingDB
IMNIC50:  200   nM  BindingDB
IMNKd:  1020   nM  BindingDB
IMNIC50:  180   nM  BindingDB
IMNIC50:  340   nM  BindingDB
IMNIC50:  300   nM  BindingDB
IMNIC50:  68   nM  BindingDB
IMNIC50:  2.9000000953674316   nM  BindingDB
IMNIC50:  220   nM  BindingDB
IMNIC50:  150   nM  BindingDB
IMNIC50:  630   nM  BindingDB
IMNIC50:  640   nM  BindingDB
IMNIC50:  600   nM  BindingDB
IMNIC50:  560   nM  BindingDB
IMNIC50:  730   nM  BindingDB
IMNIC50:  750   nM  BindingDB
IMNIC50:  700   nM  BindingDB
IMNIC50:  127   nM  BindingDB
IMNIC50:  670   nM  BindingDB
IMNIC50:  1800   nM  BindingDB
IMNIC50:  250   nM  BindingDB
IMNIC50:  430   nM  BindingDB
IMNIC50:  440   nM  BindingDB
IMNIC50:  410   nM  BindingDB
IMNIC50:  220   nM  BindingDB
IMNIC50:  400   nM  BindingDB
IMNIC50:  210   nM  BindingDB
IMNIC50:  490   nM  BindingDB
IMNIC50:  500   nM  BindingDB
IMNIC50:  200   nM  BindingDB
IMNKi:  600   nM  BindingDB
IMNIC50:  10   nM  BindingDB
IMNIC50:  460   nM  BindingDB
IMNIC50:  1200   nM  BindingDB
IMNIC50:  1170   nM  BindingDB
IMNIC50:  1100   nM  BindingDB
IMNKi:  1500   nM  BindingDB
IMNIC50:  300   nM  BindingDB
IMNKi:  9860   nM  BindingDB
IMNIC50:  900   nM  BindingDB
IMNKd:  92   nM  BindingDB
IMNIC50:  6.400000095367432   nM  BindingDB
IMNIC50:  450   nM  BindingDB
IMNKi:  1000   nM  BindingDB
IMNIC50:  1000   nM  BindingDB
IMNIC50:  960   nM  BindingDB
IMNIC50:  10   nM  BindingDB
IMNIC50:  2630   nM  BindingDB
IMNIC50:  2380   nM  BindingDB
IMNIC50:  2400   nM  BindingDB
IMNIC50:  9   nM  BindingDB
IMNIC50:  3930   nM  BindingDB
IMNIC50:  4200   nM  BindingDB
IMNIC50:  500   nM  BindingDB
IMNIC50:  3670   nM  BindingDB
IMNIC50:  1800   nM  BindingDB
IMNKi:  130   nM  BindingDB
IMNIC50:  1900   nM  BindingDB
IMNIC50:  750   nM  BindingDB
IMNKi:  440   nM  BindingDB
IMNIC50:  220   nM  BindingDB
IMNIC50:  200   nM  BindingDB
IMNKi:  370   nM  BindingDB
IMNKi:  400   nM  BindingDB
IMNIC50:  3440   nM  BindingDB
IMNIC50:  5.900000095367432   nM  BindingDB
IMNIC50:  3100   nM  BindingDB
IMNIC50:  3240   nM  BindingDB
IMNIC50:  2400   nM  BindingDB
IMNIC50:  3900   nM  BindingDB
IMNIC50:  10   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.309 
  • R-Value Work: 0.219 
  • R-Value Observed: 0.219 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 179.8α = 90
b = 133.6β = 90
c = 118.4γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
MERLOTphasing
X-PLORrefinement

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1997-12-24
    Type: Initial release
  • Version 1.1: 2008-03-03
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 1.3: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Database references, Derived calculations, Structure summary