4RRX

Crystal Structure of Apo Murine V89W Cyclooxygenase-2 Complexed with Lumiracoxib


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.78 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.249 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Action at a Distance: MUTATIONS OF PERIPHERAL RESIDUES TRANSFORM RAPID REVERSIBLE INHIBITORS TO SLOW, TIGHT BINDERS OF CYCLOOXYGENASE-2.

Blobaum, A.L.Xu, S.Rowlinson, S.W.Duggan, K.C.Banerjee, S.Kudalkar, S.N.Birmingham, W.R.Ghebreselasie, K.Marnett, L.J.

(2015) J.Biol.Chem. 290: 12793-12803

  • DOI: 10.1074/jbc.M114.635987
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Cyclooxygenase enzymes (COX-1 and COX-2) catalyze the conversion of arachidonic acid to prostaglandin G2. The inhibitory activity of rapid, reversible COX inhibitors (ibuprofen, naproxen, mefenamic acid, and lumiracoxib) demonstrated a significant in ...

    Cyclooxygenase enzymes (COX-1 and COX-2) catalyze the conversion of arachidonic acid to prostaglandin G2. The inhibitory activity of rapid, reversible COX inhibitors (ibuprofen, naproxen, mefenamic acid, and lumiracoxib) demonstrated a significant increase in potency and time dependence of inhibition against double tryptophan murine COX-2 mutants at the 89/90 and 89/119 positions. In contrast, the slow, time-dependent COX inhibitors (diclofenac, indomethacin, and flurbiprofen) were unaffected by those mutations. Further mutagenesis studies suggested that mutation at position 89 was principally responsible for the changes in inhibitory potency of rapid, reversible inhibitors, whereas mutation at position 90 may exert some effect on the potency of COX-2-selective diarylheterocycle inhibitors; no effect was observed with mutation at position 119. Several crystal structures with or without NSAIDs indicated that placement of a bulky residue at position 89 caused a closure of a gap at the lobby, and alteration of histidine to tryptophan at position 90 changed the electrostatic profile of the side pocket of COX-2. Thus, these two residues, especially Val-89 at the lobby region, are crucial for the entrance and exit of some NSAIDs from the COX active site.


    Organizational Affiliation

    From the A. B. Hancock, Jr. Memorial Laboratory for Cancer Research, Departments of Biochemistry, Chemistry, and Pharmacology, Vanderbilt Institute of Chemical Biology, Center in Molecular Toxicology, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville Tennessee 37232.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Prostaglandin G/H synthase 2
A, B
587Mus musculusMutation(s): 1 
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 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
LUR
Query on LUR

Download SDF File 
Download CCD File 
A, B
{2-[(2-chloro-6-fluorophenyl)amino]-5-methylphenyl}acetic acid
Lumiracoxib
C15 H13 Cl F N O2
KHPKQFYUPIUARC-UHFFFAOYSA-N
 Ligand Interaction
NAG
Query on NAG

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

Download SDF File 
Download CCD File 
A, B
B-OCTYLGLUCOSIDE
C14 H28 O6
HEGSGKPQLMEBJL-RKQHYHRCSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
LURKi: 320 nM (87) BINDINGDB
LURIC50: 7 - >10000 nM (87) BINDINGDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.78 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.249 
  • Space Group: I 2 2 2
Unit Cell:
Length (Å)Angle (°)
a = 180.985α = 90.00
b = 132.433β = 90.00
c = 120.354γ = 90.00
Software Package:
Software NamePurpose
PHASESphasing
PHENIXrefinement
XDSdata reduction
HKL-2000data collection
XDSdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-04-08
    Type: Initial release
  • Version 1.1: 2015-05-06
    Type: Database references
  • Version 1.2: 2015-06-03
    Type: Database references