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PDBsum entry 3kk6

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protein ligands Protein-protein interface(s) links
Oxidoreductase PDB id
3kk6
Jmol
Contents
Protein chains
553 a.a. *
Ligands
HEM ×2
NAG-NAG-MAN-BMA-
MAN
NAG-NDG ×3
CEL ×2
BOG ×4
FLC
NAG-NAG-MAN-BMA
Waters ×105
* Residue conservation analysis
PDB id:
3kk6
Name: Oxidoreductase
Title: Crystal structure of cyclooxygenase-1 in complex with celeco
Structure: Prostaglandin g/h synthase 1. Chain: a, b. Synonym: cyclooxygenase-1, cox-1, prostaglandin-endoperoxid 1, prostaglandin h2 synthase 1, pgh synthase 1, pghs-1, phs engineered: yes
Source: Ovis aries. Domestic sheep,lambs,wild sheep. Organism_taxid: 9940. Gene: cox1, ptgs1. Expressed in: spodoptera frugiperda. Expression_system_taxid: 7108.
Resolution:
2.75Å     R-factor:   0.208     R-free:   0.242
Authors: R.S.Sidhu
Key ref:
G.Rimon et al. (2010). Coxibs interfere with the action of aspirin by binding tightly to one monomer of cyclooxygenase-1. Proc Natl Acad Sci U S A, 107, 28-33. PubMed id: 19955429 DOI: 10.1073/pnas.0909765106
Date:
04-Nov-09     Release date:   15-Dec-09    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P05979  (PGH1_SHEEP) -  Prostaglandin G/H synthase 1
Seq:
Struc:
 
Seq:
Struc:
600 a.a.
553 a.a.*
Key:    PfamA domain  PfamB domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Enzyme reactions 
   Enzyme class: E.C.1.14.99.1  - Prostaglandin-endoperoxide synthase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Arachidonate + AH2 + 2 O2 = prostaglandin H2 + A + H2O
Arachidonate
Bound ligand (Het Group name = HEM)
matches with 51.16% similarity
+ AH(2)
+ 2 × O(2)
= prostaglandin H(2)
+
+ H(2)O
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     membrane   8 terms 
  Biological process     oxidation-reduction process   8 terms 
  Biochemical function     oxidoreductase activity     6 terms  

 

 
    reference    
 
 
DOI no: 10.1073/pnas.0909765106 Proc Natl Acad Sci U S A 107:28-33 (2010)
PubMed id: 19955429  
 
 
Coxibs interfere with the action of aspirin by binding tightly to one monomer of cyclooxygenase-1.
G.Rimon, R.S.Sidhu, D.A.Lauver, J.Y.Lee, N.P.Sharma, C.Yuan, R.A.Frieler, R.C.Trievel, B.R.Lucchesi, W.L.Smith.
 
  ABSTRACT  
 
Pain associated with inflammation involves prostaglandins synthesized from arachidonic acid (AA) through cyclooxygenase-2 (COX-2) pathways while thromboxane A(2) formed by platelets from AA via cyclooxygenase-1 (COX-1) mediates thrombosis. COX-1 and COX-2 are both targets of nonselective nonsteroidal antiinflammatory drugs (nsNSAIDs) including aspirin whereas COX-2 activity is preferentially blocked by COX-2 inhibitors called coxibs. COXs are homodimers composed of identical subunits, but we have shown that only one subunit is active at a time during catalysis; moreover, many nsNSAIDS bind to a single subunit of a COX dimer to inhibit the COX activity of the entire dimer. Here, we report the surprising observation that celecoxib and other coxibs bind tightly to a subunit of COX-1. Although celecoxib binding to one monomer of COX-1 does not affect the normal catalytic processing of AA by the second, partner subunit, celecoxib does interfere with the inhibition of COX-1 by aspirin in vitro. X-ray crystallographic results obtained with a celecoxib/COX-1 complex show how celecoxib can bind to one of the two available COX sites of the COX-1 dimer. Finally, we find that administration of celecoxib to dogs interferes with the ability of a low dose of aspirin to inhibit AA-induced ex vivo platelet aggregation. COX-2 inhibitors such as celecoxib are widely used for pain relief. Because coxibs exhibit cardiovascular side effects, they are often prescribed in combination with low-dose aspirin to prevent thrombosis. Our studies predict that the cardioprotective effect of low-dose aspirin on COX-1 may be blunted when taken with coxibs.
 
  Selected figure(s)  
 
Figure 5.
Celecoxib binding to ovCOX-1 as determined by x-ray crystallography. (A) A stereoview of celecoxib (yellow) in the active site of COX-1 in the celecoxib/ovCOX-1 structure shown with omit F[o]-F[c] difference density contoured at 2.8σ (gray). Residues in the active site are displayed in green, whereas celecoxib is in yellow. Residues Arg120, Tyr355, and Glu524 lie at the mouth of the COX active site, whereas the catalytic Tyr385 hydrogen bonded to Tyr348 are located at the apex of the hydrophobic channel. (B) Stereoview of celecoxib/ovCOX-1 structure with the opening from the membrane binding domain into the COX active site oriented along plane of the page. Comparison of celecoxib/ovCOX-1 complex (green) and the reference model (1Q4G) (superimposed yellow ribbon and yellow side chains) shows that Ile523, homologous to Val523 in COX-2, adopts an extended rotamer conformation allowing access to the otherwise inaccessible hydrophobic side pocket comprised of residues Leu352, Ser353, Ile517, and Phe518 (some side chains are omitted for clarity). The residues His513 and Gln192 contribute to the outer shell of the side pocket and are included in the figure. Rendering of celecoxib atoms as spheres highlight the steric clash of Ile523 (yellow sticks in bottom panel) with the reference model. In Fig. S6 the positions of the α-carbons of residues 510–520 in the celecoxib/ovCOX-1 and the AA/ovCOX-1 (1DIY) structures relative to the reference model (1Q4G) are compared. (C) Stereoview of two alternate conformations of residues 121–129 in monomer B at the dimer interface traced into the electron density. Monomer A (orange) is shown with celecoxib bound (yellow) and monomer B is shown in the two conformations representing the conformation in the absence of bound inhibitor (blue) and the shift induced by binding of celecoxib (magenta). The side chains of Ser126 and Pro127 are shown in the two conformations and represented as inhibitor bound (+) and unbound (-) next to Glu543 (E543) of the partner monomer also in an alternate conformation. The position of celecoxib in monomer A (yellow sticks) and active site residues Arg120, Glu524, Tyr355, Ser530, and Tyr385 are shown for spatial orientation. Celecoxib in monomer B, which was refined to 50% occupancy in the final model, has been removed to represent the unbound monomer. (D) Enlarged view of the boxed area at the dimer interface shown in C.
Figure 6.
Treatment of dogs with celecoxib interferes with the effect of low-dose aspirin on ex vivo platelet aggregation. Purpose-bred beagle dogs (n = 6, 10–12 kg) were administered low-dose aspirin alone (1.16 mg/kg, p.o.; LD ASA), celecoxib alone (1.43 mg/kg, po bid; CBX), or both celecoxib plus low-dose aspirin (CBX + LD ASA) for a period of three days. At the conclusion of each treatment regimen, platelet-rich plasma was prepared by centrifugation from venous whole blood collected in 3.7% sodium citrate. Ex vivo platelet aggregation responses to three platelet agonists [AA (650 μM), adenosine diphosphate (20 μM), and γ-thrombin (70 nM)] were recorded. Data are expressed as the mean ± SEM. *** indicates p < 0.001 when each time point is compared to the same agonist at day 0 by two-way ANOVA.
 
  Figures were selected by the author.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20673774 R.E.Hubbard (2011).
Structure-based drug discovery and protein targets in the CNS.
  Neuropharmacology, 60, 7.  
21522619 J.P.Jasinski, R.J.Butcher, M.S.Siddegowda, H.S.Yathirajan, and A.R.Ramesha (2010).
Etoricoxibium picrate.
  Acta Crystallogr Sect E Struct Rep Online, 67, o107-o108.  
20820196 K.Brune, B.Renner, and B.Hinz (2010).
Using pharmacokinetic principles to optimize pain therapy.
  Nat Rev Rheumatol, 6, 589-598.  
20089861 S.L.Bulfer, E.M.Scott, L.Pillus, and R.C.Trievel (2010).
Structural basis for L-lysine feedback inhibition of homocitrate synthase.
  J Biol Chem, 285, 10446-10453.
PDB codes: 3l90 3mi3
20215464 V.Limongelli, M.Bonomi, L.Marinelli, F.L.Gervasio, A.Cavalli, E.Novellino, and M.Parrinello (2010).
Molecular basis of cyclooxygenase enzymes (COXs) selective inhibition.
  Proc Natl Acad Sci U S A, 107, 5411-5416.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.