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PDBsum entry 1pxx
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Oxidoreductase
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PDB id
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1pxx
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Contents |
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* Residue conservation analysis
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References listed in PDB file
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Key reference
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Title
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A novel mechanism of cyclooxygenase-2 inhibition involving interactions with ser-530 and tyr-385.
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Authors
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S.W.Rowlinson,
J.R.Kiefer,
J.J.Prusakiewicz,
J.L.Pawlitz,
K.R.Kozak,
A.S.Kalgutkar,
W.C.Stallings,
R.G.Kurumbail,
L.J.Marnett.
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Ref.
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J Biol Chem, 2003,
278,
45763-45769.
[DOI no: ]
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PubMed id
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Abstract
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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.
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Figure 1.
FIG. 1. COX substrate binding modes. Stereo diagram of the
inhibitory binding mode of arachidonic acid to COX-2 (blue)
aligned with the productive binding mode, observed in COX-1
(beige). The substrate is nominally rotated 180° between the
two orientations, resulting in different coordination of the
carboxylic acid group. Amino acids shown are within van der
Waals contact of diclofenac except for Arg-120, Val-434, and
Arg-513, added for reference. Red text indicates the position of
the three amino acid differences between COX-1 and COX-2 within
the active site. The superposition was performed using amino
acids 113-122, 344-355, 385-391, and 522-532 and coordinate
Protein Data Bank files 1CVU [PDB]
and 1DIY [PDB]
. All molecular graphics were generated with Ribbons and
rendered with POV-Ray (36).
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Figure 6.
FIG. 6. Comparison of inhibitor binding to COX-2. a,
superposition of the structures of diclofenac (green) and
indomethacin (gold carbons; Protein Data Bank number 4COX [PDB]
) shows their differential coordination to the protein, despite
their comparable size and chemical composition. b, overlay of
the structures of diclofenac and the inhibitory mode of
arachidonic acid binding. Both ligands coordinate their acidic
groups with the side chains of Tyr-385 and Ser-530 despite their
dissimilar chemical structures.
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The above figures are
reprinted
by permission from the ASBMB:
J Biol Chem
(2003,
278,
45763-45769)
copyright 2003.
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Secondary reference #1
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Title
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Structural basis for selective inhibition of cyclooxygenase-2 by anti-Inflammatory agents.
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Authors
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R.G.Kurumbail,
A.M.Stevens,
J.K.Gierse,
J.J.Mcdonald,
R.A.Stegeman,
J.Y.Pak,
D.Gildehaus,
J.M.Miyashiro,
T.D.Penning,
K.Seibert,
P.C.Isakson,
W.C.Stallings.
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Ref.
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Nature, 1996,
384,
644-648.
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PubMed id
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Secondary reference #2
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Title
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Structural insights into the stereochemistry of the cyclooxygenase reaction.
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Authors
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J.R.Kiefer,
J.L.Pawlitz,
K.T.Moreland,
R.A.Stegeman,
W.F.Hood,
J.K.Gierse,
A.M.Stevens,
D.C.Goodwin,
S.W.Rowlinson,
L.J.Marnett,
W.C.Stallings,
R.G.Kurumbail.
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Ref.
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Nature, 2000,
405,
97.
[DOI no: ]
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PubMed id
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Figure 2.
Figure 2: COX-2 dimer interface solvent channel. The two
monomers (coloured green and blue) of the COX-2 dimer are shown
from the membrane face (a) or side (b). Cyclooxygenase and
peroxidase active sites are marked by AA (red) and haem
molecules (orange, superimposed onto the H207A-AA structure),
respectively. Solvent molecules are shown as yellow spheres.
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Figure 4.
Figure 4: Stereo diagram of the models of AA (a) and PGH[2] ( b)
bound at the cyclooxygenase active site. Dashed lines
indicate hydrogen bonds or ion pairs formed. The double bonds of
the AA and PGH[2] are coloured blue. Protein side chains shown
are within van der Waals contact of the ligand. The C13
pro(S)-hydrogen (purple) and pro(R)-hydrogen (gold) of AA are
shown for reference.
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The above figures are
reproduced from the cited reference
with permission from Macmillan Publishers Ltd
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