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PDBsum entry 2oyu

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Oxidoreductase PDB id
2oyu
Jmol
Contents
Protein chain
553 a.a.
Ligands
NAG-NAG ×2
NAG-NAG-BMA
BOG ×2
IMS
HEM
Waters ×52

References listed in PDB file
Key reference
Title Structural basis of enantioselective inhibition of cyclooxygenase-1 by s-Alpha-Substituted indomethacin ethanolamides.
Authors C.A.Harman, M.V.Turman, K.R.Kozak, L.J.Marnett, W.L.Smith, R.M.Garavito.
Ref. J Biol Chem, 2007, 282, 28096-28105. [DOI no: 10.1074/jbc.M701335200]
PubMed id 17656360
Abstract
The modification of the nonselective nonsteroidal anti-inflammatory drug, indomethacin, by amidation presents a promising strategy for designing novel cyclooxygenase (COX)-2-selective inhibitors. A series of alpha-substituted indomethacin ethanolamides, which exist as R/S-enantiomeric pairs, provides a means to study the impact of stereochemistry on COX inhibition. Comparative studies revealed that the R- and S-enantiomers of the alpha-substituted analogs inhibit COX-2 with almost equal efficacy, whereas COX-1 is selectively inhibited by the S-enantiomers. Mutagenesis studies have not been able to identify residues that manifest the enantioselectivity in COX-1. In an effort to understand the structural impact of chirality on COX-1 selectivity, the crystal structures of ovine COX-1 in complexes with an enantiomeric pair of these indomethacin ethanolamides were determined at resolutions between 2.75 and 2.85 A. These structures reveal unique, enantiomer-selective interactions within the COX-1 side pocket region that stabilize drug binding and account for the chiral selectivity observed with the (S)-alpha-substituted indomethacin ethanolamides. Kinetic analysis of binding demonstrates that both inhibitors bind quickly utilizing a two-step mechanism. However, the second binding step is readily reversible for the R-enantiomer, whereas for the S-enantiomer, it is not. These studies establish for the first time the structural and kinetic basis of high affinity binding of a neutral inhibitor to COX-1 and demonstrate that the side pocket of COX-1, previously thought to be sterically inaccessible, can serve as a binding pocket for inhibitor association.
Figure 1.
FIGURE 1. Compound 8 bound in the COX active site of COX-1. A, stereo view of 8 bound in COX active site with simulated annealing omit map difference density (blue) contoured at 3 witha3Å boundary around the ligand. Various residues within the active site are shown with carbons for 8 shown in orange, oxygen red, nitrogen blue, and chlorine purple. B, stereo representation of 8 bound in the COX site in the same manner as the parent compound indomethacin; the chlorobenzoyl group is oriented up toward the top of the channel, the methoxy group on indole ring points toward the side pocket (Leu-517, Phe-518, Ile-523, Gln-192, and Ser-516), and the ethanolamide group with the R-ethyl substitution sits next to Arg-120 and Tyr-355 at the mouth of the active site. Carbon atoms of 8 are shown with same color scheme as in A with the yellow dashed lines representing various interactions (hydrophilic) between ligand and protein residues. The hydroxyl group of the ethanolamide group makes a hydrogen bond with Arg-120 and Glu-524, whereas the (R)-ethyl group is positioned just outside the mouth of the active site. Refinement statistics for both structures are shown in Table 2. All figures presented here were created using the program PyMOL.
Figure 2.
FIGURE 2. Compound 9 bound in the COX active site of COX-1. A, stereo view of 9 fitted into simulated annealing omit map difference density (blue) contoured at 3 witha3Å boundary around the ligand. Carbon atoms of 9 are colored green with heteroatoms colored the same as in 1. B, chlorobenzoyl group of 9 is oriented toward the mouth of the active site; the methoxy group of indole ring is oriented up into the top of the channel, and the ethanolamide group with the (S)-ethyl substitution lies within the side pocket region of the channel. Yellow dashed lines represent various interactions (hydrophobic and hydrophilic) between ligand and protein. The hydroxyl group of the ethanolamide is oriented near the hydrophilic region (cyan) of the side pocket making hydrogen bonds with residues Gln-192 and His-90 whereas the S-ethyl group is oriented into the more hydrophobic region (pink) of the side pocket making van der Waals interactions with Ile-523, Phe-518, and Ile-517. For clarity, an additional polar interaction between Arg-120 and the carbonyl of the chlorobenzoyl moiety is not shown.
The above figures are reprinted by permission from the ASBMB: J Biol Chem (2007, 282, 28096-28105) copyright 2007.
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