STRUCTURAL MODELS

On this page we have made available three-dimensional models of the delta, kappa, and mu opioid receptor transmembrane regions in PDB format. A representation of these structures are shown below, as generated in the PDB file viewer Midas.


2000
Subramanian G, Paterlini MG, Portoghese PS, Ferguson, DM. Molecular Docking Reveals a Novel Binding Site Model for Fentanyl at the mu-opioid receptor. J Med. Chem., 2000,43,381-391.
Stevens, W.C., Jones, Jr. R.M., Subramanian, G., Ferguson, D.M., Portoghese, P.S. Potent and Selective Indolomorphinan Antagonists of the kappa-opiod Receptor.
Podlogar, B.L., Poda, G.I., Demeter, D.A., Zhang, S.P., Neilson, L.A., Reitz, A.B., Ferguson, D.M.Synthesis and Evaluation of 4-(N,N-Diarylamino) piperidines with High Selectivity to the delta-opioid Receptor: A Combined 3D-QSAR and Ligand Docking Study.

DELTA KAPPA MU


The kappa model was introduced in the following publication:

Metzger, T.G., Paterlini, M.G., Portoghese, P.S., Ferguson, D.M. 1996. Application of the Message-Address Concept to the Docking of Naltrexone and Selective Naltrexone-Derived Opioid Antagonists into Opioid Receptor Models. Neurochemical Research. 21(11):1287-1294.

Use any PDB file viewer to view the structures by clicking on the image or the PDB file name below it. Feel free to download the files as well.


deltamodel.pdb
kappamodel.pdb
mumodel.pdb


(1) Pearlman, D.A.; Case, D.A.; Caldwell, J.W.; Ross, W.S.; Cheatham, T.A.; DeBolt, S.; Ferguson, D.M.; Seibel, G.; Kollman, P. AMBER, a package of of computer programs for applying molecular mechanics, a normal mode analysis, molecular dynamics and free energy calculations to simulate the structural and energetic properties of molecules. Comput. Phys. Commun. 1995, 91, 1-41.

(2) Cornell, W.D.; Cieplak, P.; Bayly, C.I.; Gould, I.R.; Merz, K.M.; Ferguson, D.M.; Spellmayer, D.C.; Fox, T.; Caldwell, J.W.; Kollman, P.A. A second generation force field for the simulation of proteins, nucleic acids, and organic molecules. J. Am. Chem. Soc. 1995, 117, 5179-5197.

(3) Metzger, T.G.; Paterlini, M.G.; Portoghese, P.S.; Ferguson, D.M. An anaylsis of the conserved residues between halobacterial retinal proteins and G protein-coupled receptors: Implications for GPCR Modeling. J. Chem. Info. Comput. Sci. 1996, 36, 857-861.

(4) Donnelly, D.; Overington, J.P.; Blundell, T.L. The prediction and orientation of alpha-helices from sequence alignments: the combined use of environment-dependent substitution tables, Fourier transform methods and helix capping rules. Protein. Eng. 1994, 7, 645-653.

(5) Palczewski K, Kumasaka T, Hori T, Behnke CA, Motoshima H, Fox BA, Le Trong I, Teller DC, Okada T, Stenkamp RE, Yamamoto M, Miyano M, Crystal structure of rhodopsin: A G protein-coupled receptor. Science. 2000, 4;289(5480):733-4. The pdb file can be retrieved from the pdb bank under the ID# 1F88.

(6) Metzger, T.G. Ph. D. Thesis, University of Minnesota, 1996.

(7) Liu, J.; Schoneberg, T.; van Rhee, M.; Wess, J. Mutational Analysis of the Relative Orientation of Transmembrane Helices I and VII in G Protein-coupled Receptors. J. Biol. Chem. 1995, 270, 19532-19539.

(8) Rao, V.R.; Cohen, G.B.; Oprian, D.D. Rhodopsin Mutation G90D and a Molecular Mechanism for Congenital Night Blindness. Nature 1994, 367, 639-642.

(9) Zhou, W.; Flanagan, C.; Ballesteros, J.A.; Konvicka, K.; Davidson, J.S.; Weinstein, H.; Millar, R.P.; Sealfon, S.C. A Recipricol Mutation Supports Helix 2 and Helix 7 Proximity in the Gonadotropin-Releasing Hormone Receptor. Mol. Pharmacol. 1994, 45, 165-170. (Download file from Protein Data Bank ID# 1F88

(10) Elling, C.E.; Nielson, S.M.; Schwartz, T.H. Conversion of Antagonist-binding Site to Metal-ion Site in the Tachykinin NK-1 Receptor. Nature 1995, 374, 74-77.

(11) Thirstrup, K.; Elling, C.E.; Hjorth, S.A.; Schwartz, T.W. Construction of a High Affinity Zinc Switch in the Kappa-Opioid Receptor. J. Biol. Chem. 1996, 271, 7875-7878.