Sandbox Reserved 1440

From Proteopedia

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Revision as of 18:49, 29 January 2018

This Sandbox is Reserved from 5 Jan through 7 Feb, 2018 for use in the course Medicinal Chemistry taught by Bob Hanson at the St. Olaf College, Northfield, MN. This reservation includes Sandbox Reserved 1431 through Sandbox Reserved 1445.

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Validation of the Binding Action at the DPP-4 Protein

This page describes validity of the proposed binding structure at the catalytic triad of the DPP-4 protein. There are a variety of ligands that were tested using electron density clashes and real space R-values to flag potential clashes in the current model.

This is a default text for your page '. Click above on edit this page' to modify. Be careful with the < and > signs. You may include any references to papers as in: the use of JSmol in Proteopedia ^[1] or to the article describing Jmol ^[2] to the rescue.

1 What is a Validation Report?
2 3Q8W
3 1NU6
4 1PFQ
5 5T4B
6 6B1E
7 4N8D
8 4A5S
9 Structural highlights
10 Crystal structure of the µ-opioid receptor bound to a morphinan antagonist

What is a Validation Report?

3Q8W

1NU6

1NU6 protein along with the ligand and catalytic triad displayed. The data was captured with a 2.10 Å resolution. The ligand NDG is not found in the binding site, rather it is bound to the outside of the binding pocket. This indicates that the ligand may be binding to an allosteric site and modulating the activity at the binding site. The ligands present in this model are two sugars (NAD and NDG), a Mercury (II) ion, and water. Of these, the mercury ion is closest to the triad, but is not close enough to represent a binding interaction. NDG however is found near the opening of the binding pocket, and thus may be an allosteric site for the protein.

The catalytic triad of the protein is shown here. Important to note that there are no clashes surrounding the site, and thus the model may provide an accurate representation of the binding capabilities of this binding pocket.

1PFQ

5T4B

6B1E

4N8D

4A5S

Structural highlights

This is a sample scene created with SAT to by Group, and another to make of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.

Crystal structure of the µ-opioid receptor bound to a morphinan antagonist

Please note this way for referencing a paper using the PubmedID ^[3]. The full reference appears at the bottom of the page.

[https://www.nature.com/articles/nature10954 Nature volume 485, pages 321–326 (17 May 2012)

doi:10.1038/nature10954]

code for the above (space inserted just after the : <jmol><jmollink><text>View Figure 1a: Overall view of the µ-OR structure</text><script>exit;figure=1;SCRIPT "/wiki/images/8/8b/4dkl-local-contact.png"</script></jmollink></jmol>

↑ Hanson, R. M., Prilusky, J., Renjian, Z., Nakane, T. and Sussman, J. L. (2013), JSmol and the Next-Generation Web-Based Representation of 3D Molecular Structure as Applied to Proteopedia. Isr. J. Chem., 53:207-216. doi:http://dx.doi.org/10.1002/ijch.201300024
↑ Herraez A. Biomolecules in the computer: Jmol to the rescue. Biochem Mol Biol Educ. 2006 Jul;34(4):255-61. doi: 10.1002/bmb.2006.494034042644. PMID:21638687 doi:10.1002/bmb.2006.494034042644
↑ Manglik A, Kruse AC, Kobilka TS, Thian FS, Mathiesen JM, Sunahara RK, Pardo L, Weis WI, Kobilka BK, Granier S. Crystal structure of the micro-opioid receptor bound to a morphinan antagonist. Nature. 2012 Mar 21. doi: 10.1038/nature10954. PMID:22437502 doi:10.1038/nature10954

Authors

Lana Jevtic, Kaeli Jacobson, Tayler Aarness, Eric Ruterbories.

St. Olaf College.

Medicinal Chemistry, Interim 2018.

Professor Robert Hanson.

</StructureSection>

References

Retrieved from "http://52.214.119.220/wiki/index.php/Sandbox_Reserved_1440"

@@ Line 29: / Line 29: @@
 This is a sample scene created with SAT to <scene name="/12/3456/Sample/1">color</scene> by Group, and another to make <scene name="/12/3456/Sample/2">a transparent representation</scene> of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.
+==Crystal structure of the µ-opioid receptor bound to a morphinan antagonist==
+Please note this way for '''referencing a paper''' using the PubmedID <ref>pmid 22437502</ref>. The full reference appears at the bottom of the page.
+[https://www.nature.com/articles/nature10954 Nature volume 485, pages 321–326 (17 May 2012)
+doi:10.1038/nature10954]
+<StructureSection load='' size='340' side='right' caption='Click a green link on the left to load Figure 1' scene=''>
+<jmol><jmollink><text>View Figure 1a: Overall view of the µ-OR structure</text><script>exit;figure=1;SCRIPT "http://proteopedia.org/wiki/images/6/6b/1nu6_pocket.png"</script></jmollink></jmol>
+Shown in Figure 1a is a close-up view of a morphinan antagonist ([https://chemapps.stolaf.edu/jmol/jmol.php?pdbid=BF0&script=set%20echo%20top%20left;echo%20PDBid%20BF0;spin%20on PDBid BF0]) bound to the µ-opioid receptor. The green circles indicate hydrogen bonds.
+<jmol><jmollink><text>Animate Figure 1a</text><script>script "http://proteopedia.org/wiki/images/1/1f/Nature10954_fig1a.spt"</script></jmollink></jmol>
+</StructureSection>
+code for the above (space inserted just after the : <code>&lt;jmol><jmollink><text>View Figure 1a: Overall view of the µ-OR structure</text><script>exit;figure=1;SCRIPT "/wiki/images/8/8b/4dkl-local-contact.png"</script></jmollink></jmol></code>
+<references/>
 == Authors ==