This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.

Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.

5ntw

From Proteopedia

(Difference between revisions)

Jump to: navigation, search

Revision as of 12:12, 26 August 2020

Structural states of RORgt: X-ray elucidation of molecular mechanisms and binding interactions for natural and synthetic compounds

Structural highlights

5ntw is a 8 chain structure with sequence from [1] and Homo sapiens. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[RORG_HUMAN] Possible nuclear receptor for hydroxycholesterols, the binding of which strongly promotes coactivators recruitment. Essential for thymopoiesis and the development of several secondary lymphoid tissues, including lymph nodes. Involved in lineage specification of uncommitted CD4(+) T-helper cells into Th17 cells. Regulate the expression of several components of the circadian clock. [NRIP1_HUMAN] Modulates transcriptional activation by steroid receptors such as NR3C1, NR3C2 and ESR1. Also modulates transcriptional repression by nuclear hormone receptors.^[1] ^[2] ^[3] ^[4] ^[5] ^[6]

Publication Abstract from PubMed

The T-cell-specific retinoic acid receptor (RAR)-related orphan receptor-gamma (RORgammat) is a key transcription factor for the production of pro-inflammatory Th17 cytokines, which are implicated in the pathogenesis of autoimmune diseases. Over the years, several structurally diverse RORgammat inverse agonists have been reported, but combining high potency and good physicochemical properties has remained a challenging task. We recently reported a new series of inverse agonists based on an imidazopyridine core with good physicochemical properties and excellent selectivity. Herein we report eight new X-ray crystal structures for different classes of natural and synthetic compounds, including examples selected from the patent literature. Analysis of their respective binding modes revealed insight into the molecular mechanisms that lead to agonism, antagonism, or inverse agonism. We report new molecular mechanisms for RORgammat agonism and propose a separation of the inverse agonists into two classes: those that act via steric clash and those that act via other mechanisms (for the latter, co-crystallization with a co-activator peptide and helix 12 in the agonist position is still possible). For the non-steric clash inverse agonists, we propose a new mechanism ("water trapping") which can be combined with other mechanisms (e.g., close contacts with H479). In addition, we compare the interactions made for selected compounds in the "back pocket" near S404 and in the "sulfate pocket" near R364 and R367. Taken together, these new mechanistic insights should prove useful for the design and optimization of further RORgammat modulators.

Structural States of RORgammat: X-ray Elucidation of Molecular Mechanisms and Binding Interactions for Natural and Synthetic Compounds.,Kallen J, Izaac A, Be C, Arista L, Orain D, Kaupmann K, Guntermann C, Hoegenauer K, Hintermann S ChemMedChem. 2017 Jul 6;12(13):1014-1021. doi: 10.1002/cmdc.201700278. Epub 2017 , Jun 20. PMID:28590087^[7]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Cavailles V, Dauvois S, L'Horset F, Lopez G, Hoare S, Kushner PJ, Parker MG. Nuclear factor RIP140 modulates transcriptional activation by the estrogen receptor. EMBO J. 1995 Aug 1;14(15):3741-51. PMID:7641693
↑ Subramaniam N, Treuter E, Okret S. Receptor interacting protein RIP140 inhibits both positive and negative gene regulation by glucocorticoids. J Biol Chem. 1999 Jun 18;274(25):18121-7. PMID:10364267
↑ Vo N, Fjeld C, Goodman RH. Acetylation of nuclear hormone receptor-interacting protein RIP140 regulates binding of the transcriptional corepressor CtBP. Mol Cell Biol. 2001 Sep;21(18):6181-8. PMID:11509661
↑ Zennaro MC, Souque A, Viengchareun S, Poisson E, Lombes M. A new human MR splice variant is a ligand-independent transactivator modulating corticosteroid action. Mol Endocrinol. 2001 Sep;15(9):1586-98. PMID:11518808
↑ Teyssier C, Belguise K, Galtier F, Cavailles V, Chalbos D. Receptor-interacting protein 140 binds c-Jun and inhibits estradiol-induced activator protein-1 activity by reversing glucocorticoid receptor-interacting protein 1 effect. Mol Endocrinol. 2003 Feb;17(2):287-99. PMID:12554755 doi:http://dx.doi.org/10.1210/me.2002-0324
↑ Castet A, Boulahtouf A, Versini G, Bonnet S, Augereau P, Vignon F, Khochbin S, Jalaguier S, Cavailles V. Multiple domains of the Receptor-Interacting Protein 140 contribute to transcription inhibition. Nucleic Acids Res. 2004 Apr 1;32(6):1957-66. Print 2004. PMID:15060175 doi:http://dx.doi.org/10.1093/nar/gkh524
↑ Kallen J, Izaac A, Be C, Arista L, Orain D, Kaupmann K, Guntermann C, Hoegenauer K, Hintermann S. Structural States of RORgammat: X-ray Elucidation of Molecular Mechanisms and Binding Interactions for Natural and Synthetic Compounds. ChemMedChem. 2017 Jul 6;12(13):1014-1021. doi: 10.1002/cmdc.201700278. Epub 2017 , Jun 20. PMID:28590087 doi:http://dx.doi.org/10.1002/cmdc.201700278

1 Structural highlights
2 Function
3 Publication Abstract from PubMed
4 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/5ntw"

@@ Line 1: / Line 1: @@
 ==Structural states of RORgt: X-ray elucidation of molecular mechanisms and binding interactions for natural and synthetic compounds==
-<StructureSection load='5ntw' size='340' side='right' caption='[[5ntw]], [[Resolution|resolution]] 1.64&Aring;' scene=''>
+<StructureSection load='5ntw' size='340' side='right'caption='[[5ntw]], [[Resolution|resolution]] 1.64&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[5ntw]] is a 8 chain structure with sequence from [http://en.wikipedia.org/wiki/ ] and [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5NTW OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5NTW FirstGlance]. <br>
+<table><tr><td colspan='2'>[[5ntw]] is a 8 chain structure with sequence from [http://en.wikipedia.org/wiki/ ] and [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5NTW OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5NTW FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=98N:(S)-N-((5-(ethylsulfonyl)pyridin-2-yl)methyl)-7-isopropyl-6-(((1r,4S)-4-(trifluoromethyl)cyclohexyl)methyl)-6,7-dihydro-5H-pyrrolo[3,4-b]pyridine-3-carboxamide'>98N</scene></td></tr>
+</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=98N:(S)-N-((5-(ethylsulfonyl)pyridin-2-yl)methyl)-7-isopropyl-6-(((1r,4S)-4-(trifluoromethyl)cyclohexyl)methyl)-6,7-dihydro-5H-pyrrolo[3,4-b]pyridine-3-carboxamide'>98N</scene></td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5ntw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ntw OCA], [http://pdbe.org/5ntw PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ntw RCSB], [http://www.ebi.ac.uk/pdbsum/5ntw PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ntw ProSAT]</span></td></tr>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=5ntw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ntw OCA], [http://pdbe.org/5ntw PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ntw RCSB], [http://www.ebi.ac.uk/pdbsum/5ntw PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ntw ProSAT]</span></td></tr>
 </table>
 == Function ==
@@ Line 23: / Line 23: @@
 </StructureSection>
 [[Category: Homo sapiens]]
+[[Category: Large Structures]]
 [[Category: Kallen, J]]
 [[Category: Inverse agonist]]

5ntw

From Proteopedia

Revision as of 12:12, 26 August 2020

Structural states of RORgt: X-ray elucidation of molecular mechanisms and binding interactions for natural and synthetic compounds

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

Personal tools

Navigation

Search

Toolbox