5q1c

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==Ligand binding to FARNESOID-X-RECEPTOR==
==Ligand binding to FARNESOID-X-RECEPTOR==
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<StructureSection load='5q1c' size='340' side='right' caption='[[5q1c]], [[Resolution|resolution]] 2.30&Aring;' scene=''>
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<StructureSection load='5q1c' size='340' side='right'caption='[[5q1c]], [[Resolution|resolution]] 2.30&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
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<table><tr><td colspan='2'>[[5q1c]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5Q1C OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5Q1C FirstGlance]. <br>
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<table><tr><td colspan='2'>[[5q1c]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5Q1C OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5Q1C FirstGlance]. <br>
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</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=9NA:(2S)-2-cyclohexyl-2-[2-(2,6-dimethoxypyridin-3-yl)-5,6-difluoro-1H-benzimidazol-1-yl]-N-(trans-4-hydroxycyclohexyl)acetamide'>9NA</scene></td></tr>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.3&#8491;</td></tr>
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<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=5q1c FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5q1c OCA], [http://pdbe.org/5q1c PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5q1c RCSB], [http://www.ebi.ac.uk/pdbsum/5q1c PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5q1c ProSAT]</span></td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=9NA:(2S)-2-cyclohexyl-2-[2-(2,6-dimethoxypyridin-3-yl)-5,6-difluoro-1H-benzimidazol-1-yl]-N-(trans-4-hydroxycyclohexyl)acetamide'>9NA</scene></td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=5q1c FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5q1c OCA], [https://pdbe.org/5q1c PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5q1c RCSB], [https://www.ebi.ac.uk/pdbsum/5q1c PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5q1c ProSAT]</span></td></tr>
</table>
</table>
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== Disease ==
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[https://www.uniprot.org/uniprot/NCOA1_HUMAN NCOA1_HUMAN] Note=A chromosomal aberration involving NCOA1 is a cause of rhabdomyosarcoma. Translocation t(2;2)(q35;p23) with PAX3 generates the NCOA1-PAX3 oncogene consisting of the N-terminus part of PAX3 and the C-terminus part of NCOA1. The fusion protein acts as a transcriptional activator. Rhabdomyosarcoma is the most common soft tissue carcinoma in childhood, representing 5-8% of all malignancies in children.
== Function ==
== Function ==
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[[http://www.uniprot.org/uniprot/NR1H4_HUMAN NR1H4_HUMAN]] Ligand-activated transcription factor. Receptor for bile acids such as chenodeoxycholic acid, lithocholic acid and deoxycholic acid. Represses the transcription of the cholesterol 7-alpha-hydroxylase gene (CYP7A1) through the induction of NR0B2 or FGF19 expression, via two distinct mechanisms. Activates the intestinal bile acid-binding protein (IBABP). Activates the transcription of bile salt export pump ABCB11 by directly recruiting histone methyltransferase CARM1 to this locus.<ref>PMID:10334992</ref> <ref>PMID:10334993</ref> <ref>PMID:12815072</ref> <ref>PMID:15471871</ref> <ref>PMID:12718892</ref> <ref>PMID:18621523</ref> <ref>PMID:19410460</ref> <ref>PMID:19586769</ref>
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[https://www.uniprot.org/uniprot/NCOA1_HUMAN NCOA1_HUMAN] Nuclear receptor coactivator that directly binds nuclear receptors and stimulates the transcriptional activities in a hormone-dependent fashion. Involved in the coactivation of different nuclear receptors, such as for steroids (PGR, GR and ER), retinoids (RXRs), thyroid hormone (TRs) and prostanoids (PPARs). Also involved in coactivation mediated by STAT3, STAT5A, STAT5B and STAT6 transcription factors. Displays histone acetyltransferase activity toward H3 and H4; the relevance of such activity remains however unclear. Plays a central role in creating multisubunit coactivator complexes that act via remodeling of chromatin, and possibly acts by participating in both chromatin remodeling and recruitment of general transcription factors. Required with NCOA2 to control energy balance between white and brown adipose tissues. Required for mediating steroid hormone response. Isoform 2 has a higher thyroid hormone-dependent transactivation activity than isoform 1 and isoform 3.<ref>PMID:9427757</ref> <ref>PMID:7481822</ref> <ref>PMID:9223431</ref> <ref>PMID:9296499</ref> <ref>PMID:9223281</ref> <ref>PMID:10449719</ref> <ref>PMID:12954634</ref>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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The Drug Design Data Resource (D3R) ran Grand Challenge 2 (GC2) from September 2016 through February 2017. This challenge was based on a dataset of structures and affinities for the nuclear receptor farnesoid X receptor (FXR), contributed by F. Hoffmann-La Roche. The dataset contained 102 IC50 values, spanning six orders of magnitude, and 36 high-resolution co-crystal structures with representatives of four major ligand classes. Strong global participation was evident, with 49 participants submitting 262 prediction submission packages in total. Procedurally, GC2 mimicked Grand Challenge 2015 (GC2015), with a Stage 1 subchallenge testing ligand pose prediction methods and ranking and scoring methods, and a Stage 2 subchallenge testing only ligand ranking and scoring methods after the release of all blinded co-crystal structures. Two smaller curated sets of 18 and 15 ligands were developed to test alchemical free energy methods. This overview summarizes all aspects of GC2, including the dataset details, challenge procedures, and participant results. We also consider implications for progress in the field, while highlighting methodological areas that merit continued development. Similar to GC2015, the outcome of GC2 underscores the pressing need for methods development in pose prediction, particularly for ligand scaffolds not currently represented in the Protein Data Bank ( http://www.pdb.org ), and in affinity ranking and scoring of bound ligands.
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D3R Grand Challenge 2: blind prediction of protein-ligand poses, affinity rankings, and relative binding free energies.,Gaieb Z, Liu S, Gathiaka S, Chiu M, Yang H, Shao C, Feher VA, Walters WP, Kuhn B, Rudolph MG, Burley SK, Gilson MK, Amaro RE J Comput Aided Mol Des. 2017 Dec 4. pii: 10.1007/s10822-017-0088-4. doi:, 10.1007/s10822-017-0088-4. PMID:29204945<ref>PMID:29204945</ref>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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<div class="pdbe-citations 5q1c" style="background-color:#fffaf0;"></div>
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==See Also==
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*[[Bile acid receptor 3D structures|Bile acid receptor 3D structures]]
== References ==
== References ==
<references/>
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
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[[Category: Benz, J]]
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[[Category: Homo sapiens]]
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[[Category: Burger, D]]
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[[Category: Large Structures]]
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[[Category: Burley, S K]]
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[[Category: Benz J]]
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[[Category: Joseph, C]]
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[[Category: Burger D]]
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[[Category: Kuhn, B]]
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[[Category: Burley SK]]
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[[Category: Rudolph, M G]]
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[[Category: Joseph C]]
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[[Category: Ruf, A]]
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[[Category: Kuhn B]]
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[[Category: Shao, C]]
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[[Category: Rudolph MG]]
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[[Category: Thoma, R]]
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[[Category: Ruf A]]
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[[Category: Yang, H]]
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[[Category: Shao C]]
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[[Category: D3r]]
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[[Category: Thoma R]]
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[[Category: Docking]]
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[[Category: Yang H]]
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[[Category: Fxr]]
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[[Category: Transcription]]
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Current revision

Ligand binding to FARNESOID-X-RECEPTOR

PDB ID 5q1c

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