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.


5ofm

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
m (Protected "5ofm" [edit=sysop:move=sysop])
Current revision (16:48, 13 December 2023) (edit) (undo)
 
(One intermediate revision not shown.)
Line 1: Line 1:
==Crystal structure of human 3-phosphoglycerate dehydrogenase in complex with 5-amino-1-methyl-1H-indole==
==Crystal structure of human 3-phosphoglycerate dehydrogenase in complex with 5-amino-1-methyl-1H-indole==
-
<StructureSection load='5ofm' size='340' side='right' caption='[[5ofm]], [[Resolution|resolution]] 1.50&Aring;' scene=''>
+
<StructureSection load='5ofm' size='340' side='right'caption='[[5ofm]], [[Resolution|resolution]] 1.50&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
-
<table><tr><td colspan='2'>[[5ofm]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5OFM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5OFM FirstGlance]. <br>
+
<table><tr><td colspan='2'>[[5ofm]] is a 2 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=5OFM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5OFM FirstGlance]. <br>
-
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=9TT:1-methylindol-5-amine'>9TT</scene></td></tr>
+
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.5&#8491;</td></tr>
-
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">PHGDH, PGDH3 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</td></tr>
+
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=9TT:1-methylindol-5-amine'>9TT</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=5ofm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ofm OCA], [http://pdbe.org/5ofm PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ofm RCSB], [http://www.ebi.ac.uk/pdbsum/5ofm PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ofm ProSAT]</span></td></tr>
+
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=5ofm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ofm OCA], [https://pdbe.org/5ofm PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5ofm RCSB], [https://www.ebi.ac.uk/pdbsum/5ofm PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5ofm ProSAT]</span></td></tr>
</table>
</table>
== Disease ==
== Disease ==
-
[[http://www.uniprot.org/uniprot/SERA_HUMAN SERA_HUMAN]] Defects in PHGDH are the cause of phosphoglycerate dehydrogenase deficiency (PHGDH deficiency) [MIM:[http://omim.org/entry/601815 601815]]. It is characterized by congenital microcephaly, psychomotor retardation, and seizures.
+
[https://www.uniprot.org/uniprot/SERA_HUMAN SERA_HUMAN] Defects in PHGDH are the cause of phosphoglycerate dehydrogenase deficiency (PHGDH deficiency) [MIM:[https://omim.org/entry/601815 601815]. It is characterized by congenital microcephaly, psychomotor retardation, and seizures.
-
<div style="background-color:#fffaf0;">
+
== Function ==
-
== Publication Abstract from PubMed ==
+
[https://www.uniprot.org/uniprot/SERA_HUMAN SERA_HUMAN]
-
3-Phosphoglycerate dehydrogenase (PHGDH) has recently been identified as an attractive target in cancer therapy as it links upregulated glycolytic flux to increased biomass production in cancer cells. PHGDH catalyses the first step in the serine synthesis pathway and thus diverts glycolytic flux into serine synthesis. We have used siRNA-mediated suppression of PHGDH expression to show that PHGDH is a potential therapeutic target in PHGDH-amplified breast cancer. Knockdown caused reduced proliferation in the PHGDH-amplified cell line MDA-MB-468, whereas breast cancer cells with low PHGDH expression or with elevated PHGDH expression in the absence of genomic amplification were not affected. As a first step towards design of a chemical probe for PHGDH, we report a fragment-based drug discovery approach for the identification of PHGDH inhibitors. We designed a truncated PHGDH construct that gave crystals which diffracted to high resolution, and could be used for fragment soaking. 15 fragments stabilising PHGDH were identified using a thermal shift assay and validated by X-ray crystallography and ITC competition experiments to exhibit 1.5-26.2 mM affinity for PHGDH. A structure-guided fragment growing approach was applied to the PHGDH binders from the initial screen, yielding greater understanding of the binding site and suggesting routes to achieve higher affinity NAD-competitive inhibitors.
+
-
Validating and enabling phosphoglycerate dehydrogenase (PHGDH) as a target for fragment-based drug discovery in PHGDH-amplified breast cancer.,Unterlass JE, Basle A, Blackburn TJ, Tucker J, Cano C, Noble ME, Curtin NJ Oncotarget. 2016 Aug 22. doi: 10.18632/oncotarget.11487. PMID:27564259<ref>PMID:27564259</ref>
+
==See Also==
-
 
+
*[[Phosphoglycerate dehydrogenase|Phosphoglycerate dehydrogenase]]
-
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+
-
</div>
+
-
<div class="pdbe-citations 5ofm" style="background-color:#fffaf0;"></div>
+
-
== References ==
+
-
<references/>
+
__TOC__
__TOC__
</StructureSection>
</StructureSection>
-
[[Category: Human]]
+
[[Category: Homo sapiens]]
-
[[Category: Basle, A]]
+
[[Category: Large Structures]]
-
[[Category: Blackburn, T J]]
+
[[Category: Basle A]]
-
[[Category: Cano, C]]
+
[[Category: Blackburn TJ]]
-
[[Category: Curtin, N J]]
+
[[Category: Cano C]]
-
[[Category: Noble, M E.M]]
+
[[Category: Curtin NJ]]
-
[[Category: Tucker, J]]
+
[[Category: Noble MEM]]
-
[[Category: Unterlass, J E]]
+
[[Category: Tucker J]]
-
[[Category: Dehydrogenase]]
+
[[Category: Unterlass JE]]
-
[[Category: Fbdd]]
+
-
[[Category: Oxidoreductase]]
+
-
[[Category: Serine metabolism]]
+

Current revision

Crystal structure of human 3-phosphoglycerate dehydrogenase in complex with 5-amino-1-methyl-1H-indole

PDB ID 5ofm

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/5ofm"
Personal tools