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.


2vd0

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
m (Protected "2vd0" [edit=sysop:move=sysop])
Current revision (15:15, 13 December 2023) (edit) (undo)
 
(7 intermediate revisions not shown.)
Line 1: Line 1:
-
[[Image:2vd0.png|left|200px]]
 
-
{{STRUCTURE_2vd0| PDB=2vd0 | SCENE= }}
+
==Complex structure of prostaglandin D2 synthase at 2.2A.==
 +
<StructureSection load='2vd0' size='340' side='right'caption='[[2vd0]], [[Resolution|resolution]] 2.20&Aring;' scene=''>
 +
== Structural highlights ==
 +
<table><tr><td colspan='2'>[[2vd0]] 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=2VD0 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2VD0 FirstGlance]. <br>
 +
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.2&#8491;</td></tr>
 +
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=D27:2-{[(2E)-3-(3,4-DIMETHOXYPHENYL)PROP-2-ENOYL]AMINO}BENZOIC+ACID'>D27</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=GSH:GLUTATHIONE'>GSH</scene></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=2vd0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2vd0 OCA], [https://pdbe.org/2vd0 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2vd0 RCSB], [https://www.ebi.ac.uk/pdbsum/2vd0 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2vd0 ProSAT]</span></td></tr>
 +
</table>
 +
== Function ==
 +
[https://www.uniprot.org/uniprot/HPGDS_HUMAN HPGDS_HUMAN] Bifunctional enzyme which catalyzes both the conversion of PGH2 to PGD2, a prostaglandin involved in smooth muscle contraction/relaxation and a potent inhibitor of platelet aggregation, and the conjugation of glutathione with a wide range of aryl halides and organic isothiocyanates. Also exhibits low glutathione-peroxidase activity towards cumene hydroperoxide.<ref>PMID:10824118</ref> <ref>PMID:11672424</ref> <ref>PMID:9425264</ref> <ref>PMID:9353279</ref> <ref>PMID:12627223</ref> <ref>PMID:15113825</ref> <ref>PMID:16547010</ref> <ref>PMID:19939518</ref>
 +
== Evolutionary Conservation ==
 +
[[Image:Consurf_key_small.gif|200px|right]]
 +
Check<jmol>
 +
<jmolCheckbox>
 +
<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/vd/2vd0_consurf.spt"</scriptWhenChecked>
 +
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
 +
<text>to colour the structure by Evolutionary Conservation</text>
 +
</jmolCheckbox>
 +
</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2vd0 ConSurf].
 +
<div style="clear:both"></div>
 +
<div style="background-color:#fffaf0;">
 +
== Publication Abstract from PubMed ==
 +
We describe the discovery of novel inhibitors of prostaglandin D2 synthase (PGDS) through fragment-based lead generation and structure-based drug design. A library of 2500 low-molecular-weight compounds was screened using 2D nuclear magnetic resonance (NMR), leading to the identification of 24 primary hits. Structure determination of protein-ligand complexes with the hits enabled a hit optimization process, whereby we harvested increasingly more potent inhibitors out of our corporate compound collection. Two iterative cycles were carried out, comprising NMR screening, molecular modeling, X-ray crystallography, and in vitro biochemical testing. Six novel high-resolution PGDS complex structures were determined, and 300 hit analogues were tested. This rational drug design procedure culminated in the discovery of 24 compounds with an IC 50 below 1 microM in the in vitro assay. The best inhibitor (IC 50 = 21 nM) is one of the most potent inhibitors of PGDS to date. As such, it may enable new functional in vivo studies of PGDS and the prostaglandin metabolism pathway.
-
===COMPLEX STRUCTURE OF PROSTAGLANDIN D2 SYNTHASE AT 2.2A.===
+
Novel prostaglandin d synthase inhibitors generated by fragment-based drug design.,Hohwy M, Spadola L, Lundquist B, Hawtin P, Dahmen J, Groth-Clausen I, Nilsson E, Persdotter S, von Wachenfeldt K, Folmer RH, Edman K J Med Chem. 2008 Apr 10;51(7):2178-86. Epub 2008 Mar 15. PMID:18341273<ref>PMID:18341273</ref>
-
{{ABSTRACT_PUBMED_18341273}}
+
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-
 
+
</div>
-
==About this Structure==
+
<div class="pdbe-citations 2vd0" style="background-color:#fffaf0;"></div>
-
[[2vd0]] is a 4 chain structure of [[Prostaglandin D synthase]] with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2VD0 OCA].
+
==See Also==
==See Also==
-
*[[Prostaglandin D synthase|Prostaglandin D synthase]]
+
*[[Glutathione S-transferase 3D structures|Glutathione S-transferase 3D structures]]
-
 
+
== References ==
-
==Reference==
+
<references/>
-
<ref group="xtra">PMID:018341273</ref><references group="xtra"/>
+
__TOC__
 +
</StructureSection>
[[Category: Homo sapiens]]
[[Category: Homo sapiens]]
-
[[Category: Prostaglandin-D synthase]]
+
[[Category: Large Structures]]
-
[[Category: Dahmen, J.]]
+
[[Category: Dahmen J]]
-
[[Category: Edman, K.]]
+
[[Category: Edman K]]
-
[[Category: Folmer, R H.A.]]
+
[[Category: Folmer RHA]]
-
[[Category: Groth-Clausen, I.]]
+
[[Category: Groth-Clausen I]]
-
[[Category: Hawtin, P.]]
+
[[Category: Hawtin P]]
-
[[Category: Hohwy, M.]]
+
[[Category: Hohwy M]]
-
[[Category: Lundquist, B.]]
+
[[Category: Lundquist B]]
-
[[Category: Persdotter, S.]]
+
[[Category: Persdotter S]]
-
[[Category: Spadola, L.]]
+
[[Category: Spadola L]]
-
[[Category: Wachenfeldt, K Von.]]
+
[[Category: Von Wachenfeldt K]]
-
[[Category: Asthma]]
+
-
[[Category: Fatty acid biosynthesis]]
+
-
[[Category: Isomerase]]
+
-
[[Category: Lipid synthesis]]
+
-
[[Category: Pgd]]
+
-
[[Category: Prostaglandin biosynthesis]]
+
-
[[Category: Prostaglandin d2 synthase]]
+

Current revision

Complex structure of prostaglandin D2 synthase at 2.2A.

PDB ID 2vd0

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/2vd0"
Personal tools