5edh: Difference between revisions

Revision as of 06:54, 22 April 2020

human PDE10A, 8-ethyl-5-methyl-2-[2-(2-methyl-5-pyrrolidin-1-yl-1,2,4-triazol-3-yl)ethyl]-[1,2,4]triazolo[1,5-c]pyrimidine, 2.03A, H3, Rfree=22.7%

Structural highlights

5edh is a 4 chain structure with sequence from Human. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	5MF, MG, ZN
NonStd Res:	CME
Gene:	PDE10A (HUMAN)
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[PDE10_HUMAN] Plays a role in signal transduction by regulating the intracellular concentration of cyclic nucleotides. Can hydrolyze both cAMP and cGMP, but has higher affinity for cAMP and is more efficient with cAMP as substrate.^[1]

Publication Abstract from PubMed

We present a series of small molecule drug discovery case studies where computational methods were prospectively employed to impact Roche research projects, with the aim of highlighting those methods that provide real added value. Our brief accounts encompass a broad range of methods and techniques applied to a variety of enzymes and receptors. Most of these are based on judicious application of knowledge about molecular conformations and interactions: filling of lipophilic pockets to gain affinity or selectivity, addition of polar substituents, scaffold hopping, transfer of SAR, conformation analysis, and molecular overlays. A case study of sequence-driven focused screening is presented to illustrate how appropriate preprocessing of information enables effective exploitation of prior knowledge. We conclude that qualitative statements enabling chemists to focus on promising regions of chemical space are often more impactful than quantitative prediction.

A Real-World Perspective on Molecular Design.,Kuhn B, Guba W, Hert J, Banner D, Bissantz C, Ceccarelli S, Haap W, Korner M, Kuglstatter A, Lerner C, Mattei P, Neidhart W, Pinard E, Rudolph MG, Schulz-Gasch T, Woltering T, Stahl M J Med Chem. 2016 Feb 24. PMID:26878596^[2]

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

References

↑ Wang H, Liu Y, Hou J, Zheng M, Robinson H, Ke H. Structural insight into substrate specificity of phosphodiesterase 10. Proc Natl Acad Sci U S A. 2007 Apr 3;104(14):5782-7. Epub 2007 Mar 26. PMID:17389385
↑ Kuhn B, Guba W, Hert J, Banner D, Bissantz C, Ceccarelli S, Haap W, Korner M, Kuglstatter A, Lerner C, Mattei P, Neidhart W, Pinard E, Rudolph MG, Schulz-Gasch T, Woltering T, Stahl M. A Real-World Perspective on Molecular Design. J Med Chem. 2016 Feb 24. PMID:26878596 doi:https://dx.doi.org/10.1021/acs.jmedchem.5b01875

Proteopedia Page Contributors and Editors (what is this?)

OCA

[1] Wang H, Liu Y, Hou J, Zheng M, Robinson H, Ke H. Structural insight into substrate specificity of phosphodiesterase 10. Proc Natl Acad Sci U S A. 2007 Apr 3;104(14):5782-7. Epub 2007 Mar 26. PMID:17389385

[2] Kuhn B, Guba W, Hert J, Banner D, Bissantz C, Ceccarelli S, Haap W, Korner M, Kuglstatter A, Lerner C, Mattei P, Neidhart W, Pinard E, Rudolph MG, Schulz-Gasch T, Woltering T, Stahl M. A Real-World Perspective on Molecular Design. J Med Chem. 2016 Feb 24. PMID:26878596 doi:https://dx.doi.org/10.1021/acs.jmedchem.5b01875

[1]

[2]

@@ Line 1: / Line 1: @@
 ==human PDE10A, 8-ethyl-5-methyl-2-[2-(2-methyl-5-pyrrolidin-1-yl-1,2,4-triazol-3-yl)ethyl]-[1,2,4]triazolo[1,5-c]pyrimidine, 2.03A, H3, Rfree=22.7%==
-<StructureSection load='5edh' size='340' side='right' caption='[[5edh]], [[Resolution|resolution]] 2.03&Aring;' scene=''>
+<StructureSection load='5edh' size='340' side='right'caption='[[5edh]], [[Resolution|resolution]] 2.03&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[5edh]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5EDH OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5EDH FirstGlance]. <br>
+<table><tr><td colspan='2'>[[5edh]] is a 4 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=5EDH OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5EDH FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=5MF:8-ETHYL-5-METHYL-2-[2-(2-METHYL-5-PYRROLIDIN-1-YL-1,2,4-TRIAZOL-3-YL)ETHYL]-[1,2,4]TRIAZOLO[1,5-C]PYRIMIDINE'>5MF</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
+</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=5MF:8-ETHYL-5-METHYL-2-[2-(2-METHYL-5-PYRROLIDIN-1-YL-1,2,4-TRIAZOL-3-YL)ETHYL]-[1,2,4]TRIAZOLO[1,5-C]PYRIMIDINE'>5MF</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
 <tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CME:S,S-(2-HYDROXYETHYL)THIOCYSTEINE'>CME</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=5edh FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5edh OCA], [http://pdbe.org/5edh PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5edh RCSB], [http://www.ebi.ac.uk/pdbsum/5edh PDBsum]</span></td></tr>
+<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">PDE10A ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</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=5edh FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5edh OCA], [http://pdbe.org/5edh PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5edh RCSB], [http://www.ebi.ac.uk/pdbsum/5edh PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5edh ProSAT]</span></td></tr>
 </table>
 == Function ==
@@ Line 19: / Line 20: @@
 </div>
 <div class="pdbe-citations 5edh" style="background-color:#fffaf0;"></div>
+==See Also==
+*[[Phosphodiesterase 3D structures|Phosphodiesterase 3D structures]]
 == References ==
 <references/>
 __TOC__
 </StructureSection>
+[[Category: Human]]
+[[Category: Large Structures]]
 [[Category: Joseph, C]]
 [[Category: Rudolph, M G]]

5edh: Difference between revisions

Revision as of 06:54, 22 April 2020

human PDE10A, 8-ethyl-5-methyl-2-[2-(2-methyl-5-pyrrolidin-1-yl-1,2,4-triazol-3-yl)ethyl]-[1,2,4]triazolo[1,5-c]pyrimidine, 2.03A, H3, Rfree=22.7%

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

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