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.


3n3g

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
m (Protected "3n3g" [edit=sysop:move=sysop])
Current revision (13:14, 16 January 2019) (edit) (undo)
 
(5 intermediate revisions not shown.)
Line 1: Line 1:
-
[[Image:3n3g.png|left|200px]]
 
-
<!--
+
==4-(3-Trifluoromethylphenyl)-pyrimidine-2-carbonitrile as cathepsin S inhibitors: N3, not N1 is critically important==
-
The line below this paragraph, containing "STRUCTURE_3n3g", creates the "Structure Box" on the page.
+
<StructureSection load='3n3g' size='340' side='right' caption='[[3n3g]], [[Resolution|resolution]] 1.60&Aring;' scene=''>
-
You may change the PDB parameter (which sets the PDB file loaded into the applet)
+
== Structural highlights ==
-
or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
+
<table><tr><td colspan='2'>[[3n3g]] 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=3N3G OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3N3G FirstGlance]. <br>
-
or leave the SCENE parameter empty for the default display.
+
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=935:(E)-1-(6-{4-[3-(4-METHYLPIPERAZIN-1-YL)PROPOXY]-3-(TRIFLUOROMETHYL)PHENYL}PYRIDIN-2-YL)METHANIMINE'>935</scene>, <scene name='pdbligand=93N:6-{4-[3-(4-METHYLPIPERAZIN-1-YL)PROPOXY]-3-(TRIFLUOROMETHYL)PHENYL}PYRIDINE-2-CARBONITRILE'>93N</scene>, <scene name='pdbligand=DMS:DIMETHYL+SULFOXIDE'>DMS</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-
-->
+
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">CTSS ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</td></tr>
-
{{STRUCTURE_3n3g| PDB=3n3g | SCENE= }}
+
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Cathepsin_S Cathepsin S], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.22.27 3.4.22.27] </span></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=3n3g FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3n3g OCA], [http://pdbe.org/3n3g PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3n3g RCSB], [http://www.ebi.ac.uk/pdbsum/3n3g PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3n3g ProSAT]</span></td></tr>
 +
</table>
 +
== Function ==
 +
[[http://www.uniprot.org/uniprot/CATS_HUMAN CATS_HUMAN]] Thiol protease. Key protease responsible for the removal of the invariant chain from MHC class II molecules. The bond-specificity of this proteinase is in part similar to the specificities of cathepsin L and cathepsin N.
 +
== 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/n3/3n3g_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=3n3g ConSurf].
 +
<div style="clear:both"></div>
 +
<div style="background-color:#fffaf0;">
 +
== Publication Abstract from PubMed ==
 +
Using computer aided modelling studies, a new extended P2/S2 interaction was identified. This extended region can accommodate a variety of functional groups, such as aryls and basic amines. It was discovered that the N3 nitrogen of the pyrimidine-2-carbonitrile is critical for its cathepsin cysteine protease inhibition. N1 nitrogen also contributes to the inhibitory activity, but to a very limited degree. An 'in situ double activation' mechanism was proposed to explain these results.
-
===4-(3-Trifluoromethylphenyl)-pyrimidine-2-carbonitrile as cathepsin S inhibitors: N3, not N1 is critically important===
+
4-(3-Trifluoromethylphenyl)-pyrimidine-2-carbonitrile as cathepsin S inhibitors: N3, not N1 is critically important.,Cai J, Fradera X, van Zeeland M, Dempster M, Cameron KS, Bennett DJ, Robinson J, Popplestone L, Baugh M, Westwood P, Bruin J, Hamilton W, Kinghorn E, Long C, Uitdehaag JC Bioorg Med Chem Lett. 2010 Aug 1;20(15):4507-10. Epub 2010 Jun 10. PMID:20580231<ref>PMID:20580231</ref>
-
 
+
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-
<!--
+
</div>
-
The line below this paragraph, {{ABSTRACT_PUBMED_20580231}}, adds the Publication Abstract to the page
+
<div class="pdbe-citations 3n3g" style="background-color:#fffaf0;"></div>
-
(as it appears on PubMed at http://www.pubmed.gov), where 20580231 is the PubMed ID number.
+
-
-->
+
-
{{ABSTRACT_PUBMED_20580231}}
+
-
 
+
-
==About this Structure==
+
-
[[3n3g]] is a 2 chain structure of [[Cathepsin]] 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=3N3G OCA].
+
==See Also==
==See Also==
-
*[[Cathepsin]]
+
*[[Cathepsin|Cathepsin]]
-
 
+
== References ==
-
==Reference==
+
<references/>
-
<ref group="xtra">PMID:20580231</ref><references group="xtra"/>
+
__TOC__
 +
</StructureSection>
[[Category: Cathepsin S]]
[[Category: Cathepsin S]]
-
[[Category: Homo sapiens]]
+
[[Category: Human]]
-
[[Category: Fradera, X.]]
+
[[Category: Fradera, X]]
-
[[Category: Uitdehaag, J C.M.]]
+
[[Category: Uitdehaag, J C.M]]
-
[[Category: Zeeland, M van.]]
+
[[Category: Zeeland, M van]]
[[Category: Cathepsin s]]
[[Category: Cathepsin s]]
[[Category: Covalent inhibitor]]
[[Category: Covalent inhibitor]]
[[Category: Hydrolase]]
[[Category: Hydrolase]]

Current revision

4-(3-Trifluoromethylphenyl)-pyrimidine-2-carbonitrile as cathepsin S inhibitors: N3, not N1 is critically important

3n3g, resolution 1.60Å

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/3n3g"
Personal tools