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.


3dm6

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (06:59, 19 August 2020) (edit) (undo)
 
(7 intermediate revisions not shown.)
Line 1: Line 1:
-
{{Seed}}
 
-
[[Image:3dm6.jpg|left|200px]]
 
-
<!--
+
==Beta-secretase 1 complexed with statine-based inhibitor==
-
The line below this paragraph, containing "STRUCTURE_3dm6", creates the "Structure Box" on the page.
+
<StructureSection load='3dm6' size='340' side='right'caption='[[3dm6]], [[Resolution|resolution]] 2.60&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'>[[3dm6]] is a 3 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=3DM6 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=3DM6 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" id="ligandDat"><scene name='pdbligand=757:5-[[(2S)-2-[[(3R,4S)-5-(3,5-difluorophenoxy)-3-hydroxy-4-[[3-(methyl-methylsulfonyl-amino)-5-[[(1R)-1-phenylethyl]carbamoyl]phenyl]carbonylamino]pentanoyl]amino]-3-methyl-butanoyl]amino]benzene-1,3-dicarboxylic+acid'>757</scene>, <scene name='pdbligand=IPA:ISOPROPYL+ALCOHOL'>IPA</scene></td></tr>
-
-->
+
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Memapsin_2 Memapsin 2], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.23.46 3.4.23.46] </span></td></tr>
-
{{STRUCTURE_3dm6| PDB=3dm6 | SCENE= }}
+
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=3dm6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3dm6 OCA], [http://pdbe.org/3dm6 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3dm6 RCSB], [http://www.ebi.ac.uk/pdbsum/3dm6 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3dm6 ProSAT]</span></td></tr>
 +
</table>
 +
== Function ==
 +
[[http://www.uniprot.org/uniprot/BACE1_HUMAN BACE1_HUMAN]] Responsible for the proteolytic processing of the amyloid precursor protein (APP). Cleaves at the N-terminus of the A-beta peptide sequence, between residues 671 and 672 of APP, leads to the generation and extracellular release of beta-cleaved soluble APP, and a corresponding cell-associated C-terminal fragment which is later released by gamma-secretase.<ref>PMID:10677483</ref> <ref>PMID:20354142</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/dm/3dm6_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=3dm6 ConSurf].
 +
<div style="clear:both"></div>
 +
<div style="background-color:#fffaf0;">
 +
== Publication Abstract from PubMed ==
 +
Several BACE-1 inhibitors with low nanomolar level activities, encompassing a statine-based core structure with phenyloxymethyl- and benzyloxymethyl residues in the P1 position, are presented. The novel P1 modification introduced to allow the facile exploration of the S1 binding pocket of BACE-1, delivered highly promising inhibitors.
-
===Beta-secretase 1 complexed with statine-based inhibitor===
+
Design, synthesis and SAR of potent statine-based BACE-1 inhibitors: exploration of P1 phenoxy and benzyloxy residues.,Back M, Nyhlen J, Kvarnstrom I, Appelgren S, Borkakoti N, Jansson K, Lindberg J, Nystrom S, Hallberg A, Rosenquist S, Samuelsson B Bioorg Med Chem. 2008 Nov 1;16(21):9471-86. Epub 2008 Sep 19. PMID:18842420<ref>PMID:18842420</ref>
 +
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 +
</div>
 +
<div class="pdbe-citations 3dm6" style="background-color:#fffaf0;"></div>
-
<!--
+
==See Also==
-
The line below this paragraph, {{ABSTRACT_PUBMED_18842420}}, adds the Publication Abstract to the page
+
*[[Beta secretase 3D structures|Beta secretase 3D structures]]
-
(as it appears on PubMed at http://www.pubmed.gov), where 18842420 is the PubMed ID number.
+
== References ==
-
-->
+
<references/>
-
{{ABSTRACT_PUBMED_18842420}}
+
__TOC__
-
 
+
</StructureSection>
-
==About this Structure==
+
[[Category: Human]]
-
3DM6 is a 3 chains structure of sequences 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=3DM6 OCA].
+
[[Category: Large Structures]]
-
 
+
-
==Reference==
+
-
Design, synthesis and SAR of potent statine-based BACE-1 inhibitors: exploration of P1 phenoxy and benzyloxy residues., Back M, Nyhlen J, Kvarnstrom I, Appelgren S, Borkakoti N, Jansson K, Lindberg J, Nystrom S, Hallberg A, Rosenquist S, Samuelsson B, Bioorg Med Chem. 2008 Nov 1;16(21):9471-86. Epub 2008 Sep 19. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/18842420 18842420]
+
-
[[Category: Homo sapiens]]
+
[[Category: Memapsin 2]]
[[Category: Memapsin 2]]
-
[[Category: Borkakoti, N.]]
+
[[Category: Borkakoti, N]]
-
[[Category: Lindberg, J.]]
+
[[Category: Lindberg, J]]
-
[[Category: Nystrom, S.]]
+
[[Category: Nystrom, S]]
[[Category: Alternative splicing]]
[[Category: Alternative splicing]]
[[Category: Aspartyl protease]]
[[Category: Aspartyl protease]]
Line 41: Line 54:
[[Category: Transmembrane]]
[[Category: Transmembrane]]
[[Category: Zymogen]]
[[Category: Zymogen]]
- 
-
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Dec 17 13:43:10 2008''
 

Current revision

Beta-secretase 1 complexed with statine-based inhibitor

PDB ID 3dm6

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/3dm6"
Personal tools