5dpz

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Current revision (21:54, 28 June 2023) (edit) (undo)
 
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<StructureSection load='5dpz' size='340' side='right'caption='[[5dpz]], [[Resolution|resolution]] 1.33&Aring;' scene=''>
<StructureSection load='5dpz' size='340' side='right'caption='[[5dpz]], [[Resolution|resolution]] 1.33&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
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<table><tr><td colspan='2'>[[5dpz]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Cryphonectria_parasitica Cryphonectria parasitica]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5DPZ OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5DPZ FirstGlance]. <br>
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<table><tr><td colspan='2'>[[5dpz]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Cryphonectria_parasitica Cryphonectria parasitica]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5DPZ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5DPZ FirstGlance]. <br>
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</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=1PE:PENTAETHYLENE+GLYCOL'>1PE</scene>, <scene name='pdbligand=51V:2-METHYLANILINE'>51V</scene>, <scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene></td></tr>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.328&#8491;</td></tr>
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<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3pgi|3pgi]], [[3pld|3pld]], [[4y3y|4y3y]]</td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=1PE:PENTAETHYLENE+GLYCOL'>1PE</scene>, <scene name='pdbligand=51V:2-METHYLANILINE'>51V</scene>, <scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene></td></tr>
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<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Endothiapepsin Endothiapepsin], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.23.22 3.4.23.22] </span></td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=5dpz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5dpz OCA], [https://pdbe.org/5dpz PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5dpz RCSB], [https://www.ebi.ac.uk/pdbsum/5dpz PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5dpz ProSAT]</span></td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=5dpz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5dpz OCA], [http://pdbe.org/5dpz PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5dpz RCSB], [http://www.ebi.ac.uk/pdbsum/5dpz PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5dpz ProSAT]</span></td></tr>
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</table>
</table>
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<div style="background-color:#fffaf0;">
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== Function ==
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== Publication Abstract from PubMed ==
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[https://www.uniprot.org/uniprot/CARP_CRYPA CARP_CRYPA]
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Druglike molecules are defined by Lipinski's rule of 5, to characterize fragment thresholds, they have been reduced from 5 to 3 (Astex's rule of 3). They are applied to assemble fragment libraries, and providers use them to select fragments for commercial offer. We question whether these rules are too stringent to compose fragment libraries with candidates exhibiting sufficient room for chemical subsequent growing and merging modifications as appropriate functional groups for chemical transformations are required. Usually these groups exhibit properties as hydrogen bond donors/acceptors and provide entry points for optimization chemistry. We therefore designed a fragment library (364 entries) without strictly applying the rule of 3. For initial screening for endothiapepsin binding, we performed a biochemical cleavage assay of a fluorogenic substrate at 1 mM. "Hits" were defined to inhibit the enzyme by at least 40%. Fifty-five hits were suggested and subsequently soaked into endothiapepsin crystals. Eleven crystal structures could be determined covering fragments with diverse binding modes: (i) direct binding to the catalytic dyad aspartates, (ii) water-mediated binding to the aspartates, (iii) no direct interaction with the dyad. They occupy different specificity pockets. Only 4 of the 11 fragments are consistent with the rule of 3. Restriction to this rule would have limited the fragment hits to a strongly reduced variety of chemotypes.
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A Small Nonrule of 3 Compatible Fragment Library Provides High Hit Rate of Endothiapepsin Crystal Structures with Various Fragment Chemotypes.,Koster H, Craan T, Brass S, Herhaus C, Zentgraf M, Neumann L, Heine A, Klebe G J Med Chem. 2011 Oct 25. PMID:21972967<ref>PMID:21972967</ref>
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==See Also==
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*[[Pepsin|Pepsin]]
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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<div class="pdbe-citations 5dpz" style="background-color:#fffaf0;"></div>
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== References ==
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<references/>
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__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Cryphonectria parasitica]]
[[Category: Cryphonectria parasitica]]
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[[Category: Endothiapepsin]]
 
[[Category: Large Structures]]
[[Category: Large Structures]]
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[[Category: Heine, A]]
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[[Category: Heine A]]
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[[Category: Klebe, G]]
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[[Category: Klebe G]]
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[[Category: Radeva, N]]
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[[Category: Radeva N]]
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[[Category: Uehlein, M]]
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[[Category: Uehlein M]]
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[[Category: Weiss, M]]
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[[Category: Weiss M]]
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[[Category: Fragment screening]]
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[[Category: Hydrolase]]
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[[Category: Inhibition]]
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Current revision

Endothiapepsin in complex with fragment 31

PDB ID 5dpz

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Proteopedia Page Contributors and Editors (what is this?)

OCA

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