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7e4r
From Proteopedia
(Difference between revisions)
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| - | ==== | + | ==Crystal structure of tubulin in complex with D-DM1-SMe== |
| - | <StructureSection load='7e4r' size='340' side='right'caption='[[7e4r]]' scene=''> | + | <StructureSection load='7e4r' size='340' side='right'caption='[[7e4r]], [[Resolution|resolution]] 2.60Å' scene=''> |
== Structural highlights == | == Structural highlights == | ||
| - | <table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id= OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol= FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[7e4r]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Bos_taurus Bos taurus], [https://en.wikipedia.org/wiki/Gallus_gallus Gallus gallus] and [https://en.wikipedia.org/wiki/Rattus_norvegicus Rattus norvegicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7E4R OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7E4R FirstGlance]. <br> |
| - | </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=7e4r FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7e4r OCA], [https://pdbe.org/7e4r PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7e4r RCSB], [https://www.ebi.ac.uk/pdbsum/7e4r PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7e4r ProSAT]</span></td></tr> | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.597Å</td></tr> |
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACP:PHOSPHOMETHYLPHOSPHONIC+ACID+ADENYLATE+ESTER'>ACP</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=GDP:GUANOSINE-5-DIPHOSPHATE'>GDP</scene>, <scene name='pdbligand=GTP:GUANOSINE-5-TRIPHOSPHATE'>GTP</scene>, <scene name='pdbligand=HZ0:(10E,12E)-86-chloro-14-hydroxy-85,14-dimethoxy-33,2,7,10-tetramethyl-12,6-dioxo-7-aza-1(6,4)-oxazinana-3(2,3)-oxirana-8(1,3)-benzenacyclotetradecaphane-10,12-dien-4-yl+N-methyl-N-(3-(methylsulfinothioyl)propanoyl)-D-alaninate'>HZ0</scene>, <scene name='pdbligand=MES:2-(N-MORPHOLINO)-ETHANESULFONIC+ACID'>MES</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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=7e4r FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7e4r OCA], [https://pdbe.org/7e4r PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7e4r RCSB], [https://www.ebi.ac.uk/pdbsum/7e4r PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7e4r ProSAT]</span></td></tr> | ||
</table> | </table> | ||
| + | == Function == | ||
| + | [https://www.uniprot.org/uniprot/STMN4_RAT STMN4_RAT] Exhibits microtubule-destabilizing activity.<ref>PMID:15039434</ref> <ref>PMID:12111843</ref> <ref>PMID:15014504</ref> | ||
| + | <div style="background-color:#fffaf0;"> | ||
| + | == Publication Abstract from PubMed == | ||
| + | Maytansinoids, the chemical derivatives of Maytansine, are commonly used as potent cytotoxic payloads in antibody-drug conjugates (ADC). Structure-activity-relationship studies had identified the C3 ester side chain as a critical element for antitumor activity of maytansinoids. The maytansinoids bearing the methyl group at C3 position with D configuration were about 100 to 400-fold less cytotoxic than their corresponding L-epimers toward various cell lines. The detailed mechanism of how chirality affects the anticancer activity remains elusive. In this study, we determined the high-resolution crystal structure of tubulin in complex with maytansinol, L-DM1-SMe and D-DM1-SMe. And we found the carbonyl oxygen atom of the ester moiety and the tail thiomethyl group at C3 side chain of L-DM1-SMe form strong intramolecular interaction with the hydroxyl at position 9 and the benzene ring, respectively, fixing the bioactive conformation and enhancing the binding affinity. Additionally, ligand-based and structure-based virtually screening methods were used to screen the commercially macrocyclic compounds library, and 15 macrocyclic structures were picketed out as putatively new maytansine-site inhibitors. Our study provides a possible strategy for the rational discovery of next-generation maytansine site inhibitors. | ||
| + | |||
| + | C3 ester side chain plays a pivotal role in the antitumor activity of Maytansinoids.,Li W, Huang M, Li Y, Xia A, Tan L, Zhang Z, Wang Y, Yang J Biochem Biophys Res Commun. 2021 Aug 20;566:197-203. doi: , 10.1016/j.bbrc.2021.05.071. Epub 2021 Jun 15. PMID:34144258<ref>PMID:34144258</ref> | ||
| + | |||
| + | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | ||
| + | </div> | ||
| + | <div class="pdbe-citations 7e4r" style="background-color:#fffaf0;"></div> | ||
| + | |||
| + | ==See Also== | ||
| + | *[[Stathmin-4 3D structures|Stathmin-4 3D structures]] | ||
| + | *[[Tubulin 3D Structures|Tubulin 3D Structures]] | ||
| + | *[[Tubulin tyrosine ligase|Tubulin tyrosine ligase]] | ||
| + | == References == | ||
| + | <references/> | ||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
| + | [[Category: Bos taurus]] | ||
| + | [[Category: Gallus gallus]] | ||
[[Category: Large Structures]] | [[Category: Large Structures]] | ||
| - | [[Category: | + | [[Category: Rattus norvegicus]] |
| + | [[Category: Li W]] | ||
| + | [[Category: Wang Y]] | ||
Current revision
Crystal structure of tubulin in complex with D-DM1-SMe
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