6k9v: Difference between revisions

Latest revision as of 10:28, 22 November 2023

Crystal structure of tubulin in complex with inhibitor D64

Structural highlights

6k9v is a 6 chain structure with sequence from Bos taurus, Gallus gallus and Rattus norvegicus. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.543Å
Ligands:	ACP, CA, D3L, GDP, GTP, MES, MG
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

TBA1B_BOVIN Tubulin is the major constituent of microtubules. It binds two moles of GTP, one at an exchangeable site on the beta chain and one at a non-exchangeable site on the alpha chain.

Publication Abstract from PubMed

Microtubules are composed of alphabeta-tubulin heterodimers, and drugs that interfere with microtubule dynamics are used widely in cancer chemotherapy. Small synthetic molecules with an indole nucleus as a core structure have been identified as microtubule inhibitors and recognized as anticancer agents. However, structural information for the interactions between indole derivatives and tubulin is sparse. Here, we present the 2.55 A crystal structure of tubulin in complex with the indole derivative D64131. We compare the binding modes of D64131, colchicine, and five other indole derivatives to tubulin. These results reveal the interactions between the indole derivatives and tubulin, explain previous results of structure-activity-relationship (SAR) studies and, thus, provide insights into the development of new indole derivatives targeting the colchicine binding site.

Structural insights into the design of indole derivatives as tubulin polymerization inhibitors.,Li Y, Yang J, Niu L, Hu D, Li H, Chen L, Yu Y, Chen Q FEBS Lett. 2019 Aug 1. doi: 10.1002/1873-3468.13566. PMID:31369682^[1]

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

References

↑ Li Y, Yang J, Niu L, Hu D, Li H, Chen L, Yu Y, Chen Q. Structural insights into the design of indole derivatives as tubulin polymerization inhibitors. FEBS Lett. 2019 Aug 1. doi: 10.1002/1873-3468.13566. PMID:31369682 doi:https://dx.doi.org/10.1002/1873-3468.13566

Proteopedia Page Contributors and Editors (what is this?)

OCA

[1] Li Y, Yang J, Niu L, Hu D, Li H, Chen L, Yu Y, Chen Q. Structural insights into the design of indole derivatives as tubulin polymerization inhibitors. FEBS Lett. 2019 Aug 1. doi: 10.1002/1873-3468.13566. PMID:31369682 doi:https://dx.doi.org/10.1002/1873-3468.13566

[1]

@@ Line 3: / Line 3: @@
 <StructureSection load='6k9v' size='340' side='right'caption='[[6k9v]], [[Resolution|resolution]] 2.54&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[6k9v]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Bos_taurus Bos taurus], [http://en.wikipedia.org/wiki/Buffalo_rat Buffalo rat] and [http://en.wikipedia.org/wiki/Chick Chick]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6K9V OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6K9V FirstGlance]. <br>
+<table><tr><td colspan='2'>[[6k9v]] 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=6K9V OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6K9V FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACP:PHOSPHOMETHYLPHOSPHONIC+ACID+ADENYLATE+ESTER'>ACP</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=D3L:(5-methoxy-1H-indol-2-yl)-phenyl-methanone'>D3L</scene>, <scene name='pdbligand=GDP:GUANOSINE-5-DIPHOSPHATE'>GDP</scene>, <scene name='pdbligand=GTP:GUANOSINE-5-TRIPHOSPHATE'>GTP</scene>, <scene name='pdbligand=MES:2-(N-MORPHOLINO)-ETHANESULFONIC+ACID'>MES</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></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]] 2.543&#8491;</td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">Stmn4 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10116 Buffalo rat]), TTL ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9031 CHICK])</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=D3L:(5-methoxy-1H-indol-2-yl)-phenyl-methanone'>D3L</scene>, <scene name='pdbligand=GDP:GUANOSINE-5-DIPHOSPHATE'>GDP</scene>, <scene name='pdbligand=GTP:GUANOSINE-5-TRIPHOSPHATE'>GTP</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'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6k9v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6k9v OCA], [http://pdbe.org/6k9v PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6k9v RCSB], [http://www.ebi.ac.uk/pdbsum/6k9v PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6k9v ProSAT]</span></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=6k9v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6k9v OCA], [https://pdbe.org/6k9v PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6k9v RCSB], [https://www.ebi.ac.uk/pdbsum/6k9v PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6k9v ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/TBA1B_BOVIN TBA1B_BOVIN]] Tubulin is the major constituent of microtubules. It binds two moles of GTP, one at an exchangeable site on the beta chain and one at a non-exchangeable site on the alpha chain. [[http://www.uniprot.org/uniprot/STMN4_RAT STMN4_RAT]] Exhibits microtubule-destabilizing activity.<ref>PMID:15039434</ref> <ref>PMID:12111843</ref> <ref>PMID:15014504</ref>  [[http://www.uniprot.org/uniprot/TBB2B_BOVIN TBB2B_BOVIN]] Tubulin is the major constituent of microtubules. It binds two moles of GTP, one at an exchangeable site on the beta chain and one at a non-exchangeable site on the alpha chain (By similarity).
+[https://www.uniprot.org/uniprot/TBA1B_BOVIN TBA1B_BOVIN] Tubulin is the major constituent of microtubules. It binds two moles of GTP, one at an exchangeable site on the beta chain and one at a non-exchangeable site on the alpha chain.
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 19: / Line 19: @@
 </div>
 <div class="pdbe-citations 6k9v" 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/>
@@ Line 24: / Line 29: @@
 </StructureSection>
 [[Category: Bos taurus]]
-[[Category: Buffalo rat]]
+[[Category: Gallus gallus]]
-[[Category: Chick]]
 [[Category: Large Structures]]
-[[Category: Chen, Q]]
+[[Category: Rattus norvegicus]]
-[[Category: Yu, Y]]
+[[Category: Chen Q]]
-[[Category: Cell cycle]]
+[[Category: Yu Y]]
-[[Category: Complex]]
-[[Category: Inhibitor]]
-[[Category: Structural protein]]
-[[Category: Tubulin]]

6k9v: Difference between revisions

Latest revision as of 10:28, 22 November 2023

Crystal structure of tubulin in complex with inhibitor D64

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

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