7CNM
YDX in complex with tubulin
Summary for 7CNM
| Entry DOI | 10.2210/pdb7cnm/pdb |
| Descriptor | Tubulin alpha-1B chain, (2~{S},4~{S})-4-[[2-[(1~{R},3~{R})-1-acetyloxy-4-methyl-3-[[(2~{S},3~{S})-3-methyl-2-[[(2~{R})-1-methylpiperidin-2-yl]carbonylamino]pentanoyl]amino]pentyl]-1,3-thiazol-4-yl]carbonylamino]-5-cyclohexyl-2-methyl-pentanoic acid, PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER, ... (12 entities in total) |
| Functional Keywords | ydx, tubulin, protein-drug complex, cell cycle |
| Biological source | Mus musculus (Mouse) More |
| Total number of polymer chains | 6 |
| Total formula weight | 266248.02 |
| Authors | Wang, Y.X.,Wu, C.Y. (deposition date: 2020-08-02, release date: 2021-08-04, Last modification date: 2023-11-29) |
| Primary citation | Chengyong, W.,Jinghong, X.,Yanyan, W.,Qing-Jie, X.,Lingling, M.,Yuyan, L.,Hai, C.,Qian, L.,Quan, Z.,Bo, S.,Yuxi, W. The high-resolution X-ray structure of vinca-domain inhibitors of microtubules provides a rational approach for drug design. Febs Lett., 595:195-205, 2021 Cited by PubMed Abstract: Tubulin vinca-domain ligands can inhibit microtubule polymerization, causing cell death in mitosis, and their potential against multiple cancer types has been demonstrated. However, due to drug resistance and toxicities, development of novel vinca-domain ligands is still needed. In this study, we determined the high-resolution crystal structures of vinorelbine, YXD, and Phomopsin A in complex with tubulin at 2.5 Å. Additionally, we recapitulated all previously published high-resolution crystal structures of the vinca binding site to reveal critical residues and the molecular mechanism of vinca-domain ligands interacting with tubulin. Furthermore, we designed putatively novel triazolopyrimidine derivatives by introducing secondary amine groups to establish salt-bridge and H-bond interactions with Asp179 and Asn329 . Our studies provided the structural basis for designing novel tubulin vinca-domain ligands. PubMed: 33220079DOI: 10.1002/1873-3468.14003 PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (2.44 Å) |
Structure validation
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