Citation: Tao Lu, Yuan Yuan Qiao, Pan Wen Shen. Molecular path for ligand search[J]. Chinese Chemical Letters, ;2011, 22(9): 1130-1134. doi: 10.1016/j.cclet.2011.05.001 shu

Molecular path for ligand search

College of Chemistry, Nankai University, Tianjin 300071, China

Received Date: 28 February 2011

A ligand is a small molecule bind to several residues of a receptor. We adapt the concept of molecular path for effective ligand search with its contacting residues. Additionally, we allow wild type definitions on atoms and bonds of molecular paths for fuzzy algorithms on structural match. We choose hydrogen bond interactions to characterize the binding mode of a ligand by several proper molecular paths and use them to query the deposited ligands in PDBe that interact with their residues in the same way. Expression of molecular path and format of database entries are described with examples. Our molecular path provides a new approach to explore the ligand-receptor interactions and to provide structural framework reference on new ligand design.
- Ligand,
- Residue,
- Path,
- Database
1. [1]
  Shuaige Bai , Shuai Huang , Ting Luo , Bin Feng , Yanpeng Fang , Feiyi Chu , Jie Dong , Wenbin Zeng . Debut of a responsive chemiluminescent probe for butyrylcholinesterase: Application in biological imaging and pesticide residue detection. Chinese Chemical Letters, 2025, 36(3): 110054-. doi: 10.1016/j.cclet.2024.110054
2. [2]
  Kongchuan Wu , Dandan Lu , Jianbin Lin , Ting-Bin Wen , Wei Hao , Kai Tan , Hui-Jun Zhang . Elucidating ligand effects in rhodium(Ⅲ)-catalyzed arene–alkene coupling reactions. Chinese Chemical Letters, 2024, 35(5): 108906-. doi: 10.1016/j.cclet.2023.108906
3. [3]
  Yuanjin Chen , Xianghui Shi , Dajiang Huang , Junnian Wei , Zhenfeng Xi . Synthesis and reactivity of cobalt dinitrogen complex supported by nonsymmetrical pincer ligand. Chinese Chemical Letters, 2024, 35(7): 109292-. doi: 10.1016/j.cclet.2023.109292
4. [4]
  Luyao Lu , Chen Zhu , Fei Li , Pu Wang , Xi Kang , Yong Pei , Manzhou Zhu . Ligand effects on geometric structures and catalytic activities of atomically precise copper nanoclusters. Chinese Journal of Structural Chemistry, 2024, 43(10): 100411-100411. doi: 10.1016/j.cjsc.2024.100411
5. [5]
  Tao Yu , Vadim A. Soloshonok , Zhekai Xiao , Hong Liu , Jiang Wang . Probing the dynamic thermodynamic resolution and biological activity of Cu(Ⅱ) and Pd(Ⅱ) complexes with Schiff base ligand derived from proline. Chinese Chemical Letters, 2024, 35(4): 108901-. doi: 10.1016/j.cclet.2023.108901
6. [6]
  Tiantian Gong , Yanan Chen , Shuo Wang , Miao Wang , Junwei Zhao . Rigid-flexible-ligand-ornamented lanthanide-incorporated selenotungstates and photoluminescence properties. Chinese Journal of Structural Chemistry, 2024, 43(9): 100370-100370. doi: 10.1016/j.cjsc.2024.100370
7. [7]
  Ziyi Liu , Xunying Liu , Lubing Qin , Haozheng Chen , Ruikai Li , Zhenghua Tang . Alkynyl ligand for preparing atomically precise metal nanoclusters: Structure enrichment, property regulation, and functionality enhancement. Chinese Journal of Structural Chemistry, 2024, 43(11): 100405-100405. doi: 10.1016/j.cjsc.2024.100405
8. [8]
  Junxin Li , Chao Chen , Yuzhen Dong , Jian Lv , Jun-Mei Peng , Yuan-Ye Jiang , Daoshan Yang . Ligand-promoted reductive coupling between aryl iodides and cyclic sulfonium salts by nickel catalysis. Chinese Chemical Letters, 2024, 35(11): 109732-. doi: 10.1016/j.cclet.2024.109732
9. [9]
  Zhibin Ren , Shan Li , Xiaoying Liu , Guanghao Lv , Lei Chen , Jingli Wang , Xingyi Li , Jiaqing Wang . Penetrating efficiency of supramolecular hydrogel eye drops: Electrostatic interaction surpasses ligand-receptor interaction. Chinese Chemical Letters, 2024, 35(11): 109629-. doi: 10.1016/j.cclet.2024.109629
10. [10]
  Peipei CUI , Xin LI , Yilin CHEN , Zhilin CHENG , Feiyan GAO , Xu GUO , Wenning YAN , Yuchen DENG . Transition metal coordination polymers with flexible dicarboxylate ligand: Synthesis, characterization, and photoluminescence property. Chinese Journal of Inorganic Chemistry, 2024, 40(11): 2221-2231. doi: 10.11862/CJIC.20240234
11. [11]
  Xiaofen GUAN , Yating LIU , Jia LI , Yiwen HU , Haiyuan DING , Yuanjing SHI , Zhiqiang WANG , Wenmin WANG . Synthesis, crystal structure, and DNA-binding of binuclear lanthanide complexes based on a multidentate Schiff base ligand. Chinese Journal of Inorganic Chemistry, 2024, 40(12): 2486-2496. doi: 10.11862/CJIC.20240122
12. [12]
  Jumei Zhang , Ziheng Zhang , Gang Li , Hongjin Qiao , Hua Xie , Ling Jiang . Ligand-mediated reactivity in CO oxidation of yttrium-nickel monoxide carbonyl complexes. Chinese Chemical Letters, 2025, 36(2): 110278-. doi: 10.1016/j.cclet.2024.110278
13. [13]
  Yongsheng Xu , Lisha Yao , Jian Li , Yanzhao Dong , Dongyang Xie , Miaomiao Zhang , Feng Li , Yunsheng Dai , Jinli Zhang , Haiyang Zhang . Dual-ligand engineering over Au-based catalyst for efficient acetylene hydrochlorination. Chinese Chemical Letters, 2025, 36(3): 110318-. doi: 10.1016/j.cclet.2024.110318
14. [14]
  He Yao , Wenhao Ji , Yi Feng , Chunbo Qian , Chengguang Yue , Yue Wang , Shouying Huang , Mei-Yan Wang , Xinbin Ma . Copper-catalyzed and biphosphine ligand controlled 3,4-boracarboxylation of 1,3-dienes with carbon dioxide. Chinese Chemical Letters, 2025, 36(4): 110076-. doi: 10.1016/j.cclet.2024.110076
15. [15]
  Jia JI , Zhaoyang GUO , Wenni LEI , Jiawei ZHENG , Haorong QIN , Jiahong YAN , Yinling HOU , Xiaoyan XIN , Wenmin WANG . Two dinuclear Gd(Ⅲ)-based complexes constructed by a multidentate diacylhydrazone ligand: Crystal structure, magnetocaloric effect, and biological activity. Chinese Journal of Inorganic Chemistry, 2025, 41(4): 761-772. doi: 10.11862/CJIC.20240344
16. [16]
  Ruowen Liang , Chao Zhang , Guiyang Yan . Enhancing CO2 cycloaddition through ligand functionalization: A case study of UiO-66 metal-organic frameworks. Chinese Journal of Structural Chemistry, 2024, 43(2): 100211-100211. doi: 10.1016/j.cjsc.2023.100211
17. [17]
  Ruike Hu , Kangmin Wang , Junxiang Liu , Jingxian Zhang , Guoliang Yang , Liqiu Wan , Bijin Li . Extended π-conjugated systems by external ligand-assisted C−H olefination of heterocycles: Facile access to single-molecular white-light-emitting and NIR fluorescence materials. Chinese Chemical Letters, 2025, 36(4): 110113-. doi: 10.1016/j.cclet.2024.110113
18. [18]
  Haiming Wu , Gaya N. Andrew , Rajini Anumula , Zhixun Luo . Corrigendum to 'How ligand coordination and superatomic-states accommodate the structure and property of a metal cluster: Cu₄ (dppy)₄ Cl₂ vs. Cu₂₁ (dppy)₁₀ with altered photoluminescence' [Chin. Chem. Lett. 35 (2024) 108340]. Chinese Chemical Letters, 2024, 35(12): 109912-. doi: 10.1016/j.cclet.2024.109912

Get Citation

PDF

XML

Metrics

PDF Downloads(0)
Abstract views(664)
HTML views(16)

通讯作者: 陈斌, bchen63@163.com

1.
沈阳化工大学材料科学与工程学院沈阳 110142

Address：Zhongguancun North First Street 2,100190 Beijing, PR China Tel: +86-010-82449177-888

DownLoad: Full-Size Img PowerPoint

Return