1.结构准备 从RCSB蛋白质数据库中下载PARP1的3D晶体结构（PDB:4UND），其中PARP1与已知的BMN673的抑制剂复合。该结构用于确定PARP1的结合位点。使用UCSF Chimera程序包准备和分析PARP1晶体结构；除去溶剂和非络合离子，然后加氢和加电荷。使用AnalytiCon Discovery NP的天然化合物分子库，所包含化合物从ZINC数据库下载。
1.结构准备 从RCSB蛋白质数据库中下载PARP1的3D晶体结构(PDB:4UND),其中PARP1与已知的BMN673的抑制剂复合。该结构用于确定PARP1的结合位点。使用UCSF Chimera程序包准备和分析PARP1晶体结构;除去溶剂和非络合离子,然后加氢和加电荷。 使用AnalytiCon Discovery NP的天然化合物分子库,所包含化合物从ZINC数据库下载。所...
PARP1 has six domains from N- to C-terminus: zinc finger 1 (Zn1; PDB: 3ODA), zinc finger 2 (Zn2; PDB: 3ODE), zinc finger 3 (Zn3; PDB: 2JVN), BRCA-1 C-terminus fold (BRCT; PDB: 2COK), Tryptophan–Glycine–Arginine domain (WGR; PDB: 2CR9), and catalytic domain (CAT;...
采用分子对接技术研究化合物1与受体PARP1的结合模式(图1)。 图1.化合物1的化学结构 2.计算方法 从RCSB Protein Data Bank(http://www.rcsb.org)下载PARP1的X-ray晶体结构(PDB 编号:4RV6,分辨率:3.19 Å),以第一个构象作为受体结构。 [1].采用UCSF Chimera软件建立化合物1的三维结构,并进行能量优化。 [...
分子对接分析表明,PARP1催化结构域可以与PPFIA1 (PDB: 3TAC)和ABL1 (PDB: 5HU9)结合(图5B,C)。ABL1的结构域取自PDB (F-actin PDB),分子对接分析结果显示,ABL1的F-actin结构域可以与PARP1的催化结构域对接(图5D),而SH2结构域不能与PARP1的催化结构域对接。由于无法获得BCR/ABL融合蛋白,研究者纯化了...
Since there is no complete structural information of the PARP-1/E2F1 protein-protein interaction, a homologous structure of BRCT domain of BRCA1 complex with the phospho-peptide (PDBID: 1T2V) was utilized to identify the potential binding interface of BRCT domain of PARP-1 (PDBID: 2COK) ...
d Model of PARP1 (surface representation coloured according to domain composition) bound to a single-strand DNA break (red ribbon) created by alignment of structures from PDB accessions 4DQY, 2N8A and 2LE0. The auto-modification fragment missing from the structures is shown schematically and ...
43. These residues were defined as active site to study interactions between Banf1 and PARP1. The catalytic domain of PARP1 (pdb code 4DQY; chain C)44and Banf1 dimer (Pdb code 2BZF)45were submitted to a protein–protein docking evaluation using the ClusPro2.0 server46. This server ...
PARP_1抑制剂的研究进展_赵海龙
The 3D structures of the receptor proteins PARP1 and HMGB1 were obtained from the Protein Data Bank (PDB, https://www1.rcsb.org/). Using PyMOL 2.3.0 software, water molecules, irrelevant protein chains, and existing ligands were removed. The structures of small-molecule compounds were downloa...