2'-脱氧腺苷-5'-二磷酸酯 | 2793-06-8

• 分子结构分类: 有机化合物 - 核苷、核苷酸和类似物 - 嘌呤核苷酸
• 中文名称: 2'-脱氧腺苷-5'-二磷酸酯
• 英文名称: d-ADP
• 英文别名: 2'-deoxyadenosine 5'-diphosphate；deoxyadenosine 5'-diphosphate；deoxyadenosine diphosphate；adenosine diphosphate；D-2'-dADP；14c-dadp；2'-Deoxyadenosine-5'-diphosphate；[(2R,3S,5R)-5-(6-aminopurin-9-yl)-3-hydroxyoxolan-2-yl]methyl phosphono hydrogen phosphate
• CAS: 2793-06-8
• 化学式: C₁₀H₁₅N₅O₉P₂
• 分子量: 411.205
• InChiKey: DAEAPNUQQAICNR-RRKCRQDMSA-N

计算性质

• 辛醇/水分配系数(LogP)：
  -3.3
• 重原子数：
  26
• 可旋转键数：
  6
• 环数：
  3.0
• sp3杂化的碳原子比例：
  0.5
• 拓扑面积：
  212
• 氢给体数：
  5
• 氢受体数：
  13

反应信息

• 作为反应物：
  描述：

  2'-脱氧腺苷-5'-二磷酸酯 在 Tris-Cl buffer 、 水 、 magnesium sulfate 作用下， 生成 2'-脱氧腺苷-5'-单磷酸
  参考文献：
  名称：

  Synthesis and Stability of Novel Terminal Phosphate-Labeled Nucleotides

  摘要：

  Novel compounds consisting of a nucleotide triphosphate labeled with a PEG linker and various terminal groups attached to the -phosphate of the nucleotide were constructed for use in efforts to produce a new class of DNA sequencer. The stability of these novel compounds was investigated to determine their utility as sequencing reagents. Hydrolysis rate constants were measured for both the natural nucleoside triphosphate dATP and novel dATP derivatives. The -labeled dATP was approximately 20-fold more stable to hydrolysis than dATP.

  DOI：

  10.1080/15257770701571768
• 作为产物：
  描述：

  二磷酸腺苷 在 adenosylcobalamin 、 full-length enzyme NrdJd-wt from Stackebrandtia nassauensis 、 2'-脱氧鸟苷 5'-(四氢三磷酸酯) 、 magnesium chloride 、 Cleland's reagent 作用下， 以 aq. buffer 为溶剂， 生成 2'-脱氧腺苷-5'-二磷酸酯
  参考文献：
  名称：

  存在于大多数II类核糖核苷酸还原酶中的独特的富含半胱氨酸的锌指结构域介导催化转换。

  摘要：

  核糖核苷酸还原酶（RNR）催化核糖核苷酸还原为相应的脱氧核糖核苷酸，用于DNA合成和修复。两种不同的机制有助于将所需的电子传递到RNR活性位点。甲酸酯可直接在活性位点用作还原剂，或戊二醛毒素或硫氧还蛋白还原C端半胱氨酸对，然后将电子传递至活性位点。在这里，我们表征了一个新颖的富含半胱氨酸的C末端结构域（CRD），它存在于微生物中发现的大多数II类RNR中。来自nassauensis Stackebrandtia nassauensis细菌的NrdJd型RNR被用作模型酶。我们表明CRD参与较高的低聚物状态形成和电子转移到活性位点。高聚物（例如四聚物和六聚物）的CRD依赖性形成 通过添加dATP或dGTP而不是dTTP或dCTP来诱导细胞凋亡。电子转移是由在C末端的六个半胱氨酸残基阵列介导的，这些残基也与锌原子配位。电子转移也可能发生在亚基之间，具体取决于酶的低聚状态。对系统天然还原剂的研究

  DOI：

  10.1074/jbc.m117.806331

文献信息

• Nucleotide promiscuity of 3-phosphoglycerate kinase is in focus: implications for the design of better anti-HIV analogues
  作者：Andrea Varga、Laurent Chaloin、Gyula Sági、Róbert Sendula、Éva Gráczer、Károly Liliom、Péter Závodszky、Corinne Lionne、Mária Vas

  DOI：10.1039/c1mb05051f

  日期：——

  The wide specificity of 3-phosphoglycerate kinase (PGK) towards its nucleotide substrate is a property that allows contribution of this enzyme to the effective phosphorylation (i.e.activation) of nucleotide-based pro-drugs against HIV. Here, the structural basis of the nucleotide-PGK interaction is characterised in comparison to other kinases, namely pyruvate kinase (PK) and creatine kinase (CK), by enzyme kinetic analysis and structural modelling (docking) studies. The results provided evidence for favouring the purinevs.pyrimidine base containing nucleotides for PGK rather than for PK or CK. This is due to the exceptional ability of PGK in forming the hydrophobic contacts of the nucleotide rings that assures the appropriate positioning of the connected phosphate-chain for catalysis. As for the D-/L-configurations of the nucleotides, the L-forms (both purine and pyrimidine) are well accepted by PGK rather than either by PK or CK. Here again the dominance of the hydrophobic interactions of the L-form of pyrimidines with PGK is underlined in comparison with those of PK or CK. Furthermore, for the L-forms, the absence of the ribose OH-groups with PGK is better tolerated for the purine than for the pyrimidine containing compounds. On the other hand, the positioning of the phosphate-chain is an even more important term for PGK in the case of both purines and pyrimidines with an L-configuration, as deduced from the present kinetic studies with various nucleotide-site mutants of PGK. These characteristics of the kinase-nucleotide interactions can provide a guideline for designing new drugs.

  3-磷酸甘油酸激酶（PGK）对其核苷酸底物的广泛特异性是一种特性，使得这种酶能够有效地磷酸化（即激活）基于核苷酸的抗HIV前药。在此，通过酶动力学分析和结构建模（对接）研究，与其它激酶（即丙酮酸激酶（PK）和肌酸激酶（CK））相比，对核苷酸-PGK相互作用的结构基础进行了表征。结果提供了证据，表明对于PGK来说，含有嘌呤与嘧啶的核苷酸更受青睐，而不是对于PK或CK。这是由于PGK在形成核苷酸环疏水接触方面的特殊能力，确保了连接的磷酸链在催化中的适当定位。至于核苷酸的D-/L-构型，L型（嘌呤和嘧啶）被PGK很好地接受，而不是由PK或CK接受。在这里，与PK或CK相比，嘧啶L型的疏水相互作用的支配性再次得到强调。此外，对于L型，PGK没有核糖OH基团的存在对嘌呤比对含有嘧啶的化合物更被接受。另一方面，从PGK的各种核苷酸位点突变体的当前动力学研究中推断出，无论是在嘌呤还是嘧啶的L型化合物中，磷酸链的定位对于PGK来说都是一个更为重要的术语。这些激酶-核苷酸相互作用的特性为设计新药物提供了指导。
• REAGENTS AND METHODS FOR REPLICATION, TRANSCRIPTION, AND TRANSLATION IN SEMI-SYNTHETIC ORGANISMS
  申请人：The Scripps Research Institute

  公开号：US20200392550A1

  公开（公告）日：2020-12-17

  Disclosed herein are compositions, methods, cells, engineered microorganisms, and kits for increasing the production of proteins or polypeptides comprising one or more unnatural amino acids. Further provided are compositions, cells, engineered microorganisms, and kits for increasing the retention of unnatural nucleic acids encoding the unnatural amino acids in an engineered cell, or semi-synthetic organism.

  本文揭示了一种用于增加含有一个或多个非天然氨基酸的蛋白质或多肽的生产的组合物、方法、细胞、工程微生物和试剂盒。此外，还提供了一种用于增加编码非天然氨基酸的非天然核酸在工程细胞或半合成生物体中的保留的组合物、细胞、工程微生物和试剂盒。
• INORGANIC-ORGANIC HYBRID COMPOUNDS INCLUDING ORGANIC PLATINUM-CONTAINING ANIONS, FOR USE IN MEDICINE
  申请人：Karlsruher Institut fur Technologie

  公开号：US20210292353A1

  公开（公告）日：2021-09-23

  The present invention relates to inorganic-organic hybrid compounds for use in medicine or for use as medication, consisting of an inorganic metal cation and an organic platinum-containing cytostatic anion, in particular also a cisplatin derivative.

  本发明涉及用于医学或作为药物使用的无机-有机杂化化合物，包括无机金属阳离子和含有铂的细胞静止阴离子，特别是顺铂衍生物。
• Nucleoside Diphosphate Kinase and the Activation of Antiviral Phosphonate Analogs of Nucleotides: Binding Mode and Phosphorylation of Tenofovir Derivatives
  作者：Kerstin Koch、Yuxing Chen、Joy Y. Feng、Katyna Borroto-Esoda、Dominique Deville-Bonne、Joël Janin、Solange Moréra

  DOI：10.1080/15257770903155899

  日期：2009.9.11

  Tenofovir is an acyclic phosphonate analog of deoxyadenylate used in AIDS and hepatitis B therapy. We find that tenofovir diphosphate, its active form, can be produced by human nucleoside diphosphate kinase (NDPK), but with low efficiency, and that creatine kinase is significantly more active. The 1.65 Å x-ray structure of NDPK in complex with tenofovir mono- and diphosphate shows that the analogs

  替诺福韦是用于艾滋病和乙肝治疗的脱氧腺苷酸的无环膦酸酯类似物。我们发现替诺福韦二磷酸，其活性形式，可以由人核苷二磷酸激酶（NDPK）产生，但效率较低，并且肌酸激酶的活性明显更高。与替诺福韦单磷酸酯和二磷酸酯复合的NDPK的1.65Åx射线结构表明，类似物与天然核苷酸在同一位点结合，但构象不同，仅形成范德华力和极性相互作用的一部分天然底物，与其对酶的亲和力较低相符。
• INOSINE GUANOSINE KINASE
  申请人：KYOWA HAKKO KOGYO CO., LTD.

  公开号：EP0458971A1

  公开（公告）日：1991-12-04

  An inosine guanosine kinase and a process for producing 5'-nucleotides by using the same, said enzyme catalysing the formation of 5'-inosinic acid (5'-IMP) from inosine and adenosine triphosphate (ATP) or deoxyadenosine triphosphate (dATP) and the formation of 5'-guanylic acid (5'-GMP) from guanosine and ATP or dATP.

  一种肌苷鸟苷激酶和使用该酶生产 5'-核苷酸的工艺，所述酶催化肌苷和三磷酸腺苷（ATP）或三磷酸脱氧腺苷（dATP）形成 5'-肌苷酸（5'-IMP），以及鸟苷和 ATP 或 dATP 形成 5'-鸟苷酸（5'-GMP）。