Guanosine diphosphate (BioDeep_00000001615)

 

Secondary id: BioDeep_00000405424, BioDeep_00000413232, BioDeep_00001868316

natural product human metabolite PANOMIX_OTCML-2023 Endogenous blood metabolite BioNovoGene_Lab2019


代谢物信息卡片


[({[(2R,3S,4R,5R)-5-(2-amino-6-oxo-6,9-dihydro-3H-purin-9-yl)-3,4-dihydroxyoxolan-2-yl]methoxy}(hydroxy)phosphoryl)oxy]phosphonic acid

化学式: C10H15N5O11P2 (443.0243)
中文名称: 鸟苷-5-二磷酸, 二磷酸鸟苷
谱图信息: 最多检出来源 Homo sapiens(plant) 12.55%

Reviewed

Last reviewed on 2024-07-23.

Cite this Page

Guanosine diphosphate. BioDeep Database v3. PANOMIX ltd, a top metabolomics service provider from China. https://query.biodeep.cn/s/guanosine_diphosphate (retrieved 2024-12-23) (BioDeep RN: BioDeep_00000001615). Licensed under the Attribution-Noncommercial 4.0 International License (CC BY-NC 4.0).

分子结构信息

SMILES: C([C@@H]1[C@H]([C@H]([C@H](n2cnc3c2nc(N)[nH]c3=O)O1)O)O)OP(=O)(O)OP(=O)(O)O
InChI: InChI=1S/C10H15N5O11P2/c11-10-13-7-4(8(18)14-10)12-2-15(7)9-6(17)5(16)3(25-9)1-24-28(22,23)26-27(19,20)21/h2-3,5-6,9,16-17H,1H2,(H,22,23)(H2,19,20,21)(H3,11,13,14,18)

描述信息

Guanosine diphosphate, also known as gdp or 5-diphosphate, guanosine, is a member of the class of compounds known as purine ribonucleoside diphosphates. Purine ribonucleoside diphosphates are purine ribobucleotides with diphosphate group linked to the ribose moiety. Guanosine diphosphate is slightly soluble (in water) and a moderately acidic compound (based on its pKa). Guanosine diphosphate can be found in a number of food items such as strawberry, onion-family vegetables, walnut, and scarlet bean, which makes guanosine diphosphate a potential biomarker for the consumption of these food products. Guanosine diphosphate can be found primarily in blood and cerebrospinal fluid (CSF). Guanosine diphosphate exists in all living species, ranging from bacteria to humans. In humans, guanosine diphosphate is involved in several metabolic pathways, some of which include betahistine h1-antihistamine action, fexofenadine h1-antihistamine action, clocinizine h1-antihistamine action, and bepotastine h1-antihistamine action. Guanosine diphosphate is also involved in several metabolic disorders, some of which include adenine phosphoribosyltransferase deficiency (APRT), canavan disease, gout or kelley-seegmiller syndrome, and pyruvate dehydrogenase complex deficiency. Moreover, guanosine diphosphate is found to be associated with epilepsy, subarachnoid hemorrhage, neuroinfection, and stroke. Guanosine diphosphate, abbreviated GDP, is a nucleoside diphosphate. It is an ester of pyrophosphoric acid with the nucleoside guanosine. GDP consists of the pyrophosphate group, the pentose sugar ribose, and the nucleobase guanine .
Guanosine diphosphate, also known as 5-GDP or 5-diphosphate, guanosine, belongs to the class of organic compounds known as purine ribonucleoside diphosphates. These are purine ribobucleotides with diphosphate group linked to the ribose moiety. Guanosine diphosphate exists in all living species, ranging from bacteria to humans. In humans, guanosine diphosphate is involved in intracellular signalling through adenosine receptor A2B and adenosine. Outside of the human body, Guanosine diphosphate has been detected, but not quantified in several different foods, such as devilfish, java plums, green beans, almonds, and orange mints. Guanosine diphosphate is a purine ribonucleoside 5-diphosphate resulting from the formal condensation of the hydroxy group at the 5 position of guanosine with pyrophosphoric acid.
COVID info from COVID-19 Disease Map, PDB, Protein Data Bank
Corona-virus
Coronavirus
SARS-CoV-2
COVID-19
SARS-CoV
COVID19
SARS2
SARS

同义名列表

27 个代谢物同义名

[({[(2R,3S,4R,5R)-5-(2-amino-6-oxo-6,9-dihydro-3H-purin-9-yl)-3,4-dihydroxyoxolan-2-yl]methoxy}(hydroxy)phosphoryl)oxy]phosphonic acid; {[(2R,3S,4R,5R)-5-(2-amino-6-oxo-3H-purin-9-yl)-3,4-dihydroxyoxolan-2-yl]methoxy(hydroxy)phosphoryl}oxyphosphonic acid; 5-guanylate diphosphate (guanosine diphosphate); Guanosine mono(trihydrogen diphosphate); Guanosine 5-(trihydrogen pyrophosphate); Diphosphate, guanosine 5-trihydrogen; 5-Trihydrogen diphosphate, guanosine; Guanosine 5-trihydrogen diphosphate; Guanosine 5 trihydrogen diphosphate; Guanosine-5-diphosphate sodium salt; Guanosine 5-diphosphoric acid; Guanosine diphosphoric acid; Guanosine 5-pyrophosphate; 5-Diphosphate, guanosine; Guanosine 5-diphosphate; Guanosine pyrophosphate; Guanosine 5 diphosphate; Guanosine-5-diphosphate; Diphosphate, guanosine; guanosine diphos-phate; Guanosine-diphosphate; Guanosine diphosphate; 5-GDP; PpG; GDP; Guanosine diphosphate(GDP); GDP



数据库引用编号

27 个数据库交叉引用编号

分类词条

相关代谢途径

Reactome(29)

BioCyc(10)

PlantCyc(9)

代谢反应

3463 个相关的代谢反应过程信息。

Reactome(1067)

BioCyc(20)

WikiPathways(1)

Plant Reactome(965)

INOH(47)

PlantCyc(1036)

COVID-19 Disease Map(2)

PathBank(325)

PharmGKB(0)

4 个相关的物种来源信息

在这里通过桑基图来展示出与当前的这个代谢物在我们的BioDeep知识库中具有相关联信息的其他代谢物。在这里进行关联的信息来源主要有:

  • PubMed: 来源于PubMed文献库中的文献信息,我们通过自然语言数据挖掘得到的在同一篇文献中被同时提及的相关代谢物列表,这个列表按照代谢物同时出现的文献数量降序排序,取前10个代谢物作为相关研究中关联性很高的代谢物集合展示在桑基图中。
  • NCBI Taxonomy: 通过文献数据挖掘,得到的代谢物物种来源信息关联。这个关联信息同样按照出现的次数降序排序,取前10个代谢物作为高关联度的代谢物集合展示在桑吉图上。
  • Chemical Taxonomy: 在物质分类上处于同一个分类集合中的其他代谢物
  • Chemical Reaction: 在化学反应过程中,存在为当前代谢物相关联的生化反应过程中的反应底物或者反应产物的关联代谢物信息。

点击图上的相关代谢物的名称,可以跳转到相关代谢物的信息页面。

亚细胞结构定位 关联基因列表
Cytoplasm 11 ARHGDIA, ARHGDIB, CDC42, CMPK2, GMDS, GNAQ, RAC1, RELA, RHOA, SLC2A4RG, TUBB4B
Endoplasmic reticulum membrane 3 CDC42, RAC1, RHOA
Nucleus 7 ARHGDIA, GNAQ, RAC1, RELA, RHOA, SLC2A4RG, TUBB4B
cytosol 9 ARHGDIA, ARHGDIB, CDC42, FCSK, GMDS, RAC1, RELA, RHOA, TUBB4B
dendrite 1 RAC1
phagocytic vesicle 1 CDC42
trans-Golgi network 1 RAC1
centrosome 1 CDC42
nucleoplasm 2 CMPK2, RELA
Cell membrane 4 CDC42, GNAQ, RAC1, RHOA
Lipid-anchor 4 CDC42, GNAQ, RAC1, RHOA
Cytoplasmic side 3 CDC42, RAC1, RHOA
Cleavage furrow 1 RHOA
lamellipodium 2 RAC1, RHOA
ruffle membrane 2 RAC1, RHOA
Multi-pass membrane protein 3 RHO, UCP1, UCP2
Synapse 3 CRH, GNAQ, RAC1
cell cortex 2 RAC1, RHOA
cell junction 1 RHOA
glutamatergic synapse 4 CDC42, RAC1, RELA, RHOA
Golgi apparatus 3 FUT2, GNAQ, RHO
Golgi membrane 4 CDC42, FUT2, INS, RHO
lysosomal membrane 1 GNAQ
mitochondrial inner membrane 2 UCP1, UCP2
neuronal cell body 1 CDC42
postsynapse 2 RAC1, RHOA
Cytoplasm, cytosol 1 ARHGDIB
endosome 1 RHOA
plasma membrane 6 CDC42, GCG, GNAQ, RAC1, RHO, RHOA
Membrane 6 ARHGDIA, ARHGDIB, CDC42, GNAQ, RAC1, RHO
extracellular exosome 9 ARHGDIA, ARHGDIB, CDC42, FUT2, GMDS, GNAQ, RAC1, RHOA, TUBB4B
extracellular space 4 CRH, GCG, IL6, INS
Schaffer collateral - CA1 synapse 2 ARHGDIA, CDC42
mitochondrion 3 CMPK2, UCP1, UCP2
protein-containing complex 1 CDC42
filopodium 1 CDC42
Secreted 5 CRH, GCG, IL6, INS, RAC1
extracellular region 6 CRH, GCG, IL6, INS, RAC1, TUBB4B
cytoplasmic side of plasma membrane 1 RHOA
transcription regulator complex 1 RELA
ciliary membrane 1 RHO
photoreceptor inner segment 1 RHO
photoreceptor outer segment 2 GNAQ, RHO
Cytoplasm, cytoskeleton, microtubule organizing center, centrosome 1 CDC42
Nucleus membrane 1 GNAQ
nuclear membrane 1 GNAQ
varicosity 1 CRH
Extracellular vesicle 1 TUBB4B
dendritic spine 3 CDC42, RAC1, RHOA
neuronal dense core vesicle lumen 1 CRH
perikaryon 1 CRH
cytoplasmic vesicle 2 ARHGDIB, RAC1
microtubule cytoskeleton 1 TUBB4B
midbody 2 CDC42, RHOA
apical part of cell 1 CDC42
cell-cell junction 2 CDC42, RHO
spindle midzone 1 CDC42
Single-pass type II membrane protein 1 FUT2
vesicle 1 RHOA
Cell projection, lamellipodium 2 RAC1, RHOA
Mitochondrion inner membrane 2 UCP1, UCP2
Cytoplasm, cytoskeleton 1 TUBB4B
Cytoplasm, cytoskeleton, spindle 1 CDC42
focal adhesion 3 CDC42, RAC1, RHOA
microtubule 1 TUBB4B
secretory granule 1 CDC42
nuclear speck 1 SLC2A4RG
neuron projection 1 CDC42
chromatin 1 RELA
cell periphery 1 RHOA
mitotic spindle 2 CDC42, TUBB4B
cytoskeleton 5 ARHGDIA, ARHGDIB, RAC1, RHOA, TUBB4B
cytoplasmic ribonucleoprotein granule 2 CDC42, RAC1
Cell projection, cilium, photoreceptor outer segment 1 RHO
Cytoplasm, cell cortex 1 RHOA
sperm midpiece 1 RHO
intercellular bridge 1 TUBB4B
Cytoplasm, cytoskeleton, flagellum axoneme 1 TUBB4B
sperm flagellum 1 TUBB4B
Recycling endosome membrane 1 RAC1
endosome lumen 1 INS
axonemal microtubule 1 TUBB4B
heterotrimeric G-protein complex 1 GNAQ
leading edge membrane 1 CDC42
Cell projection, dendrite 3 CDC42, RAC1, RHOA
Melanosome 1 RAC1
Golgi cisterna membrane 1 FUT2
Golgi-associated vesicle membrane 1 RHO
secretory granule lumen 2 GCG, INS
secretory granule membrane 2 RAC1, RHOA
Golgi lumen 1 INS
endoplasmic reticulum lumen 3 GCG, IL6, INS
Photoreceptor inner segment membrane 1 RHO
transport vesicle 1 INS
azurophil granule lumen 1 TUBB4B
Golgi apparatus, Golgi stack membrane 1 FUT2
Endoplasmic reticulum-Golgi intermediate compartment membrane 1 INS
immunological synapse 1 ARHGDIA
ficolin-1-rich granule membrane 2 RAC1, RHOA
apical junction complex 1 RHOA
photoreceptor outer segment membrane 1 RHO
sperm head plasma membrane 1 RHO
photoreceptor disc membrane 1 RHO
[Glucagon-like peptide 1]: Secreted 1 GCG
NADPH oxidase complex 1 RAC1
interleukin-6 receptor complex 1 IL6
rod photoreceptor outer segment 1 RHO
NF-kappaB p50/p65 complex 1 RELA
NF-kappaB complex 1 RELA
Golgi transport complex 1 CDC42
storage vacuole 1 CDC42


文献列表

  • Xiangning Liu, Xiang Yu, Yue Shi, Liang Ma, Ying Fu, Yan Guo. Phosphorylation of RhoGDI1, a Rho GDP dissociation inhibitor, regulates root hair development in Arabidopsis under salt stress. Proceedings of the National Academy of Sciences of the United States of America. 2023 08; 120(34):e2217957120. doi: 10.1073/pnas.2217957120. [PMID: 37590409]
  • H Y Bao, W Wang, H B Sun, J Z Chen. Binding modes of GDP, GTP and GNP to NRAS deciphered by using Gaussian accelerated molecular dynamics simulations. SAR and QSAR in environmental research. 2023 Jan; 34(1):65-89. doi: 10.1080/1062936x.2023.2165542. [PMID: 36762439]
  • Bowen Zhan, Yanqing Gao, Wenqing Gao, Ye Li, Zhengyang Li, Qi Qi, Xin Lan, Hongbo Shen, Jianhua Gan, Guoping Zhao, Jixi Li. Structural insights of the elongation factor EF-Tu complexes in protein translation of Mycobacterium tuberculosis. Communications biology. 2022 10; 5(1):1052. doi: 10.1038/s42003-022-04019-y. [PMID: 36192483]
  • Giang Pham, Dong-Min Shin, Yoon Kim, Soo-Hwan Kim. Ran-GTP/-GDP-dependent nuclear accumulation of NONEXPRESSOR OF PATHOGENESIS-RELATED GENES1 and TGACG-BINDING FACTOR2 controls salicylic acid-induced leaf senescence. Plant physiology. 2022 06; 189(3):1774-1793. doi: 10.1093/plphys/kiac164. [PMID: 35417014]
  • Yuan Chen, Peng Shu, Ruochen Wang, Xiaofei Du, Yue Xie, Kui Du, Heng Deng, Mingzhang Li, Yang Zhang, Don Grierson, Mingchun Liu. Ethylene response factor AcERF91 affects ascorbate metabolism via regulation of GDP-galactose phosphorylase encoding gene (AcGGP3) in kiwifruit. Plant science : an international journal of experimental plant biology. 2021 Dec; 313(?):111063. doi: 10.1016/j.plantsci.2021.111063. [PMID: 34763857]
  • Hiroshi Senoo, Daisuke Murata, May Wai, Kenta Arai, Wakiko Iwata, Hiromi Sesaki, Miho Iijima. KARATE: PKA-induced KRAS4B-RHOA-mTORC2 supercomplex phosphorylates AKT in insulin signaling and glucose homeostasis. Molecular cell. 2021 11; 81(22):4622-4634.e8. doi: 10.1016/j.molcel.2021.09.001. [PMID: 34551282]
  • Natsumi Maruta, Yuri Trusov, Alan M Jones, Jose R Botella. Heterotrimeric G Proteins in Plants: Canonical and Atypical Gα Subunits. International journal of molecular sciences. 2021 Oct; 22(21):. doi: 10.3390/ijms222111841. [PMID: 34769272]
  • Ying Liu, Xiaoyun Wang, Danhui Dong, Luqin Guo, Xiaonan Dong, Jing Leng, Bing Zhao, Yang-Dong Guo, Na Zhang. Research Advances in Heterotrimeric G-Protein α Subunits and Uncanonical G-Protein Coupled Receptors in Plants. International journal of molecular sciences. 2021 Aug; 22(16):. doi: 10.3390/ijms22168678. [PMID: 34445383]
  • Jianzhong Chen, Lifei Wang, Wei Wang, Haibo Sun, Laixue Pang, Huayin Bao. Conformational transformation of switch domains in GDP/K-Ras induced by G13 mutants: An investigation through Gaussian accelerated molecular dynamics simulations and principal component analysis. Computers in biology and medicine. 2021 08; 135(?):104639. doi: 10.1016/j.compbiomed.2021.104639. [PMID: 34247129]
  • Mario Fenech, Vítor Amorim-Silva, Alicia Esteban Del Valle, Dominique Arnaud, Noemi Ruiz-Lopez, Araceli G Castillo, Nicholas Smirnoff, Miguel A Botella. The role of GDP-l-galactose phosphorylase in the control of ascorbate biosynthesis. Plant physiology. 2021 04; 185(4):1574-1594. doi: 10.1093/plphys/kiab010. [PMID: 33793952]
  • Meng Zhang, Miao Gui, Zi-Fu Wang, Christoph Gorgulla, James J Yu, Hao Wu, Zhen-Yu J Sun, Christoph Klenk, Lisa Merklinger, Lena Morstein, Franz Hagn, Andreas Plückthun, Alan Brown, Mahmoud L Nasr, Gerhard Wagner. Cryo-EM structure of an activated GPCR-G protein complex in lipid nanodiscs. Nature structural & molecular biology. 2021 03; 28(3):258-267. doi: 10.1038/s41594-020-00554-6. [PMID: 33633398]
  • Toshihiro Kishikawa, Yuichi Maeda, Takuro Nii, Noriko Arase, Jun Hirata, Ken Suzuki, Kenichi Yamamoto, Tatsuo Masuda, Kotaro Ogawa, Shigeyoshi Tsuji, Masato Matsushita, Hidetoshi Matsuoka, Maiko Yoshimura, Shinichiro Tsunoda, Shiro Ohshima, Masashi Narazaki, Atsushi Ogata, Yukihiko Saeki, Hidenori Inohara, Atsushi Kumanogoh, Kiyoshi Takeda, Yukinori Okada. Increased levels of plasma nucleotides in patients with rheumatoid arthritis. International immunology. 2021 01; 33(2):119-124. doi: 10.1093/intimm/dxaa059. [PMID: 32866240]
  • Andrés Tolosa-Díaz, Víctor G Almendro-Vedia, Paolo Natale, Iván López-Montero. The GDP-Bound State of Mitochondrial Mfn1 Induces Membrane Adhesion of Apposing Lipid Vesicles through a Cooperative Binding Mechanism. Biomolecules. 2020 07; 10(7):. doi: 10.3390/biom10071085. [PMID: 32708307]
  • Li Wan, Yingying Zhu, Wen Li, Wenli Zhang, Wanmeng Mu. Combinatorial Modular Pathway Engineering for Guanosine 5'-Diphosphate-l-fucose Production in Recombinant Escherichia coli. Journal of agricultural and food chemistry. 2020 May; 68(20):5668-5675. doi: 10.1021/acs.jafc.0c01064. [PMID: 32336091]
  • Liming Yan, Yuanbo Qi, Derek Ricketson, Lei Li, Kelly Subramanian, Jinghua Zhao, Caiting Yu, Lijie Wu, Reta Sarsam, Melissa Wong, Zhiyong Lou, Zihe Rao, Jodi Nunnari, Junjie Hu. Structural analysis of a trimeric assembly of the mitochondrial dynamin-like GTPase Mgm1. Proceedings of the National Academy of Sciences of the United States of America. 2020 02; 117(8):4061-4070. doi: 10.1073/pnas.1919116117. [PMID: 32041880]
  • Matías L Alegre, Charlotte Steelheart, Pierre Baldet, Christophe Rothan, Daniel Just, Yoshihiro Okabe, Hiroshi Ezura, Nicholas Smirnoff, Gustavo E Gergoff Grozeff, Carlos G Bartoli. Deficiency of GDP-L-galactose phosphorylase, an enzyme required for ascorbic acid synthesis, reduces tomato fruit yield. Planta. 2020 Jan; 251(2):54. doi: 10.1007/s00425-020-03345-x. [PMID: 31970534]
  • Sanchaita Das, Andrew W Malaby, Agata Nawrotek, Wenhua Zhang, Mahel Zeghouf, Sarah Maslen, Mark Skehel, Srinivas Chakravarthy, Thomas C Irving, Osman Bilsel, Jacqueline Cherfils, David G Lambright. Structural Organization and Dynamics of Homodimeric Cytohesin Family Arf GTPase Exchange Factors in Solution and on Membranes. Structure (London, England : 1993). 2019 12; 27(12):1782-1797.e7. doi: 10.1016/j.str.2019.09.007. [PMID: 31601460]
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