dGDP (BioDeep_00000001618)

 

Secondary id: BioDeep_00001868838

natural product human metabolite Endogenous BioNovoGene_Lab2019


Metabolite Card


[({[(2R,3S,5R)-5-(2-amino-6-oxo-6,9-dihydro-1H-purin-9-yl)-3-hydroxyoxolan-2-yl]methoxy}(hydroxy)phosphoryl)oxy]phosphonic acid

  Formula: C10H15N5O10P2 (427.0294)
Chinese Names: 2'-脱氧鸟苷-5'-二磷酸
  Spectrum Hits: Top Source Homo sapiens(plant) 3.9%

Molecular Structure

SMILES: C1C(C(OC1N2C=NC3=C2N=C(NC3=O)N)COP(=O)(O)OP(=O)(O)O)O
InChI: InChI=1/C10H15N5O10P2/c11-10-13-8-7(9(17)14-10)12-3-15(8)6-1-4(16)5(24-6)2-23-27(21,22)25-26(18,19)20/h3-6,16H,1-2H2,(H,21,22)(H2,18,19,20)(H3,11,13,14,17)/t4-,5+,6+/m0/s1/f/h13,18-19,21H,11H2


Description

dGDP is a derivative of the common nucleic acid GTP, or guanosine triphosphate, in which the -OH (hydroxyl) group on the 2 carbon on the nucleotides pentose has been removed (hence the deoxy- part of the name). Additionally, the diphosphate of the name indicates that one of the phosphoryl groups of GTP has been removed, most likely by hydrolysis . [HMDB]. dGDP is found in many foods, some of which are tea, black chokeberry, european plum, and roman camomile.
dGDP is a derivative of the common nucleic acid GTP, or guanosine triphosphate, in which the -OH (hydroxyl) group on the 2 carbon on the nucleotides pentose has been removed (hence the deoxy- part of the name). Additionally, the diphosphate of the name indicates that one of the phosphoryl groups of GTP has been removed, most likely by hydrolysis (Wikipedia).
Acquisition and generation of the data is financially supported in part by CREST/JST.
COVID info from COVID-19 Disease Map
Corona-virus
Coronavirus
SARS-CoV-2
COVID-19
SARS-CoV
COVID19
SARS2
SARS

Synonyms

26 synonym names

[({[(2R,3S,5R)-5-(2-amino-6-oxo-6,9-dihydro-1H-purin-9-yl)-3-hydroxyoxolan-2-yl]methoxy}(hydroxy)phosphoryl)oxy]phosphonic acid; 2-Deoxyguanosine-5-diphosphate sodium salt; 2-Deoxyguanosine 5-diphosphoric acid; Deoxyguanosine diphosphate (dGDP); Deoxyguanosine diphosphoric acid; 2-Deoxyguanosine 5-diphosphate; 2-Deoxyguanosine-5-diphosphate; Deoxyguanosine 5-diphosphate; Deoxyguanosine-diphosphate; deoxyguanosine diphosphate; 2-Deoxy-GDP; 5-dGDP; dGDP; DGI; 2'-Deoxyguanosine 5'-diphosphate(dGDP); ((2R,3S,5R)-5-(2-amino-6-oxo-1H-purin-9-yl)-3-hydroxyoxolan-2-yl)methyl phosphono hydrogen phosphate; [(2R,3S,5R)-5-(2-amino-6-oxo-1H-purin-9-yl)-3-hydroxyoxolan-2-yl]methyl phosphono hydrogen phosphate; 2 inverted exclamation marka-Deoxyguanosine 5 inverted exclamation marka-(trihydrogen diphosphate); 2'-Deoxy-GDP; 2'-deoxyguanosine 5'-(trihydrogen diphosphate); 2'-Deoxyguanosine 5'-diphosphate; 2'-deoxyguanosine-5'-diphosphate; 2invertedexclamationmarka-Deoxyguanosine5invertedexclamationmarka-(trihydrogendiphosphate); 5'-dGDP; Deoxyguanosine 5'-diphosphate; 2'-Deoxyguanosine 5'-diphosphoric acid



Cross Reference

32 cross reference id

Classification Terms

Related Pathways

Reactome()

BioCyc(3)

PlantCyc(2)

Biological Process

439 related biological process reactions.

Reactome()

BioCyc(4)

WikiPathways(1)

Plant Reactome()

INOH(3)

PlantCyc(378)

COVID-19 Disease Map(2)

PathBank(51)

PharmGKB()

2 organism taxonomy source information

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。

Sub-cellular location Genes
Cytoplasm 14 CFTR, CMPK2, DGUOK, DTYMK, GTPBP4, HPRT1, MAPT, NME1, NUDT3, PKM, PNP, PNPT1, POLB, TUBB4B
Peripheral membrane protein 2 MAPT, PNPT1
Endosome membrane 1 CFTR
Endoplasmic reticulum membrane 2 CFTR, PNPT1
Nucleus 13 CFTR, DACH1, DGUOK, DTYMK, GTPBP4, MAPT, NME1, NUDT3, NUDT5, PKM, PLCZ1, POLB, TUBB4B
cytosol 16 CFTR, DACH1, DGUOK, DTYMK, GTPBP4, GUK1, HPRT1, MAPT, NME1, NUDT3, NUDT5, PKM, PLCZ1, PNP, PNPT1, TUBB4B
dendrite 1 MAPT
nucleoplasm 5 CMPK2, DACH1, GTPBP4, PLCZ1, POLB
Cell membrane 2 CFTR, MAPT
Cytoplasmic side 1 MAPT
ruffle membrane 1 NME1
Cell projection, axon 1 MAPT
Early endosome membrane 1 CFTR
Multi-pass membrane protein 1 CFTR
cell surface 1 CFTR
glutamatergic synapse 1 NUDT3
Golgi apparatus 1 DACH1
growth cone 1 MAPT
lysosomal membrane 2 CFTR, GAA
neuronal cell body 1 MAPT
Cytoplasm, cytosol 2 GUK1, MAPT
Lysosome 1 GAA
plasma membrane 3 CFTR, GAA, MAPT
Membrane 4 CFTR, GAA, GTPBP4, NME1
apical plasma membrane 1 CFTR
axon 1 MAPT
extracellular exosome 7 GAA, HPRT1, NME1, NUDT5, PKM, PNP, TUBB4B
Lysosome membrane 1 GAA
extracellular space 1 PNP
lysosomal lumen 1 GAA
perinuclear region of cytoplasm 2 GTPBP4, PLCZ1
mitochondrion 7 CMPK2, DGUOK, DTYMK, GUK1, MAPT, PKM, PNPT1
protein-containing complex 2 CFTR, POLB
intracellular membrane-bounded organelle 1 GAA
pronucleus 1 PLCZ1
Secreted 3 GAA, MAPT, PNP
extracellular region 5 GAA, MAPT, PKM, PNP, TUBB4B
Mitochondrion matrix 1 PNPT1
mitochondrial matrix 3 DGUOK, DTYMK, PNPT1
transcription regulator complex 1 DACH1
photoreceptor inner segment 1 GUK1
nuclear membrane 1 GTPBP4
Extracellular vesicle 2 PKM, TUBB4B
dendritic spine 1 MAPT
microtubule cytoskeleton 2 MAPT, TUBB4B
nucleolus 2 GTPBP4, PLCZ1
axon cytoplasm 1 MAPT
Early endosome 2 CFTR, NME1
recycling endosome 1 CFTR
vesicle 1 PKM
Apical cell membrane 1 CFTR
Cytoplasm, perinuclear region 1 PLCZ1
Membrane raft 1 MAPT
Cytoplasm, cytoskeleton 2 MAPT, TUBB4B
microtubule 3 MAPT, POLB, TUBB4B
axolemma 1 MAPT
Mitochondrion intermembrane space 1 PNPT1
mitochondrial intermembrane space 1 PNPT1
collagen-containing extracellular matrix 1 PKM
nuclear speck 2 DACH1, MAPT
neuron projection 1 MAPT
cilium 1 PKM
mitotic spindle 1 TUBB4B
cytoskeleton 1 TUBB4B
cytoplasmic ribonucleoprotein granule 1 MAPT
Nucleus, nucleolus 1 GTPBP4
intercellular bridge 1 TUBB4B
Cytoplasm, cytoskeleton, flagellum axoneme 1 TUBB4B
sperm flagellum 1 TUBB4B
Recycling endosome membrane 1 CFTR
chloride channel complex 1 CFTR
axonemal microtubule 1 TUBB4B
Cell projection, dendrite 1 MAPT
tertiary granule membrane 1 GAA
Golgi-associated vesicle membrane 1 CFTR
cell body 1 MAPT
ficolin-1-rich granule lumen 2 PKM, PNP
secretory granule lumen 2 PKM, PNP
azurophil granule membrane 1 GAA
azurophil granule lumen 1 TUBB4B
clathrin-coated endocytic vesicle membrane 1 CFTR
ficolin-1-rich granule membrane 1 GAA
spindle microtubule 1 POLB
Rough endoplasmic reticulum 1 PKM
somatodendritic compartment 1 MAPT
nuclear periphery 1 MAPT
glial cell projection 1 MAPT
ribosome 1 PNPT1
sperm head 1 PLCZ1
catalytic complex 1 PNPT1
neurofibrillary tangle 1 MAPT
autolysosome lumen 1 GAA
main axon 1 MAPT
tubulin complex 1 MAPT
[Isoform M2]: Cytoplasm 1 PKM
[Isoform M1]: Cytoplasm 1 PKM
mitochondrial degradosome 1 PNPT1


Literature Reference

  • Martin Pabst, Josephine Grass, Richard Fischl, Renaud Léonard, Chunsheng Jin, Georg Hinterkörner, Nicole Borth, Friedrich Altmann. Nucleotide and nucleotide sugar analysis by liquid chromatography-electrospray ionization-mass spectrometry on surface-conditioned porous graphitic carbon. Analytical chemistry. 2010 Dec; 82(23):9782-8. doi: 10.1021/ac101975k. [PMID: 21043458]