Human Metabolome Database: Showing metabocard for Adenosine 3',5'-diphosphate (HMDB0000061)

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Identification Taxonomy Ontology Physical properties Spectra Biological properties Concentrations Links References enzymes (39) Show 39 proteins XML

enzymes (39) Show 39 proteins

Record Information

Version

4.0

Status

Detected and Quantified

Creation Date

2005-11-16 15:48:42 UTC

Update Date

2020-05-14 21:41:43 UTC

HMDB ID

HMDB0000061

Secondary Accession Numbers

HMDB0001468
HMDB00061
HMDB01468

Metabolite Identification

Common Name

Adenosine 3',5'-diphosphate

Description

Adenosine 3', 5'-diphosphate or PAP is a nucleotide that is closely related to ADP. It has two phosphate groups attached to the 5' and 3' positions of the pentose sugar ribose (instead of pyrophosphoric acid at the 5' position, as found in ADP), and the nucleobase adenine. PAP is converted to PAPS by Sulfotransferase and then back to PAP after the sulfotransferase reaction. Sulfotransferase (STs) catalyze the transfer reaction of the sulfate group from the ubiquitous donor 3'-phosphoadenosine 5'-phosphosulfate (PAPS) to an acceptor group of numerous substrates. This reaction, often referred to as sulfuryl transfer, sulfation, or sulfonation, is widely observed from bacteria to humans and plays a key role in various biological processes such as cell communication, growth and development, and defense. PAP also appears to a role in bipolar depression. Phosphatases converting 3'-phosphoadenosine 5'-phosphate (PAP) into adenosine 5'-phosphate are of fundamental importance in living cells as the accumulation of PAP is toxic to several cellular systems. These enzymes are lithium-sensitive and we have characterized a human PAP phosphatase as a potential target of lithium therapy.

Structure

MOL SDF PDB SMILES InChI

Synonyms

Value	Source
3'-Phosphoadenylate	ChEBI
Adenosine 3',5'-bisphosphate	ChEBI
PAP	ChEBI
Phosphoadenosine phosphate	ChEBI
3'-Phosphoadenylic acid	Generator
Adenosine 3',5'-bisphosphoric acid	Generator
Phosphoadenosine phosphoric acid	Generator
Adenosine 3',5'-diphosphoric acid	Generator
3'-Phosphoryl-AMP	HMDB
3,5-ADP	HMDB
3,5-Diphosphoadenosine	HMDB
3-Phosphoadenosine 5-phosphate	HMDB
5-(Dihydrogen phosphate) 3-adenylate	HMDB
5-(Dihydrogen phosphate)3'-adenylic acid	HMDB
Adenosine 3,5-bis	HMDB
Adenosine 3,5-bisphosphate	HMDB
Adenosine 3'-phosphate-5'-phosphate, disodium salt	HMDB
3'-Phosphoadenosine 5'-phosphate	HMDB
Adenosine 3'-phosphate-5'-phosphate, monosodium salt	HMDB
3',5'-ADP	HMDB
Adenosine 3'-phosphate-5'-phosphate	HMDB

Chemical Formula

C₁₀H₁₅N₅O₁₀P₂

Average Molecular Weight

427.2011

Monoisotopic Molecular Weight

427.029414749

IUPAC Name

{[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-4-hydroxy-3-(phosphonooxy)oxolan-2-yl]methoxy}phosphonic acid

Traditional Name

adenosine 3',5'-bisphosphate

CAS Registry Number

1053-73-2

SMILES

NC1=C2N=CN([C@@H]3O[C@H](COP(O)(O)=O)[C@@H](OP(O)(O)=O)[C@H]3O)C2=NC=N1

InChI Identifier

InChI=1S/C10H15N5O10P2/c11-8-5-9(13-2-12-8)15(3-14-5)10-6(16)7(25-27(20,21)22)4(24-10)1-23-26(17,18)19/h2-4,6-7,10,16H,1H2,(H2,11,12,13)(H2,17,18,19)(H2,20,21,22)/t4-,6-,7-,10-/m1/s1

InChI Key

WHTCPDAXWFLDIH-KQYNXXCUSA-N

Chemical Taxonomy

Description

belongs to the class of organic compounds known as purine ribonucleoside 3',5'-bisphosphates. These are purine ribobucleotides with one phosphate group attached to 3' and 5' hydroxyl groups of the ribose moiety.

Kingdom

Organic compounds

Super Class

Nucleosides, nucleotides, and analogues

Class

Purine nucleotides

Sub Class

Purine ribonucleotides

Direct Parent

Purine ribonucleoside 3',5'-bisphosphates

Alternative Parents

Substituents

Purine ribonucleoside 3',5'-bisphosphate
Purine ribonucleoside monophosphate
Pentose phosphate
Ribonucleoside 3'-phosphate
Pentose-5-phosphate
Glycosyl compound
N-glycosyl compound
6-aminopurine
Pentose monosaccharide
Monosaccharide phosphate
Imidazopyrimidine
Purine
Aminopyrimidine
Monoalkyl phosphate
Organic phosphoric acid derivative
N-substituted imidazole
Phosphoric acid ester
Monosaccharide
Imidolactam
Pyrimidine
Alkyl phosphate
Imidazole
Azole
Tetrahydrofuran
Heteroaromatic compound
Secondary alcohol
Oxacycle
Azacycle
Organoheterocyclic compound
Amine
Alcohol
Organic nitrogen compound
Hydrocarbon derivative
Organic oxide
Organopnictogen compound
Organic oxygen compound
Primary amine
Organooxygen compound
Organonitrogen compound
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic heteropolycyclic compounds

External Descriptors

adenosine bisphosphate (CHEBI:17985 )

Ontology

Disposition

Route of exposure:

Enteral:

Ingestion

Source:

Biological:

Animal

Plant:

Biological location:

Tissue and substructures:

Placenta

Subcellular:

Organ and components:

Process

Naturally occurring process:

Biological process:

Biochemical pathway:

Role

Industrial application:

Pharmaceutical industry:

Pharmaceutical

Physical Properties

State

Solid

Experimental Properties

Property	Value	Reference
Melting Point	Not Available	Not Available
Boiling Point	Not Available	Not Available
Water Solubility	614.5 mg/mL	Not Available
LogP	Not Available	Not Available

Predicted Properties

Property	Value	Source
Water Solubility	3.33 g/L	ALOGPS
logP	-1.6	ALOGPS
logP	-4.8	ChemAxon
logS	-2.1	ALOGPS
pKa (Strongest Acidic)	0.7	ChemAxon
pKa (Strongest Basic)	3.92	ChemAxon
Physiological Charge	-4	ChemAxon
Hydrogen Acceptor Count	12	ChemAxon
Hydrogen Donor Count	6	ChemAxon
Polar Surface Area	232.6 Å²	ChemAxon
Rotatable Bond Count	6	ChemAxon
Refractivity	84.94 m³·mol⁻¹	ChemAxon
Polarizability	34.28 Å³	ChemAxon
Number of Rings	3	ChemAxon
Bioavailability	No	ChemAxon
Rule of Five	No	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	Yes	ChemAxon

Spectra

Spectrum Type	Description	Splash Key	View
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	splash10-0002-9332100000-c2cf1343058e5c460684	Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (1 TMS) - 70eV, Positive	splash10-0002-9141400000-8e8cf251eecd6d39cf02	Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-000i-0902300000-77268ef9fe8672f81e9f	Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-000i-0900000000-6986eb10675f363acf42	Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-000i-1900000000-493254661a51349997bd	Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-004i-7801900000-b4b0af4deca129a6a12c	Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-0059-9800000000-4a1ffcf05d9938fe121e	Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-004i-9200000000-fb4a5bf16d0e5bcaa1e0	Spectrum
1D NMR	1H NMR Spectrum	Not Available	Spectrum
2D NMR	[1H,13C] 2D NMR Spectrum	Not Available	Spectrum

Biological Properties

Cellular Locations

Golgi apparatus

Biospecimen Locations

Cellular Cytoplasm

Tissue Locations

Brain
Liver
Placenta

Pathways

Name	SMPDB/Pathwhiz	KEGG
Sulfate/Sulfite Metabolism
Sulfite oxidase deficiency		Not Available
Sphingolipid Metabolism
Gaucher Disease		Not Available
Globoid Cell Leukodystrophy		Not Available

Normal Concentrations

Biospecimen	Status	Value	Age	Sex	Condition	Reference	Details
Cellular Cytoplasm	Detected and Quantified	137 uM	Adult (>18 years old)	Both	Normal	7877593	details

Abnormal Concentrations

Not Available

Associated Disorders and Diseases

Disease References

None

Associated OMIM IDs

None

External Links

DrugBank ID

DB01812

Phenol Explorer Compound ID

Not Available

FooDB ID

KNApSAcK ID

Chemspider ID

KEGG Compound ID

BioCyc ID

BiGG ID

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

159296

PDB ID

Not Available

ChEBI ID

17985

Food Biomarker Ontology

Not Available

VMH ID

PAP

References

Synthesis Reference

Tsunako, Mitsutomo; Kotone, Akira. Preparation of nucleoside-2',5'- and 3',5'-diphosphoric acids. Jpn. Kokai Tokkyo Koho (1991), 13 pp.

Material Safety Data Sheet (MSDS)

Download (PDF)

General References

Lewis AJ, Otake Y, Walle UK, Walle T: Sulphonation of N-hydroxy-2-acetylaminofluorene by human dehydroepiandrosterone sulphotransferase. Xenobiotica. 2000 Mar;30(3):253-61. [PubMed:10752640 ]
Gasmi L, McLennan AG: The mouse Nudt7 gene encodes a peroxisomal nudix hydrolase specific for coenzyme A and its derivatives. Biochem J. 2001 Jul 1;357(Pt 1):33-8. [PubMed:11415433 ]
Leonidas DD, Chavali GB, Oikonomakos NG, Chrysina ED, Kosmopoulou MN, Vlassi M, Frankling C, Acharya KR: High-resolution crystal structures of ribonuclease A complexed with adenylic and uridylic nucleotide inhibitors. Implications for structure-based design of ribonucleolytic inhibitors. Protein Sci. 2003 Nov;12(11):2559-74. [PubMed:14573867 ]
Turner NA, Moake JL, McIntire LV: Blockade of adenosine diphosphate receptors P2Y(12) and P2Y(1) is required to inhibit platelet aggregation in whole blood under flow. Blood. 2001 Dec 1;98(12):3340-5. [PubMed:11719372 ]
Traut TW: Physiological concentrations of purines and pyrimidines. Mol Cell Biochem. 1994 Nov 9;140(1):1-22. [PubMed:7877593 ]
Russo N, Acharya KR, Vallee BL, Shapiro R: A combined kinetic and modeling study of the catalytic center subsites of human angiogenin. Proc Natl Acad Sci U S A. 1996 Jan 23;93(2):804-8. [PubMed:8570639 ]
Elshenawy S, Pinney SE, Stuart T, Doulias PT, Zura G, Parry S, Elovitz MA, Bennett MJ, Bansal A, Strauss JF 3rd, Ischiropoulos H, Simmons RA: The Metabolomic Signature of the Placenta in Spontaneous Preterm Birth. Int J Mol Sci. 2020 Feb 4;21(3). pii: ijms21031043. doi: 10.3390/ijms21031043. [PubMed:32033212 ]

Only showing the first 10 proteins. There are 39 proteins in total.

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Enzymes

Enzyme Details

1. Ectonucleotide pyrophosphatase/phosphodiesterase family member 1

General function:: Involved in catalytic activity
Specific function:: Involved primarily in ATP hydrolysis at the plasma membrane. Plays a role in regulating pyrophosphate levels, and functions in bone mineralization and soft tissue calcification. In vitro, has a broad specificity, hydrolyzing other nucleoside 5' triphosphates such as GTP, CTP, TTP and UTP to their corresponding monophosphates with release of pyrophosphate and diadenosine polyphosphates, and also 3',5'-cAMP to AMP. May also be involved in the regulation of the availability of nucleotide sugars in the endoplasmic reticulum and Golgi, and the regulation of purinergic signaling. Appears to modulate insulin sensitivity.
Gene Name:: ENPP1
Uniprot ID:: P22413
Molecular weight:: 104923.58

Reactions

Phosphoadenosine phosphosulfate + Water → Oat gum + Adenosine 3',5'-diphosphate	details

Enzyme Details

2. Ectonucleotide pyrophosphatase/phosphodiesterase family member 3

General function:: Involved in catalytic activity
Specific function:: Cleaves a variety of phosphodiester and phosphosulfate bonds including deoxynucleotides, nucleotide sugars, and NAD (By similarity).
Gene Name:: ENPP3
Uniprot ID:: O14638
Molecular weight:: 100123.54

Reactions

Phosphoadenosine phosphosulfate + Water → Oat gum + Adenosine 3',5'-diphosphate	details

Enzyme Details

3. Carbohydrate sulfotransferase 11

General function:: Involved in sulfotransferase activity
Specific function:: Catalyzes the transfer of sulfate to position 4 of the N-acetylgalactosamine (GalNAc) residue of chondroitin. Chondroitin sulfate constitutes the predominant proteoglycan present in cartilage and is distributed on the surfaces of many cells and extracellular matrices. Can also sulfate Gal residues in desulfated dermatan sulfate. Preferentially sulfates in GlcA->GalNAc unit than in IdoA->GalNAc unit. Does not form 4, 6-di-O-sulfated GalNAc when chondroitin sulfate C is used as an acceptor.
Gene Name:: CHST11
Uniprot ID:: Q9NPF2
Molecular weight:: 41002.97

Reactions

Phosphoadenosine phosphosulfate + Chondroitin → Adenosine 3',5'-diphosphate + chondroitin 4'-sulfate	details
Phosphoadenosine phosphosulfate + Chondroitin → Adenosine 3',5'-diphosphate + Chondroitin 4-sulfate	details

Enzyme Details

4. Carbohydrate sulfotransferase 3

General function:: Involved in sulfotransferase activity
Specific function:: Sulfotransferase that utilizes 3'-phospho-5'-adenylyl sulfate (PAPS) as sulfonate donor to catalyze the transfer of sulfate to position 6 of the N-acetylgalactosamine (GalNAc) residue of chondroitin. Chondroitin sulfate constitutes the predominant proteoglycan present in cartilage and is distributed on the surfaces of many cells and extracellular matrices. Can also sulfate Gal residues of keratan sulfate, another glycosaminoglycan, and the Gal residues in sialyl N-acetyllactosamine (sialyl LacNAc) oligosaccharides. May play a role in the maintenance of naive T-lymphocytes in the spleen.
Gene Name:: CHST3
Uniprot ID:: Q7LGC8
Molecular weight:: 54705.5

Reactions

Phosphoadenosine phosphosulfate + Chondroitin → Adenosine 3',5'-diphosphate + Chondroitin 6-sulfate	details

Enzyme Details

5. Carbohydrate sulfotransferase 13

General function:: Involved in sulfotransferase activity
Specific function:: Catalyzes the transfer of sulfate to position 4 of the N-acetylgalactosamine (GalNAc) residue of chondroitin. Chondroitin sulfate constitutes the predominant proteoglycan present in cartilage and is distributed on the surfaces of many cells and extracellular matrices. Transfers sulfate to the C4 hydroxyl of beta1,4-linked GalNAc that is substituted with a beta-linked glucuronic acid at the C-3 hydroxyl. No activity toward dermatan.
Gene Name:: CHST13
Uniprot ID:: Q8NET6
Molecular weight:: 38919.34

Reactions

Phosphoadenosine phosphosulfate + Chondroitin → Adenosine 3',5'-diphosphate + chondroitin 4'-sulfate	details
Phosphoadenosine phosphosulfate + Chondroitin → Adenosine 3',5'-diphosphate + Chondroitin 4-sulfate	details

Enzyme Details

6. Carbohydrate sulfotransferase 12

General function:: Involved in sulfotransferase activity
Specific function:: Catalyzes the transfer of sulfate to position 4 of the N-acetylgalactosamine (GalNAc) residue of chondroitin and desulfated dermatan sulfate. Chondroitin sulfate constitutes the predominant proteoglycan present in cartilage and is distributed on the surfaces of many cells and extracellular matrices. Activity toward partially desulfated dermatan sulfate is however lower. Does not form 4, 6-di-O-sulfated GalNAc when chondroitin sulfate C is used as an acceptor.
Gene Name:: CHST12
Uniprot ID:: Q9NRB3
Molecular weight:: 48413.945

Reactions

Phosphoadenosine phosphosulfate + Chondroitin → Adenosine 3',5'-diphosphate + chondroitin 4'-sulfate	details
Phosphoadenosine phosphosulfate + Chondroitin → Adenosine 3',5'-diphosphate + Chondroitin 4-sulfate	details

Enzyme Details

7. Galactosylceramide sulfotransferase

General function:: Involved in galactosylceramide sulfotransferase activity
Specific function:: Catalyzes the sulfation of membrane glycolipids. Seems to prefer beta-glycosides at the non-reducing termini of sugar chains attached to a lipid moiety. Catalyzes the synthesis of galactosylceramide sulfate (sulfatide), a major lipid component of the myelin sheath and of monogalactosylalkylacylglycerol sulfate (seminolipid), present in spermatocytes (By similarity). Also acts on lactosylceramide, galactosyl 1-alkyl-2-sn-glycerol and galactosyl diacylglycerol (in vitro).
Gene Name:: GAL3ST1
Uniprot ID:: Q99999
Molecular weight:: 48763.63

Reactions

Phosphoadenosine phosphosulfate + a galactosylceramide → Adenosine 3',5'-diphosphate + a galactosylceramidesulfate	details
Phosphoadenosine phosphosulfate + monogalactosylalkylacylglycerol → Adenosine 3',5'-diphosphate + monogalactosylalkylacylglycerol sulfate	details
Phosphoadenosine phosphosulfate + Galactosylceramide → Adenosine 3',5'-diphosphate + Sulfatide	details
Phosphoadenosine phosphosulfate + Digalactosylceramide → Adenosine 3',5'-diphosphate + Digalactosylceramidesulfate	details

Enzyme Details

8. Heparan sulfate glucosamine 3-O-sulfotransferase 3B1

General function:: Involved in sulfotransferase activity
Specific function:: Sulfotransferase that utilizes 3'-phospho-5'-adenylyl sulfate (PAPS) to catalyze the transfer of a sulfo group to an N-unsubstituted glucosamine linked to a 2-O-sulfo iduronic acid unit on heparan sulfate. Catalyzes the O-sulfation of glucosamine in IdoUA2S-GlcNS and also in IdoUA2S-GlcNH2. The substrate-specific O-sulfation generates an enzyme-modified heparan sulfate which acts as a binding receptor to Herpes simplex virus-1 (HSV-1) and permits its entry. Unlike 3-OST-1, does not convert non-anticoagulant heparan sulfate to anticoagulant heparan sulfate.
Gene Name:: HS3ST3B1
Uniprot ID:: Q9Y662
Molecular weight:: 43323.605

Reactions

Phosphoadenosine phosphosulfate + [heparan sulfate]-glucosamine → Adenosine 3',5'-diphosphate + [heparan sulfate]-glucosamine 3-sulfate	details

Enzyme Details

9. Heparan sulfate glucosamine 3-O-sulfotransferase 3A1

General function:: Involved in sulfotransferase activity
Specific function:: Sulfotransferase that utilizes 3'-phospho-5'-adenylyl sulfate (PAPS) to catalyze the transfer of a sulfo group to an N-unsubstituted glucosamine linked to a 2-O-sulfo iduronic acid unit on heparan sulfate. Catalyzes the O-sulfation of glucosamine in IdoUA2S-GlcNS and also in IdoUA2S-GlcNH2. The substrate-specific O-sulfation generates an enzyme-modified heparan sulfate which acts as a binding receptor to Herpes simplex virus-1 (HSV-1) and permits its entry. Unlike 3-OST-1, does not convert non-anticoagulant heparan sulfate to anticoagulant heparan sulfate.
Gene Name:: HS3ST3A1
Uniprot ID:: Q9Y663
Molecular weight:: 44899.155

Reactions

Phosphoadenosine phosphosulfate + [heparan sulfate]-glucosamine → Adenosine 3',5'-diphosphate + [heparan sulfate]-glucosamine 3-sulfate	details

Enzyme Details

10. Sulfotransferase 1A1

General function:: Involved in sulfotransferase activity
Specific function:: Sulfotransferase that utilizes 3'-phospho-5'-adenylyl sulfate (PAPS) as sulfonate donor to catalyze the sulfate conjugation of catecholamines, phenolic drugs and neurotransmitters. Has also estrogen sulfotransferase activity. responsible for the sulfonation and activation of minoxidil. Is Mediates the metabolic activation of carcinogenic N-hydroxyarylamines to DNA binding products and could so participate as modulating factor of cancer risk.
Gene Name:: SULT1A1
Uniprot ID:: P50225
Molecular weight:: 34165.13

Reactions

Phosphoadenosine phosphosulfate + a phenol → Adenosine 3',5'-diphosphate + an aryl sulfate	details
Phosphoadenosine phosphosulfate + Phenol → Adenosine 3',5'-diphosphate + Phenol sulphate	details

Only showing the first 10 proteins. There are 39 proteins in total.

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Showing metabocard for Adenosine 3',5'-diphosphate (HMDB0000061)

Structure for HMDB0000061 (Adenosine 3',5'-diphosphate)

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