MiMeDB: Showing metabocard for 3',5'-cyclic dAMP (MMDBc0032985)

Record Information

Version

2.0

Status

Detected and Quantified

Creation Date

2021-11-19 04:29:59 UTC

Update Date

2025-10-07 16:07:53 UTC

Metabolite ID

MMDBc0032985

Metabolite Identification

Common Name

3',5'-cyclic dAMP

Description

3',5'-cyclic dAMP is a nucleotide derivative belonging to the class of cyclic adenosine monophosphates. There is limited literature available on this metabolite, indicating that further research is needed to fully understand its biological significance and functions.

Structure

MOL SDF PDB SMILES InChI


  Mrv0541 02241222192D          

 21 24  0  0  1  0            999 V2000
   -0.7145    0.4125    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000   -0.8250    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.7540   -1.4521    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.2691   -2.1195    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.7540   -2.7869    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.5387   -2.5320    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.5387   -1.7070    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1517   -3.0840    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.5825   -3.5939    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1956   -4.1459    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.7872   -4.0625    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.9802   -3.8910    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
    3.2352   -4.6756    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4991   -0.6674    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.9840    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4991    0.6674    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    1.6500    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0  0  0  0
  3 20  1  0  0  0  0
  3  4  1  0  0  0  0
  4 18  1  0  0  0  0
  5  1  1  0  0  0  0
  3  5  2  0  0  0  0
 21  5  1  0  0  0  0
  6  2  1  0  0  0  0
  4  6  2  0  0  0  0
  7 18  1  1  0  0  0
  8  7  1  0  0  0  0
  7 11  1  0  0  0  0
  9  8  1  0  0  0  0
  9 13  1  1  0  0  0
  9 10  1  0  0  0  0
 10 12  1  6  0  0  0
 10 11  1  0  0  0  0
 12 16  1  0  0  0  0
 14 13  1  0  0  0  0
 16 14  1  0  0  0  0
 16 15  2  0  0  0  0
 16 17  1  0  0  0  0
 19 18  1  0  0  0  0
 20 19  2  0  0  0  0
M  END
> <DATABASE_ID>
MMDBc0032985

> <DATABASE_NAME>
MIME

> <SMILES>
NC1=C2N=CN([C@H]3C[C@@H]4OP(O)(=O)OC[C@H]4O3)C2=NC=N1

> <INCHI_IDENTIFIER>
InChI=1S/C10H12N5O5P/c11-9-8-10(13-3-12-9)15(4-14-8)7-1-5-6(19-7)2-18-21(16,17)20-5/h3-7H,1-2H2,(H,16,17)(H2,11,12,13)/t5-,6+,7+/m0/s1

> <INCHI_KEY>
MKMZAENVDZADSW-RRKCRQDMSA-N

> <FORMULA>
C10H12N5O5P

> <MOLECULAR_WEIGHT>
313.2065

> <EXACT_MASS>
313.057605031

> <JCHEM_ACCEPTOR_COUNT>
7

> <JCHEM_AVERAGE_POLARIZABILITY>
27.83042554894695

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(4aR,6R,7aS)-6-(6-amino-9H-purin-9-yl)-2-hydroxy-hexahydro-2λ⁵-furo[3,2-d][1,3,2]dioxaphosphinin-2-one

> <ALOGPS_LOGP>
-2.00

> <JCHEM_LOGP>
-2.908970341306835

> <ALOGPS_LOGS>
-2.03

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
4

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
18.53996070325955

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.857516571801571

> <JCHEM_PKA_STRONGEST_BASIC>
5.001510161284282

> <JCHEM_POLAR_SURFACE_AREA>
134.61

> <JCHEM_REFRACTIVITY>
68.7788

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
2.92e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
3',5'-Cyclic dAMP

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 24-FEB-12   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   24-FEB-12         0                                  
HETATM    1  N   UNK     0      -1.334   0.770   0.000  0.00  0.00           N+0
HETATM    2  C   UNK     0      -1.334  -0.770   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       1.334   0.770   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       0.000   1.540   0.000  0.00  0.00           C+0
HETATM    6  N   UNK     0       0.000  -1.540   0.000  0.00  0.00           N+0
HETATM    7  C   UNK     0       3.274  -2.711   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0       2.369  -3.956   0.000  0.00  0.00           O+0
HETATM    9  C   UNK     0       3.274  -5.202   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       4.739  -4.726   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       4.739  -3.186   0.000  0.00  0.00           C+0
HETATM   12  O   UNK     0       5.883  -5.757   0.000  0.00  0.00           O+0
HETATM   13  C   UNK     0       2.954  -6.709   0.000  0.00  0.00           C+0
HETATM   14  O   UNK     0       4.098  -7.739   0.000  0.00  0.00           O+0
HETATM   15  O   UNK     0       7.069  -7.583   0.000  0.00  0.00           O+0
HETATM   16  P   UNK     0       5.563  -7.263   0.000  0.00  0.00           P+0
HETATM   17  O   UNK     0       6.039  -8.728   0.000  0.00  0.00           O+0
HETATM   18  N   UNK     0       2.798  -1.246   0.000  0.00  0.00           N+0
HETATM   19  C   UNK     0       3.703   0.000   0.000  0.00  0.00           C+0
HETATM   20  N   UNK     0       2.798   1.246   0.000  0.00  0.00           N+0
HETATM   21  N   UNK     0       0.000   3.080   0.000  0.00  0.00           N+0
CONECT    1    2    5                                                       
CONECT    2    1    6                                                       
CONECT    3   20    4    5                                                  
CONECT    4    3   18    6                                                  
CONECT    5    1    3   21                                                  
CONECT    6    2    4                                                       
CONECT    7   18    8   11                                                  
CONECT    8    7    9                                                       
CONECT    9    8   13   10                                                  
CONECT   10    9   12   11                                                  
CONECT   11    7   10                                                       
CONECT   12   10   16                                                       
CONECT   13    9   14                                                       
CONECT   14   13   16                                                       
CONECT   15   16                                                            
CONECT   16   12   14   15   17                                             
CONECT   17   16                                                            
CONECT   18    4    7   19                                                  
CONECT   19   18   20                                                       
CONECT   20    3   19                                                       
CONECT   21    5                                                            
MASTER        0    0    0    0    0    0    0    0   21    0   48    0
END

Synonyms

Value	Source
2'-Deoxy cyclic AMP	ChEBI
2'-Deoxyadenosine cyclic 3',5'-(hydrogen phosphate)	ChEBI
3',5'-Cyclic deoxyadenylic acid	ChEBI
3',5'-Cyclic-2'-dAMP	ChEBI
2'-Deoxyadenosine cyclic 3',5'-(hydrogen phosphoric acid)	Generator
3',5'-Cyclic deoxyadenylate	Generator

Molecular Formula

C₁₀H₁₂N₅O₅P

Average Mass

313.2065

Monoisotopic Mass

313.057605031

IUPAC Name

(4aR,6R,7aS)-6-(6-amino-9H-purin-9-yl)-2-hydroxy-hexahydro-2λ⁵-furo[3,2-d][1,3,2]dioxaphosphinin-2-one

Traditional Name

3',5'-Cyclic dAMP

CAS Registry Number

13342-50-2

SMILES

NC1=C2N=CN([C@H]3C[C@@H]4OP(O)(=O)OC[C@H]4O3)C2=NC=N1

InChI Identifier

InChI=1S/C10H12N5O5P/c11-9-8-10(13-3-12-9)15(4-14-8)7-1-5-6(19-7)2-18-21(16,17)20-5/h3-7H,1-2H2,(H,16,17)(H2,11,12,13)/t5-,6+,7+/m0/s1

InChI Key

MKMZAENVDZADSW-RRKCRQDMSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as 6-aminopurines. These are purines that carry an amino group at position 6. Purine is a bicyclic aromatic compound made up of a pyrimidine ring fused to an imidazole ring.

Kingdom

Organic compounds

Super Class

Organoheterocyclic compounds

Class

Imidazopyrimidines

Sub Class

Purines and purine derivatives

Direct Parent

6-aminopurines

Alternative Parents

Substituents

6-aminopurine
Aminopyrimidine
N-substituted imidazole
Organic phosphoric acid derivative
Pyrimidine
Imidolactam
Azole
Imidazole
Tetrahydrofuran
Heteroaromatic compound
Azacycle
Oxacycle
Hydrocarbon derivative
Primary amine
Organooxygen compound
Organonitrogen compound
Organic oxide
Organopnictogen compound
Amine
Organic nitrogen compound
Organic oxygen compound
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic heteropolycyclic compounds

External Descriptors

3',5'-cyclic purine nucleotide (CHEBI:28074 )
3',5'-Cyclic nuclcleotides (C00968 )

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
Water Solubility	2.92 g/L	ALOGPS
logP	-2	ALOGPS
logP	-2.9	ChemAxon
logS	-2	ALOGPS
pKa (Strongest Acidic)	1.86	ChemAxon
pKa (Strongest Basic)	5	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	7	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	134.61 Å²	ChemAxon
Rotatable Bond Count	1	ChemAxon
Refractivity	68.78 m³·mol⁻¹	ChemAxon
Polarizability	27.83 Å³	ChemAxon
Number of Rings	4	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

Spectra

Spectrum Type	Description	Splash Key	Deposition Date	View
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_2) - 70eV, Positive	Not Available	2022-08-08	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-000i-0901000000-e70cf63b59de33e74ce7	2016-09-12	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-000i-0900000000-4a0a72e1cbde78c9bdcd	2016-09-12	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-000i-2900000000-209a627933c84bba0d29	2016-09-12	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-03di-1229000000-b3711fdf9137c12b0e44	2016-09-12	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-003r-5931000000-ad6c3e355ed82b8c344c	2016-09-12	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-003r-9400000000-3f85236530810bd3a295	2016-09-12	View Spectrum

Chromatographic Retention Times and Retention Indices

Retention Times

Chromatography Type	Technique	Column	Deposition Date	Retention Time (s)
Liquid Chromatography	HILIC	Waters Acquity UPLC-BEH Amide column (eluted)	2025-10-24	438.2
Liquid Chromatography	HILIC	Accucore 150 Amide HILIC (eluted)	2025-10-24	259.0
Liquid Chromatography	Reversed-phase	Hypersil Gold 1.9 µm C18 (void)	2025-10-24	197.4
Liquid Chromatography	Reversed-phase	Agilent Zorbax Eclipse Plus C18 (2.1 mm x 150 mm, 3.5 um) (eluted)	2025-10-24	290.4
Liquid Chromatography	Reversed-phase	XBridge C18 3.5u 2.1x50 mm (eluted)	2025-10-24	307.6
Liquid Chromatography	Reversed-phase	Ascentis Express C18 (eluted)	2025-10-24	216.0
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC HSS T3 C18 (eluted)	2025-10-24	1311.1
Liquid Chromatography	HILIC	Merck SeQuant ZIC-HILIC (eluted)	2025-10-24	498.7
Liquid Chromatography	HILIC	Merck SeQuant ZIC-pHILIC (eluted)	2025-10-24	610.8
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC HSS T3 C18 (eluted)	2025-10-24	137.9
Liquid Chromatography	HILIC	Merck SeQuant ZIC-HILIC (eluted)	2025-10-24	255.6
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC HSS T3 C18 (eluted)	2025-10-24	152.5
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC BEH C18 (eluted)	2025-10-24	78.2
Liquid Chromatography	HILIC	Merck SeQuant ZIC-pHILIC column (eluted)	2025-10-24	194.1
Liquid Chromatography	HILIC	Merck SeQuant ZIC-pHILIC column (eluted)	2025-10-24	408.6
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC BEH C18 (eluted)	2025-10-24	70.4
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC BEH C18 (eluted)	2025-10-24	162.1
Liquid Chromatography	Reversed-phase	Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex (eluted)	2025-10-24	645.1
Liquid Chromatography	Reversed-phase	Waters Atlantis T3 (2.1 x 150 mm, 5 um) (eluted)	2025-10-24	613.0

Retention Indices

Chromatography Type	Peak Label	SMILES	Stationary Phase	Deposition Date	Retention Index
Gas Chromatography	3',5'-cyclic dAMP_TMS_1	C[Si](C)(C)OP1(=O)OC[C@H]2O[C@@H](N3C=NC4=C(N)N=CN=C43)C[C@@H]2O1	standard non polar	2025-10-24	2247.79
Gas Chromatography	3',5'-cyclic dAMP_TMS_2	C[Si](C)(C)NC1=NC=NC2=C1N=CN2[C@H]1C[C@@H]2OP(=O)(O)OC[C@H]2O1	standard non polar	2025-10-24	2173.94
Gas Chromatography	3',5'-cyclic dAMP_TMS_3	C[Si](C)(C)NC1=NC=NC2=C1N=CN2[C@H]1C[C@@H]2OP(=O)(O[Si](C)(C)C)OC[C@H]2O1	standard non polar	2025-10-24	2167.26
Gas Chromatography	3',5'-cyclic dAMP_TMS_4	C[Si](C)(C)N(C1=NC=NC2=C1N=CN2[C@H]1C[C@@H]2OP(=O)(O)OC[C@H]2O1)[Si](C)(C)C	standard non polar	2025-10-24	2770.46
Gas Chromatography	3',5'-cyclic dAMP_TMS_5	C[Si](C)(C)OP1(=O)OC[C@H]2O[C@@H](N3C=NC4=C(N([Si](C)(C)C)[Si](C)(C)C)N=CN=C43)C[C@@H]2O1	standard non polar	2025-10-24	2495.67
Gas Chromatography	3',5'-cyclic dAMP_TMS_1	C[Si](C)(C)OP1(=O)OC[C@H]2O[C@@H](N3C=NC4=C(N)N=CN=C43)C[C@@H]2O1	standard polar	2025-10-24	2050.95
Gas Chromatography	3',5'-cyclic dAMP_TMS_2	C[Si](C)(C)NC1=NC=NC2=C1N=CN2[C@H]1C[C@@H]2OP(=O)(O)OC[C@H]2O1	standard polar	2025-10-24	2230.51
Gas Chromatography	3',5'-cyclic dAMP_TMS_3	C[Si](C)(C)NC1=NC=NC2=C1N=CN2[C@H]1C[C@@H]2OP(=O)(O[Si](C)(C)C)OC[C@H]2O1	standard polar	2025-10-24	2327.84
Gas Chromatography	3',5'-cyclic dAMP_TMS_4	C[Si](C)(C)N(C1=NC=NC2=C1N=CN2[C@H]1C[C@@H]2OP(=O)(O)OC[C@H]2O1)[Si](C)(C)C	standard polar	2025-10-24	2136.8
Gas Chromatography	3',5'-cyclic dAMP_TMS_5	C[Si](C)(C)OP1(=O)OC[C@H]2O[C@@H](N3C=NC4=C(N([Si](C)(C)C)[Si](C)(C)C)N=CN=C43)C[C@@H]2O1	standard polar	2025-10-24	820.413

Biological Properties

Cellular Locations

Not Available

Biospecimen Locations

Not Available

Tissue Locations

Not Available

Associated OMIM IDs

114500 (Colorectal cancer)
610247 (Eosinophilic esophagitis)

Human Proteins and Enzymes

Protein ID	Protein Name	Protein Type	Uniprot ID	Species

Human Pathways

Pathways

Name	SMPDB/PathBank

Microbial Pathways

Pathways

Not Available

Metabolic Reactions

Reactions

This table shows at most 20 reactions. For the full list of associated reactions:

See All Associated Reactions

Reaction ID	Precursor	Product	Enzyme	Reaction Type	Data Source	Reference

Health Effects and Bioactivity

Health Outcome/Bioactivity	Metabolite Response/Effect	Evidence Type	Host and Biospecimen	Data Source	Reference

Microbial Sources

Superkingdom/Kingdom	Phylum	Total species	Hosts and Body Sites	Microbial Links
Eukaryota/Fungi	Ascomycota	1	Human feces; Human saliva	Unknown

Exposure Sources

Other Exposures

Source Type	Data Source	Reference

Host Biospecimen and Location

Host and Biospecimen	Status	Mean	Std	Min	Max	Units	Age	Sex	Health Condition	Data Source	Reference

External Links

HMDB ID

Not Available

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

Not Available

KNApSAcK ID

Not Available

Chemspider ID

Not Available

KEGG Compound ID

C00968

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

188955

PDB ID

Not Available

ChEBI ID

28074

Food Biomarker Ontology

Not Available

CMMC Knowledgebase

Not Available

General References

Londesborough J: Characterization of an adenosine 3':5'-cyclic monophosphate phosphodiesterase from baker's yeast. Its binding to subcellular particles, catalytic properties and gel-filtration behaviour. Biochem J. 1977 Jun 1;163(3):467-76. doi: 10.1042/bj1630467. [PubMed:18135 ]
Herrgard MJ, Swainston N, Dobson P, Dunn WB, Arga KY, Arvas M, Bluthgen N, Borger S, Costenoble R, Heinemann M, Hucka M, Le Novere N, Li P, Liebermeister W, Mo ML, Oliveira AP, Petranovic D, Pettifer S, Simeonidis E, Smallbone K, Spasic I, Weichart D, Brent R, Broomhead DS, Westerhoff HV, Kirdar B, Penttila M, Klipp E, Palsson BO, Sauer U, Oliver SG, Mendes P, Nielsen J, Kell DB: A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology. Nat Biotechnol. 2008 Oct;26(10):1155-60. doi: 10.1038/nbt1492. [PubMed:18846089 ]

Showing metabocard for 3',5'-cyclic dAMP (MMDBc0032985)

MOL for #<Metabolite:0x00007f8afc261608>

3D MOL for #<Metabolite:0x00007f8afc261608>

3D SDF for #<Metabolite:0x00007f8afc261608>

3D-SDF for #<Metabolite:0x00007f8afc261608>

PDB for #<Metabolite:0x00007f8afc261608>

3D PDB for #<Metabolite:0x00007f8afc261608>

SMILES for #<Metabolite:0x00007f8afc261608>

INCHI for #<Metabolite:0x00007f8afc261608>

Structure for #<Metabolite:0x00007f8afc261608>

3D Structure for #<Metabolite:0x00007f8afc261608>