MiMeDB: Showing metabocard for 2'-Deoxyadenosine 3'-phosphate (MMDBc0057147)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2022-11-09 19:15:31 UTC

Update Date

2022-11-09 19:15:31 UTC

Metabolite ID

MMDBc0057147

Metabolite Identification

Common Name

2'-Deoxyadenosine 3'-phosphate

Description

2'-deoxyadenosine 3'-monophosphate, also known as 2'-deoxy-3'-AMP, belongs to the class of organic compounds known as ribonucleoside 3'-phosphates. These are ribonucleosides that contain a phosphate group attached to the C-3 carbon of the ribose or deoxyribose moiety. The nucleobases here are limited to purine, pyrimidine, and pyridine derivatives. 2'-deoxyadenosine 3'-monophosphate is a strong basic compound (based on its pKa).

Structure

MOL SDF PDB SMILES InChI


  Mrv0541 05031419232D          

 25 27  0  0  1  0            999 V2000
    0.0992   -0.1841    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1387   -2.0486    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3523    1.1104    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6538    1.5229    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0992   -1.0091    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.8838   -1.2640    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.8838    0.0709    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.9233    1.9354    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6378    2.3479    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9233    1.1104    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6378    3.1729    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.3523    1.9354    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.6378    0.6979    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.1387    2.1904    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.1387    0.8555    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.9457   -2.2201    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3958   -3.1349    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3025   -2.4007    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.3384   -2.2282    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.3687   -0.5966    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5683   -1.4940    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4820   -2.3145    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6359   -0.6345    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3004   -1.8474    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3004    0.6542    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  5  1  1  0  0  0  0
  6  2  1  6  0  0  0
  6  5  1  0  0  0  0
  7  1  1  0  0  0  0
  9  8  2  0  0  0  0
 10  8  1  0  0  0  0
 11  9  1  0  0  0  0
 12  3  2  0  0  0  0
 12  9  1  0  0  0  0
 13  3  1  0  0  0  0
 13 10  2  0  0  0  0
 14  4  2  0  0  0  0
 14  8  1  0  0  0  0
 15  4  1  0  0  0  0
  7 15  1  6  0  0  0
 15 10  1  0  0  0  0
 16  2  1  0  0  0  0
 20  6  1  0  0  0  0
 20  7  1  0  0  0  0
  5 21  1  1  0  0  0
 22 17  1  0  0  0  0
 22 18  1  0  0  0  0
 22 19  2  0  0  0  0
 22 21  1  0  0  0  0
  5 23  1  6  0  0  0
  6 24  1  1  0  0  0
  7 25  1  1  0  0  0
M  END
> <DATABASE_ID>
MMDBc0057147

> <DATABASE_NAME>
MIME

> <SMILES>
[H][C@@]1(C[C@]([H])(OP(O)(O)=O)[C@@]([H])(CO)O1)N1C=NC2=C(N)N=CN=C12

> <INCHI_IDENTIFIER>
InChI=1S/C10H14N5O6P/c11-9-8-10(13-3-12-9)15(4-14-8)7-1-5(6(2-16)20-7)21-22(17,18)19/h3-7,16H,1-2H2,(H2,11,12,13)(H2,17,18,19)/t5-,6+,7+/m0/s1

> <INCHI_KEY>
UEUPTUCWIHOIMK-RRKCRQDMSA-N

> <FORMULA>
C10H14N5O6P

> <MOLECULAR_WEIGHT>
331.2218

> <EXACT_MASS>
331.068169717

> <JCHEM_ACCEPTOR_COUNT>
9

> <JCHEM_AVERAGE_POLARIZABILITY>
29.234766955078957

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
{[(2R,3S,5R)-5-(6-amino-9H-purin-9-yl)-2-(hydroxymethyl)oxolan-3-yl]oxy}phosphonic acid

> <ALOGPS_LOGP>
-2.44

> <JCHEM_LOGP>
-4.331708102745633

> <ALOGPS_LOGS>
-2.06

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-2

> <JCHEM_PKA>
6.144670000430156

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.0831717006787223

> <JCHEM_PKA_STRONGEST_BASIC>
4.968708874985157

> <JCHEM_POLAR_SURFACE_AREA>
165.83999999999997

> <JCHEM_REFRACTIVITY>
72.55779999999999

> <JCHEM_ROTATABLE_BOND_COUNT>
4

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
2.87e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
2'-Deoxy-3'-AMP

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 03-MAY-14   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   03-MAY-14         0                                  
HETATM    1  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM   11  N   UNK     0       0.000   0.000   0.000  0.00  0.00           N+0
HETATM   12  N   UNK     0       0.000   0.000   0.000  0.00  0.00           N+0
HETATM   13  N   UNK     0       0.000   0.000   0.000  0.00  0.00           N+0
HETATM   14  N   UNK     0       0.000   0.000   0.000  0.00  0.00           N+0
HETATM   15  N   UNK     0       0.000   0.000   0.000  0.00  0.00           N+0
HETATM   16  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   17  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   18  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   19  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   20  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   21  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   22  P   UNK     0       0.000   0.000   0.000  0.00  0.00           P+0
HETATM   23  H   UNK     0       0.000   0.000   0.000  0.00  0.00           H+0
HETATM   24  H   UNK     0       0.000   0.000   0.000  0.00  0.00           H+0
HETATM   25  H   UNK     0       0.000   0.000   0.000  0.00  0.00           H+0
CONECT    1    5    7                                                       
CONECT    2    6   16                                                       
CONECT    3   12   13                                                       
CONECT    4   14   15                                                       
CONECT    5    1    6   21   23                                             
CONECT    6    2    5   20   24                                             
CONECT    7    1   15   20   25                                             
CONECT    8    9   10   14                                                  
CONECT    9    8   11   12                                                  
CONECT   10    8   13   15                                                  
CONECT   11    9                                                            
CONECT   12    3    9                                                       
CONECT   13    3   10                                                       
CONECT   14    4    8                                                       
CONECT   15    4    7   10                                                  
CONECT   16    2                                                            
CONECT   17   22                                                            
CONECT   18   22                                                            
CONECT   19   22                                                            
CONECT   20    6    7                                                       
CONECT   21    5   22                                                       
CONECT   22   17   18   19   21                                             
CONECT   23    5                                                            
CONECT   24    6                                                            
CONECT   25    7                                                            
MASTER        0    0    0    0    0    0    0    0   25    0   54    0
END

Synonyms

Value	Source
2'-Deoxy-3'-adenosine monophosphate	ChEBI
2'-Deoxy-3'-AMP	ChEBI
2'-Deoxy-3'-adenosine monophosphoric acid	Generator
2'-Deoxyadenosine 3'-monophosphoric acid	Generator

Molecular Formula

C₁₀H₁₄N₅O₆P

Average Mass

331.2218

Monoisotopic Mass

331.068169717

IUPAC Name

{[(2R,3S,5R)-5-(6-amino-9H-purin-9-yl)-2-(hydroxymethyl)oxolan-3-yl]oxy}phosphonic acid

Traditional Name

2'-Deoxy-3'-AMP

CAS Registry Number

Not Available

SMILES

[H][C@@]1(C[C@]([H])(OP(O)(O)=O)[C@@]([H])(CO)O1)N1C=NC2=C(N)N=CN=C12

InChI Identifier

InChI=1S/C10H14N5O6P/c11-9-8-10(13-3-12-9)15(4-14-8)7-1-5(6(2-16)20-7)21-22(17,18)19/h3-7,16H,1-2H2,(H2,11,12,13)(H2,17,18,19)/t5-,6+,7+/m0/s1

InChI Key

UEUPTUCWIHOIMK-RRKCRQDMSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as ribonucleoside 3'-phosphates. These are ribonucleosides that contain a phosphate group attached to the C-3 carbon of the ribose or deoxyribose moiety. The nucleobases here are limited to purine, pyrimidine, and pyridine derivatives.

Kingdom

Organic compounds

Super Class

Nucleosides, nucleotides, and analogues

Class

Ribonucleoside 3'-phosphates

Sub Class

Not Available

Direct Parent

Ribonucleoside 3'-phosphates

Alternative Parents

Substituents

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

Molecular Framework

Aromatic heteropolycyclic compounds

External Descriptors

purine 2'-deoxyribonucleoside 3'-monophosphate (CHEBI:580387 )
2'-deoxyadenosine phosphate (CHEBI:580387 )

Functional Ontology

Not Available

Physical Properties

State

Not Available

Predicted Properties

Property	Value	Source
Water Solubility	2.87 g/L	ALOGPS
logP	-2.4	ALOGPS
logP	-4.3	ChemAxon
logS	-2.1	ALOGPS
pKa (Strongest Acidic)	1.08	ChemAxon
pKa (Strongest Basic)	4.97	ChemAxon
Physiological Charge	-2	ChemAxon
Hydrogen Acceptor Count	9	ChemAxon
Hydrogen Donor Count	4	ChemAxon
Polar Surface Area	165.84 Å²	ChemAxon
Rotatable Bond Count	4	ChemAxon
Refractivity	72.56 m³·mol⁻¹	ChemAxon
Polarizability	29.23 Å³	ChemAxon
Number of Rings	3	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

Spectra

Not Available

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

Metabolic Reactions

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

Exposure Sources

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

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

167350

PDB ID

Not Available

ChEBI ID

580387

Food Biomarker Ontology

Not Available

References

Synthesis Reference

Not Available

General References

Bansal P, Morgat A, Axelsen KB, Muthukrishnan V, Coudert E, Aimo L, Hyka-Nouspikel N, Gasteiger E, Kerhornou A, Neto TB, Pozzato M, Blatter MC, Ignatchenko A, Redaschi N, Bridge A: Rhea, the reaction knowledgebase in 2022. Nucleic Acids Res. 2022 Jan 7;50(D1):D693-D700. doi: 10.1093/nar/gkab1016. [PubMed:34755880 ]

Showing metabocard for 2'-Deoxyadenosine 3'-phosphate (MMDBc0057147)

MOL for #<Metabolite:0x00007fdb489e6878>

3D MOL for #<Metabolite:0x00007fdb489e6878>

3D SDF for #<Metabolite:0x00007fdb489e6878>

3D-SDF for #<Metabolite:0x00007fdb489e6878>

PDB for #<Metabolite:0x00007fdb489e6878>

3D PDB for #<Metabolite:0x00007fdb489e6878>

SMILES for #<Metabolite:0x00007fdb489e6878>

INCHI for #<Metabolite:0x00007fdb489e6878>

Structure for #<Metabolite:0x00007fdb489e6878>

3D Structure for #<Metabolite:0x00007fdb489e6878>