MiMeDB: Showing metabocard for adenosine 5'-phosphoramidate (MMDBc0055682)

Record Information

Version

2.0

Status

Detected and Quantified

Creation Date

2022-06-17 20:02:03 UTC

Update Date

2025-10-07 16:09:17 UTC

Metabolite ID

MMDBc0055682

Metabolite Identification

Common Name

adenosine 5'-phosphoramidate

Description

Adenosine 5'-phosphoramidate is a nucleoside 5'-phosphoramidate, a class of uncommon nucleotides characterized by the presence of an amide group attached to the phosphate moiety. Its chemical structure features an adenosine base linked to a phosphate group, which is further modified by an amine, distinguishing it from more common nucleotides. In cellular metabolism, adenosine 5'-phosphoramidate (NH2-pA) is involved in various biochemical pathways, including signaling mechanisms in plants where it acts as a signaling molecule that enhances the metabolism of phenylpropanoids and salicylic acid in Arabidopsis thaliana seedlings (PMID:26079287 ). Additionally, it is formed through the ammonolysis of adenosine 5'-phosphosulfate, catalyzed by Fhit proteins, which also hydrolyze other nucleotides (PMID:26181368 , PMID:18694747 ). Despite its presence in cells and potential roles in signaling and metabolic processes, the biochemistry and biological functions of adenosine 5'-phosphoramidate remain poorly understood (PMID:23772423 , PMID:21403921 ). Its rarity and the complexity of its pathways contribute to the intrigue surrounding this nucleotide.

Structure

MOL SDF PDB SMILES InChI


  Mrv1652306172222022D          

 27 29  0  0  1  0            999 V2000
   -0.5683   -1.4940    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  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
    0.8838   -1.2640    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.3687   -0.5966    0.0000 C   0  0  2  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
    0.8838    0.0709    0.0000 C   0  0  2  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
   -2.6568   -2.1283    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
    1.1387   -2.0486    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1937   -0.5966    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4743   -0.9759    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
   -1.5045   -2.3108    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3220   -1.1584    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0992   -0.1841    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9894   -1.6433    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
    0.2282   -1.8239    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6986   -1.3931    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7432    0.1385    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
  4  1  1  1  0  0  0
  6  4  1  0  0  0  0
  7  6  1  0  0  0  0
  8  5  2  0  0  0  0
  9  5  1  0  0  0  0
 10  7  1  0  0  0  0
 11  8  1  0  0  0  0
 13  2  2  0  0  0  0
 13  8  1  0  0  0  0
 14  2  1  0  0  0  0
 14  9  2  0  0  0  0
 15  3  2  0  0  0  0
 15  5  1  0  0  0  0
 16  3  1  0  0  0  0
 16  9  1  0  0  0  0
 10 16  1  1  0  0  0
  6 17  1  6  0  0  0
  7 18  1  6  0  0  0
 21  1  1  0  0  0  0
 22  4  1  0  0  0  0
 22 10  1  0  0  0  0
 23 12  1  0  0  0  0
 23 19  1  0  0  0  0
 23 20  2  0  0  0  0
 23 21  1  0  0  0  0
  4 24  1  6  0  0  0
  6 25  1  1  0  0  0
  7 26  1  1  0  0  0
 10 27  1  6  0  0  0
M  CHG  1  19  -1
M  END


  Mrv1652306172222022D          

 27 29  0  0  1  0            999 V2000
   -0.5683   -1.4940    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  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
    0.8838   -1.2640    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.3687   -0.5966    0.0000 C   0  0  2  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
    0.8838    0.0709    0.0000 C   0  0  2  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
   -2.6568   -2.1283    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
    1.1387   -2.0486    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1937   -0.5966    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4743   -0.9759    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
   -1.5045   -2.3108    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3220   -1.1584    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0992   -0.1841    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9894   -1.6433    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
    0.2282   -1.8239    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6986   -1.3931    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7432    0.1385    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
  4  1  1  1  0  0  0
  6  4  1  0  0  0  0
  7  6  1  0  0  0  0
  8  5  2  0  0  0  0
  9  5  1  0  0  0  0
 10  7  1  0  0  0  0
 11  8  1  0  0  0  0
 13  2  2  0  0  0  0
 13  8  1  0  0  0  0
 14  2  1  0  0  0  0
 14  9  2  0  0  0  0
 15  3  2  0  0  0  0
 15  5  1  0  0  0  0
 16  3  1  0  0  0  0
 16  9  1  0  0  0  0
 10 16  1  1  0  0  0
  6 17  1  6  0  0  0
  7 18  1  6  0  0  0
 21  1  1  0  0  0  0
 22  4  1  0  0  0  0
 22 10  1  0  0  0  0
 23 12  1  0  0  0  0
 23 19  1  0  0  0  0
 23 20  2  0  0  0  0
 23 21  1  0  0  0  0
  4 24  1  6  0  0  0
  6 25  1  1  0  0  0
  7 26  1  1  0  0  0
 10 27  1  6  0  0  0
M  CHG  1  19  -1
M  END
> <DATABASE_ID>
MMDBc0055682

> <DATABASE_NAME>
MIME

> <SMILES>
[H][C@]1(COP(N)([O-])=O)O[C@@]([H])(N2C=NC3=C(N)N=CN=C23)[C@]([H])(O)[C@]1([H])O

> <INCHI_IDENTIFIER>
InChI=1S/C10H15N6O6P/c11-8-5-9(14-2-13-8)16(3-15-5)10-7(18)6(17)4(22-10)1-21-23(12,19)20/h2-4,6-7,10,17-18H,1H2,(H2,11,13,14)(H3,12,19,20)/p-1/t4-,6-,7-,10-/m1/s1

> <INCHI_KEY>
LDEMREUBLBGZBO-KQYNXXCUSA-M

> <FORMULA>
C10H14N6O6P

> <MOLECULAR_WEIGHT>
345.232

> <EXACT_MASS>
345.071792773

> <JCHEM_ACCEPTOR_COUNT>
9

> <JCHEM_ATOM_COUNT>
37

> <JCHEM_AVERAGE_POLARIZABILITY>
29.952239393426716

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
-1

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
amino({[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxyoxolan-2-yl]methoxy})phosphinate

> <JCHEM_LOGP>
-4.212384313712803

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
12.457206439093081

> <JCHEM_PKA_STRONGEST_ACIDIC>
2.6450179538445933

> <JCHEM_PKA_STRONGEST_BASIC>
3.944896576198745

> <JCHEM_POLAR_SURFACE_AREA>
194.69

> <JCHEM_REFRACTIVITY>
74.4822

> <JCHEM_ROTATABLE_BOND_COUNT>
4

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
adenosine 5'-phosphoramidate

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 17-JUN-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   17-JUN-22         0                                  
HETATM    1  C   UNK     0      -1.061  -2.789   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       6.258   2.073   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       1.220   2.843   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       0.185  -1.884   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       3.590   3.613   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       1.650  -2.359   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       2.555  -1.114   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       4.924   4.383   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       3.590   2.073   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       1.650   0.132   0.000  0.00  0.00           C+0
HETATM   11  N   UNK     0       4.924   5.923   0.000  0.00  0.00           N+0
HETATM   12  N   UNK     0      -4.959  -3.973   0.000  0.00  0.00           N+0
HETATM   13  N   UNK     0       6.258   3.613   0.000  0.00  0.00           N+0
HETATM   14  N   UNK     0       4.924   1.303   0.000  0.00  0.00           N+0
HETATM   15  N   UNK     0       2.126   4.089   0.000  0.00  0.00           N+0
HETATM   16  N   UNK     0       2.126   1.597   0.000  0.00  0.00           N+0
HETATM   17  O   UNK     0       2.126  -3.824   0.000  0.00  0.00           O+0
HETATM   18  O   UNK     0       4.095  -1.114   0.000  0.00  0.00           O+0
HETATM   19  O   UNK     0      -4.619  -1.822   0.000  0.00  0.00           O-1
HETATM   20  O   UNK     0      -2.808  -4.313   0.000  0.00  0.00           O+0
HETATM   21  O   UNK     0      -2.468  -2.162   0.000  0.00  0.00           O+0
HETATM   22  O   UNK     0       0.185  -0.344   0.000  0.00  0.00           O+0
HETATM   23  P   UNK     0      -3.714  -3.068   0.000  0.00  0.00           P+0
HETATM   24  H   UNK     0       0.426  -3.405   0.000  0.00  0.00           H+0
HETATM   25  H   UNK     0       3.171  -2.600   0.000  0.00  0.00           H+0
HETATM   26  H   UNK     0       3.254   0.259   0.000  0.00  0.00           H+0
HETATM   27  H   UNK     0       0.561   1.221   0.000  0.00  0.00           H+0
CONECT    1    4   21                                                       
CONECT    2   13   14                                                       
CONECT    3   15   16                                                       
CONECT    4    1    6   22   24                                             
CONECT    5    8    9   15                                                  
CONECT    6    4    7   17   25                                             
CONECT    7    6   10   18   26                                             
CONECT    8    5   11   13                                                  
CONECT    9    5   14   16                                                  
CONECT   10    7   16   22   27                                             
CONECT   11    8                                                            
CONECT   12   23                                                            
CONECT   13    2    8                                                       
CONECT   14    2    9                                                       
CONECT   15    3    5                                                       
CONECT   16    3    9   10                                                  
CONECT   17    6                                                            
CONECT   18    7                                                            
CONECT   19   23                                                            
CONECT   20   23                                                            
CONECT   21    1   23                                                       
CONECT   22    4   10                                                       
CONECT   23   12   19   20   21                                             
CONECT   24    4                                                            
CONECT   25    6                                                            
CONECT   26    7                                                            
CONECT   27   10                                                            
MASTER        0    0    0    0    0    0    0    0   27    0   58    0
END

Synonyms

Value	Source
Adenosine 5'-phosphoramidate	ChEBI
Adenosine 5'-phosphoramidate anion	ChEBI
Adenosine 5'-phosphoramidic acid	Generator
Adenosine 5'-phosphoramidic acid anion	Generator
Adenosine 5'-phosphoramidic acid(1-)	Generator

Molecular Formula

C₁₀H₁₄N₆O₆P

Average Mass

345.232

Monoisotopic Mass

345.071792773

IUPAC Name

amino({[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxyoxolan-2-yl]methoxy})phosphinate

Traditional Name

adenosine 5'-phosphoramidate

CAS Registry Number

Not Available

SMILES

[H][C@]1(COP(N)([O-])=O)O[C@@]([H])(N2C=NC3=C(N)N=CN=C23)[C@]([H])(O)[C@]1([H])O

InChI Identifier

InChI=1S/C10H15N6O6P/c11-8-5-9(14-2-13-8)16(3-15-5)10-7(18)6(17)4(22-10)1-21-23(12,19)20/h2-4,6-7,10,17-18H,1H2,(H2,11,13,14)(H3,12,19,20)/p-1/t4-,6-,7-,10-/m1/s1

InChI Key

LDEMREUBLBGZBO-KQYNXXCUSA-M

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as glycosylamines. Glycosylamines are compounds consisting of an amine with a beta-N-glycosidic bond to a carbohydrate, thus forming a cyclic hemiaminal ether bond (alpha-amino ether).

Kingdom

Organic compounds

Super Class

Organic oxygen compounds

Class

Organooxygen compounds

Sub Class

Carbohydrates and carbohydrate conjugates

Direct Parent

Glycosylamines

Alternative Parents

Substituents

N-glycosyl compound
6-aminopurine
Pentose monosaccharide
Imidazopyrimidine
Purine
Aminopyrimidine
Phosphoric monoester monoamide
Monosaccharide
N-substituted imidazole
Organic phosphoric acid derivative
Imidolactam
Organic phosphoric acid amide
Phosphoric acid ester
Pyrimidine
Azole
Imidazole
Heteroaromatic compound
Tetrahydrofuran
1,2-diol
Secondary alcohol
Organoheterocyclic compound
Azacycle
Oxacycle
Organonitrogen compound
Alcohol
Hydrocarbon derivative
Organic nitrogen compound
Organic oxide
Organopnictogen compound
Primary amine
Amine
Organic anion
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic heteropolycyclic compounds

External Descriptors

organic phosphoramidate anion (CHEBI:57890 )

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
logP	-4.2	ChemAxon
pKa (Strongest Acidic)	2.65	ChemAxon
pKa (Strongest Basic)	3.94	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	9	ChemAxon
Hydrogen Donor Count	4	ChemAxon
Polar Surface Area	194.69 Å²	ChemAxon
Rotatable Bond Count	4	ChemAxon
Refractivity	74.48 m³·mol⁻¹	ChemAxon
Polarizability	29.95 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

Chromatographic Retention Times and Retention Indices

Retention Times

Not Available

Retention Indices

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

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	3

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

19951262

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

23615303

PDB ID

Not Available

ChEBI ID

57890

Food Biomarker Ontology

Not Available

CMMC Knowledgebase

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 adenosine 5'-phosphoramidate (MMDBc0055682)

MOL for #<Metabolite:0x00007fade0123dc0>

3D MOL for #<Metabolite:0x00007fade0123dc0>

3D SDF for #<Metabolite:0x00007fade0123dc0>

3D-SDF for #<Metabolite:0x00007fade0123dc0>

PDB for #<Metabolite:0x00007fade0123dc0>

3D PDB for #<Metabolite:0x00007fade0123dc0>

SMILES for #<Metabolite:0x00007fade0123dc0>

INCHI for #<Metabolite:0x00007fade0123dc0>

Structure for #<Metabolite:0x00007fade0123dc0>

3D Structure for #<Metabolite:0x00007fade0123dc0>