MiMeDB: Showing metabocard for 5-Amino-2,6-dioxy-4-(5'-phospho-D-ribitylamino)pyrimidine (MMDBc0047873)

Microbial

Record Information

Version

2.0

Status

Detected and Quantified

Creation Date

2021-11-19 15:46:58 UTC

Update Date

2025-10-07 16:08:08 UTC

Metabolite ID

MMDBc0047873

Metabolite Identification

Common Name

5-Amino-2,6-dioxy-4-(5'-phospho-D-ribitylamino)pyrimidine

Description

5-Amino-2,6-dioxy-4-(5'-phospho-D-ribitylamino)pyrimidine is a pyrimidine derivative. There is little literature available on this metabolite, indicating that its biological significance and potential roles in metabolic pathways remain largely unexplored.

Structure

MOL SDF PDB SMILES InChI


  Mrv1572001051620482D          

 23 23  0  0  0  0            999 V2000
   -3.7500    3.3919    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4645    2.9794    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4645    2.1543    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7500    1.7419    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0355    2.1543    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0355    2.9794    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7500    4.2169    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3210    1.7418    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.1789    1.7418    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -5.1788    0.9168    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4643    0.5043    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4643   -0.3206    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7499    0.9169    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
   -5.1787   -0.7331    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
   -3.7498   -0.7330    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7498   -1.5580    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0353   -1.9705    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0530   -1.9374    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0354   -0.3205    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
   -5.1789    3.3919    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0665   -1.0755    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
   -1.1925   -1.9456    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
   -2.0617   -2.9779    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  2  0  0  0  0
 10 11  1  0  0  0  0
 11 12  1  0  0  0  0
 12 15  1  0  0  0  0
 15 16  1  0  0  0  0
 16 17  1  0  0  0  0
 17 18  1  0  0  0  0
 15 19  1  0  0  0  0
 12 14  1  0  0  0  0
 11 13  1  0  0  0  0
  3  9  1  0  0  0  0
  9 10  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  1  6  1  0  0  0  0
  5  6  1  0  0  0  0
  2 20  1  0  0  0  0
  5  8  2  0  0  0  0
  1  7  2  0  0  0  0
 18 21  1  0  0  0  0
 18 23  2  0  0  0  0
 18 22  1  0  0  0  0
M  CHG  5  13  -1  14  -1  19  -1  21  -1  22  -1
M  END
> <DATABASE_ID>
MMDBc0047873

> <DATABASE_NAME>
MIME

> <SMILES>
NC1=C(NCC([O-])C([O-])C([O-])COP([O-])([O-])=O)NC(=O)NC1=O

> <INCHI_IDENTIFIER>
InChI=1S/C9H14N4O9P/c10-5-7(12-9(18)13-8(5)17)11-1-3(14)6(16)4(15)2-22-23(19,20)21/h3-4,6H,1-2,10H2,(H2,19,20,21)(H3,11,12,13,17,18)/q-3/p-2

> <INCHI_KEY>
XFQQOMMQTVPCOB-UHFFFAOYSA-L

> <FORMULA>
C9H12N4O9P

> <MOLECULAR_WEIGHT>
351.191

> <EXACT_MASS>
351.03693288

> <JCHEM_ACCEPTOR_COUNT>
10

> <JCHEM_ATOM_COUNT>
35

> <JCHEM_AVERAGE_POLARIZABILITY>
29.128050600210322

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
-5

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
1-[(5-amino-2,6-dioxo-1,2,3,6-tetrahydropyrimidin-4-yl)amino]-5-(phosphonatooxy)pentane-2,3,4-tris(olate)

> <ALOGPS_LOGP>
-1.35

> <JCHEM_LOGP>
-4.512588078333334

> <ALOGPS_LOGS>
-1.72

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-2

> <JCHEM_PKA>
6.513137596770021

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.4921085022698914

> <JCHEM_PKA_STRONGEST_BASIC>
-2.743613426263204

> <JCHEM_POLAR_SURFACE_AREA>
237.85

> <JCHEM_REFRACTIVITY>
111.76499999999999

> <JCHEM_ROTATABLE_BOND_COUNT>
8

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
8.43e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
1-[(5-amino-2,6-dioxo-1,3-dihydropyrimidin-4-yl)amino]-5-(phosphonatooxy)pentane-2,3,4-tris(olate)

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 05-JAN-16   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   05-JAN-16         0                                  
HETATM    1  C   UNK     0      -7.000   6.332   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -8.334   5.562   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -8.334   4.021   0.000  0.00  0.00           C+0
HETATM    4  N   UNK     0      -7.000   3.252   0.000  0.00  0.00           N+0
HETATM    5  C   UNK     0      -5.666   4.021   0.000  0.00  0.00           C+0
HETATM    6  N   UNK     0      -5.666   5.562   0.000  0.00  0.00           N+0
HETATM    7  O   UNK     0      -7.000   7.872   0.000  0.00  0.00           O+0
HETATM    8  O   UNK     0      -4.333   3.251   0.000  0.00  0.00           O+0
HETATM    9  N   UNK     0      -9.667   3.251   0.000  0.00  0.00           N+0
HETATM   10  C   UNK     0      -9.667   1.711   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      -8.333   0.941   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      -8.333  -0.598   0.000  0.00  0.00           C+0
HETATM   13  O   UNK     0      -7.000   1.712   0.000  0.00  0.00           O-1
HETATM   14  O   UNK     0      -9.667  -1.368   0.000  0.00  0.00           O-1
HETATM   15  C   UNK     0      -7.000  -1.368   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0      -7.000  -2.908   0.000  0.00  0.00           C+0
HETATM   17  O   UNK     0      -5.666  -3.678   0.000  0.00  0.00           O+0
HETATM   18  P   UNK     0      -3.832  -3.616   0.000  0.00  0.00           P+0
HETATM   19  O   UNK     0      -5.666  -0.598   0.000  0.00  0.00           O-1
HETATM   20  N   UNK     0      -9.667   6.332   0.000  0.00  0.00           N+0
HETATM   21  O   UNK     0      -3.857  -2.008   0.000  0.00  0.00           O-1
HETATM   22  O   UNK     0      -2.226  -3.632   0.000  0.00  0.00           O-1
HETATM   23  O   UNK     0      -3.849  -5.559   0.000  0.00  0.00           O+0
CONECT    1    2    6    7                                                  
CONECT    2    1    3   20                                                  
CONECT    3    2    9    4                                                  
CONECT    4    3    5                                                       
CONECT    5    4    6    8                                                  
CONECT    6    1    5                                                       
CONECT    7    1                                                            
CONECT    8    5                                                            
CONECT    9    3   10                                                       
CONECT   10   11    9                                                       
CONECT   11   10   12   13                                                  
CONECT   12   11   15   14                                                  
CONECT   13   11                                                            
CONECT   14   12                                                            
CONECT   15   12   16   19                                                  
CONECT   16   15   17                                                       
CONECT   17   16   18                                                       
CONECT   18   17   21   23   22                                             
CONECT   19   15                                                            
CONECT   20    2                                                            
CONECT   21   18                                                            
CONECT   22   18                                                            
CONECT   23   18                                                            
MASTER        0    0    0    0    0    0    0    0   23    0   46    0
END

Synonyms

Not Available

Molecular Formula

C₉H₁₂N₄O₉P

Average Mass

351.191

Monoisotopic Mass

351.03693288

IUPAC Name

1-[(5-amino-2,6-dioxo-1,2,3,6-tetrahydropyrimidin-4-yl)amino]-5-(phosphonatooxy)pentane-2,3,4-tris(olate)

Traditional Name

1-[(5-amino-2,6-dioxo-1,3-dihydropyrimidin-4-yl)amino]-5-(phosphonatooxy)pentane-2,3,4-tris(olate)

CAS Registry Number

Not Available

SMILES

NC1=C(NCC([O-])C([O-])C([O-])COP([O-])([O-])=O)NC(=O)NC1=O

InChI Identifier

InChI=1S/C9H14N4O9P/c10-5-7(12-9(18)13-8(5)17)11-1-3(14)6(16)4(15)2-22-23(19,20)21/h3-4,6H,1-2,10H2,(H2,19,20,21)(H3,11,12,13,17,18)/q-3/p-2

InChI Key

XFQQOMMQTVPCOB-UHFFFAOYSA-L

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as monosaccharide phosphates. These are monosaccharides comprising a phosphated group linked to the carbohydrate unit.

Kingdom

Organic compounds

Super Class

Organic oxygen compounds

Class

Organooxygen compounds

Sub Class

Carbohydrates and carbohydrate conjugates

Direct Parent

Monosaccharide phosphates

Alternative Parents

Substituents

Monosaccharide phosphate
Monoalkyl phosphate
Secondary aliphatic/aromatic amine
Aminopyrimidine
Imidolactam
Alkyl phosphate
Pyrimidine
Phosphoric acid ester
Organic phosphoric acid derivative
Heteroaromatic compound
Azacycle
Organoheterocyclic compound
Secondary amine
Organic nitrogen compound
Organopnictogen compound
Organic oxide
Hydrocarbon derivative
Alkoxide
Primary amine
Organonitrogen compound
Amine
Organic anion
Aromatic heteromonocyclic compound

Molecular Framework

Aromatic heteromonocyclic compounds

External Descriptors

Not Available

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
Water Solubility	8.43 g/L	ALOGPS
logP	-1.4	ALOGPS
logP	-4.5	ChemAxon
logS	-1.7	ALOGPS
pKa (Strongest Acidic)	1.49	ChemAxon
pKa (Strongest Basic)	-2.7	ChemAxon
Physiological Charge	-2	ChemAxon
Hydrogen Acceptor Count	10	ChemAxon
Hydrogen Donor Count	4	ChemAxon
Polar Surface Area	237.85 Å²	ChemAxon
Rotatable Bond Count	8	ChemAxon
Refractivity	111.76 m³·mol⁻¹	ChemAxon
Polarizability	29.13 Å³	ChemAxon
Number of Rings	1	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 LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-0udi-0019000000-0a49e19058eb50c56bab	2016-09-14	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-0002-3319000000-f268f1685cc37f825537	2016-09-14	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-01ow-9432000000-8aabd1a849a22c9a3a1a	2016-09-14	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-0udi-2209000000-c69e60e3885d3d25518b	2016-09-14	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-004l-9100000000-188a19d2fa388c07f3c7	2016-09-14	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-004i-9000000000-f42e4d7b6dd4a3e92f30	2016-09-14	View Spectrum

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

This table shows at most 5 pathways. For the full list of associated pathways:

See All Associated Bacterial Pathways

Name	SMPDB/PathBank	Species

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
MMDBr0019645	2,5-Diamino-6-(1-D-ribitylamino)pyrimidin-4(3H)-one 5'-phosphate	5-Amino-2,6-dioxy-4-(5'-phospho-D-ribitylamino)pyrimidine	Bifunctional protein RIB2	Synthesis	PathBank	31602464

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

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

Not Available

PDB ID

Not Available

ChEBI ID

Not Available

Food Biomarker Ontology

Not Available

CMMC Knowledgebase

Not Available

References

Synthesis Reference

Not Available

General References

Wishart DS, Li C, Marcu A, Badran H, Pon A, Budinski Z, Patron J, Lipton D, Cao X, Oler E, Li K, Paccoud M, Hong C, Guo AC, Chan C, Wei W, Ramirez-Gaona M: PathBank: a comprehensive pathway database for model organisms. Nucleic Acids Res. 2020 Jan 8;48(D1):D470-D478. doi: 10.1093/nar/gkz861. [PubMed:31602464 ]

Showing metabocard for 5-Amino-2,6-dioxy-4-(5'-phospho-D-ribitylamino)pyrimidine (MMDBc0047873)

MOL for #<Metabolite:0x00007f2add372f80>

3D MOL for #<Metabolite:0x00007f2add372f80>

3D SDF for #<Metabolite:0x00007f2add372f80>

3D-SDF for #<Metabolite:0x00007f2add372f80>

PDB for #<Metabolite:0x00007f2add372f80>

3D PDB for #<Metabolite:0x00007f2add372f80>

SMILES for #<Metabolite:0x00007f2add372f80>

INCHI for #<Metabolite:0x00007f2add372f80>

Structure for #<Metabolite:0x00007f2add372f80>

3D Structure for #<Metabolite:0x00007f2add372f80>