MiMeDB: Showing metabocard for 5-Amino-6-ribitylamino uracil (MMDBc0029807)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2021-11-17 23:42:32 UTC

Update Date

2022-08-31 17:18:33 UTC

Metabolite ID

MMDBc0029807

Metabolite Identification

Common Name

5-Amino-6-ribitylamino uracil

Description

5-Amino-6-ribitylamino uracil is an intermediate in riboflavin metabolism. It is converted from 5-Amino-6-(5'-phosphoribitylamino)uracil via dephosphorylation by the enzyme phosphohistidine phosphatase 1 (EC 3.1.3.-). (HMDB, KEGG)

Structure

MOL SDF PDB SMILES InChI


  Mrv0541 02241201182D          

 19 19  0  0  0  0            999 V2000
   19.1644   -8.8929    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   19.1637   -8.1146    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   19.8476   -7.7193    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   20.5268   -8.1112    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   20.5222   -8.8986    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   19.8437   -9.2848    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   18.4799   -7.7201    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   19.8431   -6.9267    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   18.4804   -9.2882    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   21.2061   -9.2932    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   17.0514  -12.5885    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   17.0514  -11.7635    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   17.7659  -11.3509    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   17.7659  -10.5258    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   18.4804  -10.1133    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   16.3368  -13.0011    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   16.3368  -11.3509    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   18.4804  -11.7635    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   17.0514  -10.1133    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  6  1  1  0  0  0  0
  2  7  1  0  0  0  0
  3  8  2  0  0  0  0
  1  9  1  0  0  0  0
  5 10  2  0  0  0  0
 12 11  1  0  0  0  0
 13 12  1  0  0  0  0
 14 13  1  0  0  0  0
 15 14  1  0  0  0  0
 11 16  1  0  0  0  0
 12 17  1  0  0  0  0
 13 18  1  0  0  0  0
 14 19  1  0  0  0  0
 15  9  1  0  0  0  0
M  END
> <DATABASE_ID>
MMDBc0029807

> <DATABASE_NAME>
MIME

> <SMILES>
NC1=C(NCC(O)C(O)C(O)CO)NC(=O)NC1=O

> <INCHI_IDENTIFIER>
InChI=1S/C9H16N4O6/c10-5-7(12-9(19)13-8(5)18)11-1-3(15)6(17)4(16)2-14/h3-4,6,14-17H,1-2,10H2,(H3,11,12,13,18,19)

> <INCHI_KEY>
XKQZIXVJVUPORE-UHFFFAOYSA-N

> <FORMULA>
C9H16N4O6

> <MOLECULAR_WEIGHT>
276.2465

> <EXACT_MASS>
276.106984264

> <JCHEM_ACCEPTOR_COUNT>
8

> <JCHEM_AVERAGE_POLARIZABILITY>
25.92093591924372

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
8

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
5-amino-6-[(2,3,4,5-tetrahydroxypentyl)amino]-1,2,3,4-tetrahydropyrimidine-2,4-dione

> <ALOGPS_LOGP>
-2.44

> <JCHEM_LOGP>
-4.389022046999999

> <ALOGPS_LOGS>
-1.29

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
12.660773298965573

> <JCHEM_PKA_STRONGEST_ACIDIC>
9.412531420932337

> <JCHEM_PKA_STRONGEST_BASIC>
4.356375443965954

> <JCHEM_POLAR_SURFACE_AREA>
177.17

> <JCHEM_REFRACTIVITY>
71.4846

> <JCHEM_ROTATABLE_BOND_COUNT>
6

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
1.43e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
5-amino-6-[(2,3,4,5-tetrahydroxypentyl)amino]-1,3-dihydropyrimidine-2,4-dione

> <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  C   UNK     0      35.774 -16.600   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      35.772 -15.147   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      37.049 -14.409   0.000  0.00  0.00           C+0
HETATM    4  N   UNK     0      38.317 -15.141   0.000  0.00  0.00           N+0
HETATM    5  C   UNK     0      38.308 -16.611   0.000  0.00  0.00           C+0
HETATM    6  N   UNK     0      37.042 -17.332   0.000  0.00  0.00           N+0
HETATM    7  N   UNK     0      34.496 -14.411   0.000  0.00  0.00           N+0
HETATM    8  O   UNK     0      37.040 -12.930   0.000  0.00  0.00           O+0
HETATM    9  N   UNK     0      34.497 -17.338   0.000  0.00  0.00           N+0
HETATM   10  O   UNK     0      39.585 -17.347   0.000  0.00  0.00           O+0
HETATM   11  C   UNK     0      31.829 -23.499   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      31.829 -21.958   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      33.163 -21.188   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      33.163 -19.648   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0      34.497 -18.878   0.000  0.00  0.00           C+0
HETATM   16  O   UNK     0      30.495 -24.269   0.000  0.00  0.00           O+0
HETATM   17  O   UNK     0      30.495 -21.188   0.000  0.00  0.00           O+0
HETATM   18  O   UNK     0      34.497 -21.958   0.000  0.00  0.00           O+0
HETATM   19  O   UNK     0      31.829 -18.878   0.000  0.00  0.00           O+0
CONECT    1    2    6    9                                                  
CONECT    2    1    3    7                                                  
CONECT    3    2    4    8                                                  
CONECT    4    3    5                                                       
CONECT    5    4    6   10                                                  
CONECT    6    5    1                                                       
CONECT    7    2                                                            
CONECT    8    3                                                            
CONECT    9    1   15                                                       
CONECT   10    5                                                            
CONECT   11   12   16                                                       
CONECT   12   11   13   17                                                  
CONECT   13   12   14   18                                                  
CONECT   14   13   15   19                                                  
CONECT   15   14    9                                                       
CONECT   16   11                                                            
CONECT   17   12                                                            
CONECT   18   13                                                            
CONECT   19   14                                                            
MASTER        0    0    0    0    0    0    0    0   19    0   38    0
END

Synonyms

Value	Source
1-[(5-Amino-2,6-dihydroxypyrimidin-4-yl)amino]-1-deoxy-D-ribitol	HMDB
1-[(5-Amino-2,6-dioxo-1,2,3,6-tetrahydropyrimidin-4-yl)amino]-1-deoxy-D-ribitol	HMDB
4-(1-D-Ribitylamino)-5-amino-2,6 dihydroxypyrimidine	HMDB
4-(1-D-Ribitylamino)-5-amino-2,6-dihydroxypyrimidine	HMDB
4-(1-D-Ribitylamino)-5-aminouracil	HMDB
5-Amino-6-(2,3,4,5-tetrahydroxypentylamino)-1H-pyrimidine-2,4-dione	HMDB
6-Ribitylamino-5-aminouracil	HMDB

Molecular Formula

C₉H₁₆N₄O₆

Average Mass

276.2465

Monoisotopic Mass

276.106984264

IUPAC Name

5-amino-6-[(2,3,4,5-tetrahydroxypentyl)amino]-1,2,3,4-tetrahydropyrimidine-2,4-dione

Traditional Name

5-amino-6-[(2,3,4,5-tetrahydroxypentyl)amino]-1,3-dihydropyrimidine-2,4-dione

CAS Registry Number

Not Available

SMILES

NC1=C(NCC(O)C(O)C(O)CO)NC(=O)NC1=O

InChI Identifier

InChI=1S/C9H16N4O6/c10-5-7(12-9(19)13-8(5)18)11-1-3(15)6(17)4(16)2-14/h3-4,6,14-17H,1-2,10H2,(H3,11,12,13,18,19)

InChI Key

XKQZIXVJVUPORE-UHFFFAOYSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as pentoses. These are monosaccharides in which the carbohydrate moiety contains five carbon atoms.

Kingdom

Organic compounds

Super Class

Organic oxygen compounds

Class

Organooxygen compounds

Sub Class

Carbohydrates and carbohydrate conjugates

Direct Parent

Pentoses

Alternative Parents

Substituents

Pentose monosaccharide
Aminopyrimidine
Pyrimidone
Secondary aliphatic/aromatic amine
Hydropyrimidine
Pyrimidine
Heteroaromatic compound
Vinylogous amide
Lactam
Urea
Secondary alcohol
Polyol
Azacycle
Organoheterocyclic compound
Secondary amine
Primary alcohol
Alcohol
Hydrocarbon derivative
Organonitrogen compound
Organic oxide
Organopnictogen compound
Primary amine
Amine
Organic nitrogen compound
Aromatic heteromonocyclic compound

Molecular Framework

Aromatic heteromonocyclic compounds

External Descriptors

a small molecule (AMINO-RIBOSYLAMINO-1H-3H-PYR-DIONE )

Functional Ontology

Not Available

Physical Properties

State

Solid

Predicted Properties

Property	Value	Source
Water Solubility	14.3 g/L	ALOGPS
logP	-2.4	ALOGPS
logP	-4.4	ChemAxon
logS	-1.3	ALOGPS
pKa (Strongest Acidic)	9.41	ChemAxon
pKa (Strongest Basic)	4.36	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	8	ChemAxon
Hydrogen Donor Count	8	ChemAxon
Polar Surface Area	177.17 Å²	ChemAxon
Rotatable Bond Count	6	ChemAxon
Refractivity	71.48 m³·mol⁻¹	ChemAxon
Polarizability	25.92 Å³	ChemAxon
Number of Rings	1	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	No	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 (Non-derivatized) - 70eV, Positive	splash10-0903-9440000000-d4b6a6cff43cc761315f	2016-09-22	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (4 TMS) - 70eV, Positive	splash10-056r-6294350000-61d4d076b5309ed14bcb	2017-10-06	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-056r-1190000000-2514b630f375b2189bfe	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-08fu-9750000000-779ce19c1a0e6b0c6932	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-0a4i-9300000000-2f9fc8d8f57a4b3ca8c6	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-01x0-5490000000-40e672b419cf2a89e723	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-0006-9210000000-e4e8a4b406ad4dfd459f	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-052f-9200000000-0e769fc743b8cee3b542	2015-09-15	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 100 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 200 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 300 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 400 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 500 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 600 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 700 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 800 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 900 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, H₂O, predicted)		2022-08-20	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

Metabolic Reactions

Reaction ID	Precursor	Product	Enzyme	Reaction Type	Data Source	Reference
MMDBr0019050	Water	Phosphate	5-amino-6-(5-phospho-D-ribitylamino)uracil phosphatase YigB	Dephosphorylation	PathBank	31602464
MMDBr0019052	5-Amino-6-ribitylamino uracil	Hydrogen Ion	Riboflavin synthase	Synthesis	PathBank	31602464
MMDBr0019058	Hydrogen Ion	Riboflavin	Riboflavin synthase	Synthesis	PathBank	31602464
MMDBr0019171	3,4-Dihydroxy-2-butanone-4-P	Water	Riboflavin synthase	Synthesis	PathBank	31602464
MMDBr0019647	5-Amino-6-ribitylamino uracil	6,7-Dimethyl-8-(1-D-ribityl)lumazine	6,7-dimethyl-8-ribityllumazine synthase	Synthesis	PathBank	31602464
MMDBr0019648	6,7-Dimethyl-8-(1-D-ribityl)lumazine	Riboflavin	Riboflavin synthase	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
Bacteria	Proteobacteria	1	Human ; Human feces; Human feces; pleural fluid plaque; bal; Human stool	Unknown
Eukaryota/Fungi	Ascomycota	1	Human feces; Human saliva	Unknown

Exposure Sources

Source Type	Source Sub-type	Species	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

HMDB0011106

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

FDB027889

KNApSAcK ID

Not Available

Chemspider ID

216

KEGG Compound ID

C04732

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

221

PDB ID

Not Available

ChEBI ID

15934

Food Biomarker Ontology

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-6-ribitylamino uracil (MMDBc0029807)

MOL for #<Metabolite:0x00007fa5084b8e58>

3D MOL for #<Metabolite:0x00007fa5084b8e58>

3D SDF for #<Metabolite:0x00007fa5084b8e58>

3D-SDF for #<Metabolite:0x00007fa5084b8e58>

PDB for #<Metabolite:0x00007fa5084b8e58>

3D PDB for #<Metabolite:0x00007fa5084b8e58>

SMILES for #<Metabolite:0x00007fa5084b8e58>

INCHI for #<Metabolite:0x00007fa5084b8e58>

Structure for #<Metabolite:0x00007fa5084b8e58>

3D Structure for #<Metabolite:0x00007fa5084b8e58>