MiMeDB: Showing metabocard for 5-Amino-6-(5'-phosphoribosylamino)uracil (MMDBc0030024)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2021-11-17 23:51:04 UTC

Update Date

2022-08-31 17:38:49 UTC

Metabolite ID

MMDBc0030024

Metabolite Identification

Common Name

5-Amino-6-(5'-phosphoribosylamino)uracil

Description

5-amino-6-(5'-phosphoribosylamino)uracil is a member of the chemical class known as Pentoses. These are monosaccharides in which the carbohydrate moiety contains five carbon atoms.

Structure

MOL SDF PDB SMILES InChI

 
  Mrv1652303082006202D          
 
 23 24  0  0  1  0            999 V2000
   16.8516  -14.5977    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
   17.6752  -14.5977    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   16.0319  -14.5977    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   16.8516  -13.7779    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   16.8516  -15.4212    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   18.4144  -14.6014    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   19.3613  -15.1114    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   19.6106  -15.8972    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   20.0225  -14.6316    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   20.4380  -15.8972    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   19.1270  -16.5582    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   20.6911  -15.1114    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   20.9215  -16.5620    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   21.5574  -14.5429    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   22.2715  -14.1349    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   22.2715  -13.3038    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   22.9816  -14.5964    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   22.9816  -12.8920    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   21.5996  -12.9342    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   23.7032  -14.1349    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   23.7032  -13.3038    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   22.9778  -12.2409    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   24.4134  -14.5429    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  1  3  1  0  0  0  0
  1  4  1  0  0  0  0
  1  5  2  0  0  0  0
  2  6  1  0  0  0  0
  7  6  1  1  0  0  0
  7  8  1  0  0  0  0
  7  9  1  0  0  0  0
  8 10  1  0  0  0  0
  8 11  1  6  0  0  0
  9 12  1  0  0  0  0
 10 13  1  6  0  0  0
 12 14  1  1  0  0  0
 14 15  1  0  0  0  0
 15 16  2  0  0  0  0
 15 17  1  0  0  0  0
 16 18  1  0  0  0  0
 16 19  1  0  0  0  0
 17 20  1  0  0  0  0
 18 21  1  0  0  0  0
 18 22  2  0  0  0  0
 20 23  2  0  0  0  0
 10 12  1  0  0  0  0
 20 21  1  0  0  0  0
M  END
> <DATABASE_ID>
MMDBc0030024

> <DATABASE_NAME>
MIME

> <SMILES>
NC1=C(N[C@@H]2O[C@H](COP(O)(O)=O)[C@@H](O)[C@H]2O)NC(=O)NC1=O

> <INCHI_IDENTIFIER>
InChI=1S/C9H15N4O9P/c10-3-6(12-9(17)13-7(3)16)11-8-5(15)4(14)2(22-8)1-21-23(18,19)20/h2,4-5,8,14-15H,1,10H2,(H2,18,19,20)(H3,11,12,13,16,17)/t2-,4-,5-,8-/m1/s1

> <INCHI_KEY>
LZEXYCAGPMYXLX-UMMCILCDSA-N

> <FORMULA>
C9H15N4O9P

> <MOLECULAR_WEIGHT>
354.2106

> <EXACT_MASS>
354.05766461

> <JCHEM_ACCEPTOR_COUNT>
10

> <JCHEM_ATOM_COUNT>
38

> <JCHEM_AVERAGE_POLARIZABILITY>
29.551298197476896

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
8

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
{[(2R,3S,4R,5R)-5-[(5-amino-2,6-dioxo-1,2,3,6-tetrahydropyrimidin-4-yl)amino]-3,4-dihydroxyoxolan-2-yl]methoxy}phosphonic acid

> <ALOGPS_LOGP>
-1.84

> <JCHEM_LOGP>
-3.7151084476666667

> <ALOGPS_LOGS>
-1.99

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-2

> <JCHEM_PKA>
6.248803119147884

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.2255771173733017

> <JCHEM_PKA_STRONGEST_BASIC>
-3.6640269455988914

> <JCHEM_POLAR_SURFACE_AREA>
212.7

> <JCHEM_REFRACTIVITY>
79.87729999999998

> <JCHEM_ROTATABLE_BOND_COUNT>
5

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
3.64e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
[(2R,3S,4R,5R)-5-[(5-amino-2,6-dioxo-1,3-dihydropyrimidin-4-yl)amino]-3,4-dihydroxyoxolan-2-yl]methoxyphosphonic acid

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 08-MAR-20   NONE
TITLE     NULL                                                        
COMPND    MOLECULE:                                                   
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   08-MAR-20         0                                  
HETATM    1  P   UNK     0      31.456 -27.249   0.000  0.00  0.00           P+0
HETATM    2  O   UNK     0      32.994 -27.249   0.000  0.00  0.00           O+0
HETATM    3  O   UNK     0      29.926 -27.249   0.000  0.00  0.00           O+0
HETATM    4  O   UNK     0      31.456 -25.719   0.000  0.00  0.00           O+0
HETATM    5  O   UNK     0      31.456 -28.786   0.000  0.00  0.00           O+0
HETATM    6  C   UNK     0      34.374 -27.256   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      36.141 -28.208   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      36.606 -29.675   0.000  0.00  0.00           C+0
HETATM    9  O   UNK     0      37.375 -27.312   0.000  0.00  0.00           O+0
HETATM   10  C   UNK     0      38.151 -29.675   0.000  0.00  0.00           C+0
HETATM   11  O   UNK     0      35.704 -30.909   0.000  0.00  0.00           O+0
HETATM   12  C   UNK     0      38.623 -28.208   0.000  0.00  0.00           C+0
HETATM   13  O   UNK     0      39.053 -30.916   0.000  0.00  0.00           O+0
HETATM   14  N   UNK     0      40.240 -27.147   0.000  0.00  0.00           N+0
HETATM   15  C   UNK     0      41.573 -26.385   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0      41.573 -24.834   0.000  0.00  0.00           C+0
HETATM   17  N   UNK     0      42.899 -27.247   0.000  0.00  0.00           N+0
HETATM   18  C   UNK     0      42.899 -24.065   0.000  0.00  0.00           C+0
HETATM   19  N   UNK     0      40.319 -24.144   0.000  0.00  0.00           N+0
HETATM   20  C   UNK     0      44.246 -26.385   0.000  0.00  0.00           C+0
HETATM   21  N   UNK     0      44.246 -24.834   0.000  0.00  0.00           N+0
HETATM   22  O   UNK     0      42.892 -22.850   0.000  0.00  0.00           O+0
HETATM   23  O   UNK     0      45.572 -27.147   0.000  0.00  0.00           O+0
CONECT    1    2    3    4    5                                             
CONECT    2    1    6                                                       
CONECT    3    1                                                            
CONECT    4    1                                                            
CONECT    5    1                                                            
CONECT    6    2    7                                                       
CONECT    7    6    8    9                                                  
CONECT    8    7   10   11                                                  
CONECT    9    7   12                                                       
CONECT   10    8   13   12                                                  
CONECT   11    8                                                            
CONECT   12    9   14   10                                                  
CONECT   13   10                                                            
CONECT   14   12   15                                                       
CONECT   15   14   16   17                                                  
CONECT   16   15   18   19                                                  
CONECT   17   15   20                                                       
CONECT   18   16   21   22                                                  
CONECT   19   16                                                            
CONECT   20   17   23   21                                                  
CONECT   21   18   20                                                       
CONECT   22   18                                                            
CONECT   23   20                                                            
MASTER        0    0    0    0    0    0    0    0   23    0   48    0
END

Synonyms

Value	Source
5-Amino-6-(5-phosphoribosylamino)uracil	ChEBI
5-Amino-6-(ribosylamino)-2,4-(1H,3H)-pyrimidinedione 5'-phosphate	ChEBI
5-Amino-6-(ribosylamino)-2,4-(1H,3H)-pyrimidinedione 5'-phosphoric acid	Generator

Molecular Formula

C₉H₁₅N₄O₉P

Average Mass

354.2106

Monoisotopic Mass

354.05766461

IUPAC Name

{[(2R,3S,4R,5R)-5-[(5-amino-2,6-dioxo-1,2,3,6-tetrahydropyrimidin-4-yl)amino]-3,4-dihydroxyoxolan-2-yl]methoxy}phosphonic acid

Traditional Name

[(2R,3S,4R,5R)-5-[(5-amino-2,6-dioxo-1,3-dihydropyrimidin-4-yl)amino]-3,4-dihydroxyoxolan-2-yl]methoxyphosphonic acid

CAS Registry Number

Not Available

SMILES

NC1=C(N[C@@H]2O[C@H](COP(O)(O)=O)[C@@H](O)[C@H]2O)NC(=O)NC1=O

InChI Identifier

InChI=1S/C9H15N4O9P/c10-3-6(12-9(17)13-7(3)16)11-8-5(15)4(14)2(22-8)1-21-23(18,19)20/h2,4-5,8,14-15H,1,10H2,(H2,18,19,20)(H3,11,12,13,16,17)/t2-,4-,5-,8-/m1/s1

InChI Key

LZEXYCAGPMYXLX-UMMCILCDSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as pentose phosphates. These are carbohydrate derivatives containing a pentose substituted by one or more phosphate groups.

Kingdom

Organic compounds

Super Class

Organic oxygen compounds

Class

Organooxygen compounds

Sub Class

Carbohydrates and carbohydrate conjugates

Direct Parent

Pentose phosphates

Alternative Parents

Substituents

Pentose phosphate
Pentose-5-phosphate
Glycosyl compound
N-glycosyl compound
Monosaccharide phosphate
Aminopyrimidine
Monoalkyl phosphate
Pyrimidone
Secondary aliphatic/aromatic amine
Hydropyrimidine
Organic phosphoric acid derivative
Phosphoric acid ester
Alkyl phosphate
Pyrimidine
Heteroaromatic compound
Vinylogous amide
Tetrahydrofuran
Urea
Secondary alcohol
Lactam
1,2-diol
Secondary amine
Organoheterocyclic compound
Oxacycle
Azacycle
Alcohol
Hydrocarbon derivative
Organic oxide
Organopnictogen compound
Primary amine
Amine
Organonitrogen compound
Organic nitrogen compound
Aromatic heteromonocyclic compound

Molecular Framework

Aromatic heteromonocyclic compounds

External Descriptors

N-glycosyl compound (CHEBI:18337 )
ribose monophosphate (CHEBI:18337 )
aminouracil (CHEBI:18337 )

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
Water Solubility	3.64 g/L	ALOGPS
logP	-1.8	ALOGPS
logP	-3.7	ChemAxon
logS	-2	ALOGPS
pKa (Strongest Acidic)	1.23	ChemAxon
pKa (Strongest Basic)	-3.7	ChemAxon
Physiological Charge	-2	ChemAxon
Hydrogen Acceptor Count	10	ChemAxon
Hydrogen Donor Count	8	ChemAxon
Polar Surface Area	212.7 Å²	ChemAxon
Rotatable Bond Count	5	ChemAxon
Refractivity	79.88 m³·mol⁻¹	ChemAxon
Polarizability	29.55 Å³	ChemAxon
Number of Rings	2	ChemAxon
Bioavailability	No	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 (TMS_4_63) - 70eV, Positive	Not Available	2022-08-08	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-052f-0914000000-bfd0154077cf7db50381	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-0006-2900000000-d3488d63b0eee9406798	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-0006-8900000000-a92cbdbfe038ca5bbe5d	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-03fv-9607000000-5c4c690d1a011ac633e3	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-004l-9000000000-328e8307ada72eb610e4	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-004i-9000000000-67b8e3d0ec6c70e5c24c	2015-09-15	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 100 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 200 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 300 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 400 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 500 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 600 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 700 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 800 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 900 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, H₂O, predicted)		2022-08-18	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
MMDBr0019045	Hydrogen Ion	5-Amino-6-(5'-phosphoribosylamino)uracil	Riboflavin biosynthesis protein RibD	Synthesis	PathBank	31602464
MMDBr0019046	Hydrogen Ion	5-Amino-6-(5'-phosphoribosylamino)uracil	Riboflavin biosynthesis protein RibD	Synthesis	PathBank	31602464
MMDBr0019047	Hydrogen Ion	NADP	Riboflavin biosynthesis protein RibD	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

Not Available

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

Not Available

KNApSAcK ID

C00019665

Chemspider ID

Not Available

KEGG Compound ID

C01268

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

439462

PDB ID

Not Available

ChEBI ID

18337

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-(5'-phosphoribosylamino)uracil (MMDBc0030024)

MOL for #<Metabolite:0x00007fa48ba729c0>

3D MOL for #<Metabolite:0x00007fa48ba729c0>

3D SDF for #<Metabolite:0x00007fa48ba729c0>

3D-SDF for #<Metabolite:0x00007fa48ba729c0>

PDB for #<Metabolite:0x00007fa48ba729c0>

3D PDB for #<Metabolite:0x00007fa48ba729c0>

SMILES for #<Metabolite:0x00007fa48ba729c0>

INCHI for #<Metabolite:0x00007fa48ba729c0>

Structure for #<Metabolite:0x00007fa48ba729c0>

3D Structure for #<Metabolite:0x00007fa48ba729c0>