MiMeDB: Showing metabocard for 5-amino-5-(4-hydroxybenzyl)-6-(D-ribitylimino)-5,6-dihydrouracil (MMDBc0055551)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2022-06-17 19:58:41 UTC

Update Date

2022-08-12 20:09:24 UTC

MiMeDB ID

MMDBc0055551

Metabolite Identification

Common Name

5-amino-5-(4-hydroxybenzyl)-6-(D-ribitylimino)-5,6-dihydrouracil

Description

5-amino-5-(4-hydroxybenzyl)-6-(D-ribitylimino)-5,6-dihydrouracil belongs to the class of organic compounds known as pentoses. These are monosaccharides in which the carbohydrate moiety contains five carbon atoms. Based on a literature review very few articles have been published on 5-amino-5-(4-hydroxybenzyl)-6-(D-ribitylimino)-5,6-dihydrouracil.

Structure

MOL SDF PDB SMILES InChI


  Mrv1652306172221582D          

 30 31  0  0  1  0            999 V2000
   -3.9185   -0.3860    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0131   -1.3045    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4488    0.2460    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.5434   -0.6725    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6704   -1.7933    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4289    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2007   -1.1613    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.2612    0.1027    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145   -0.4125    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.7145   -0.4125    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.1434   -1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8579   -2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4289   -2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8579   -1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1401   -0.8748    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1434   -0.4125    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4289   -1.6500    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1434   -2.8875    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -0.4125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.7915    0.7347    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145   -1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.8250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5724   -2.8875    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145   -2.8875    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145    0.4125    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    0.4125    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000   -0.8250    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  3  1  1  0  0  0  0
  4  2  2  0  0  0  0
  8  1  2  0  0  0  0
  8  2  1  0  0  0  0
  8  5  1  0  0  0  0
  9  3  2  0  0  0  0
  9  4  1  0  0  0  0
 10  6  1  0  0  0  0
 11  7  1  0  0  0  0
 12 10  1  0  0  0  0
 12 11  1  0  0  0  0
 16  5  1  0  0  0  0
 16 13  1  0  0  0  0
 16 14  1  0  0  0  0
 17 16  1  0  0  0  0
 18  6  1  4  0  0  0
 18 13  2  0  0  0  0
 19 13  1  0  0  0  0
 19 15  2  0  0  0  0
 20 14  2  0  0  0  0
 20 15  1  0  0  0  0
 21  7  1  0  0  0  0
 22  9  1  0  0  0  0
 10 23  1  6  0  0  0
 11 24  1  6  0  0  0
 12 25  1  1  0  0  0
 26 14  1  0  0  0  0
 27 15  1  0  0  0  0
 10 28  1  6  0  0  0
 11 29  1  6  0  0  0
 12 30  1  1  0  0  0
M  END


  Mrv1652306172221582D          

 30 31  0  0  1  0            999 V2000
   -3.9185   -0.3860    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0131   -1.3045    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4488    0.2460    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.5434   -0.6725    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6704   -1.7933    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4289    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2007   -1.1613    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.2612    0.1027    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145   -0.4125    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.7145   -0.4125    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.1434   -1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8579   -2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4289   -2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8579   -1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1401   -0.8748    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1434   -0.4125    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4289   -1.6500    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1434   -2.8875    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -0.4125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.7915    0.7347    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145   -1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.8250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5724   -2.8875    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145   -2.8875    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145    0.4125    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    0.4125    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000   -0.8250    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  3  1  1  0  0  0  0
  4  2  2  0  0  0  0
  8  1  2  0  0  0  0
  8  2  1  0  0  0  0
  8  5  1  0  0  0  0
  9  3  2  0  0  0  0
  9  4  1  0  0  0  0
 10  6  1  0  0  0  0
 11  7  1  0  0  0  0
 12 10  1  0  0  0  0
 12 11  1  0  0  0  0
 16  5  1  0  0  0  0
 16 13  1  0  0  0  0
 16 14  1  0  0  0  0
 17 16  1  0  0  0  0
 18  6  1  4  0  0  0
 18 13  2  0  0  0  0
 19 13  1  0  0  0  0
 19 15  2  0  0  0  0
 20 14  2  0  0  0  0
 20 15  1  0  0  0  0
 21  7  1  0  0  0  0
 22  9  1  0  0  0  0
 10 23  1  6  0  0  0
 11 24  1  6  0  0  0
 12 25  1  1  0  0  0
 26 14  1  0  0  0  0
 27 15  1  0  0  0  0
 10 28  1  6  0  0  0
 11 29  1  6  0  0  0
 12 30  1  1  0  0  0
M  END
> <DATABASE_ID>
MMDBc0055551

> <DATABASE_NAME>
MIME

> <SMILES>
[H][C@@](O)(CO)[C@@]([H])(O)[C@@]([H])(O)CN=C1N=C(O)N=C(O)C1(N)CC1=CC=C(O)C=C1

> <INCHI_IDENTIFIER>
InChI=1S/C16H22N4O7/c17-16(5-8-1-3-9(22)4-2-8)13(19-15(27)20-14(16)26)18-6-10(23)12(25)11(24)7-21/h1-4,10-12,21-25H,5-7,17H2,(H2,18,19,20,26,27)/t10-,11+,12-,16?/m0/s1

> <INCHI_KEY>
XETIGMNRSOUDLK-USDBNLMRSA-N

> <FORMULA>
C16H22N4O7

> <MOLECULAR_WEIGHT>
382.373

> <EXACT_MASS>
382.148849064

> <JCHEM_ACCEPTOR_COUNT>
11

> <JCHEM_ATOM_COUNT>
49

> <JCHEM_AVERAGE_POLARIZABILITY>
36.4002410013571

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
8

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2R,3S,4S)-5-({5-amino-2,6-dihydroxy-5-[(4-hydroxyphenyl)methyl]-4,5-dihydropyrimidin-4-ylidene}amino)pentane-1,2,3,4-tetrol

> <JCHEM_LOGP>
-4.197443194020119

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
1

> <JCHEM_PKA>
3.1061895082208344

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.6364939198511026

> <JCHEM_PKA_STRONGEST_BASIC>
8.254769614344136

> <JCHEM_POLAR_SURFACE_AREA>
204.70999999999998

> <JCHEM_REFRACTIVITY>
92.4607

> <JCHEM_ROTATABLE_BOND_COUNT>
7

> <JCHEM_RULE_OF_FIVE>
0

> <JCHEM_TRADITIONAL_IUPAC>
(2R,3S,4S)-5-({5-amino-2,6-dihydroxy-5-[(4-hydroxyphenyl)methyl]pyrimidin-4-ylidene}amino)pentane-1,2,3,4-tetrol

> <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      -7.315  -0.721   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -9.358  -2.435   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -8.304   0.459   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0     -10.348  -1.255   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      -6.851  -3.347   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      -2.667   0.000   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       2.667   0.000   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      -7.841  -2.168   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      -9.821   0.192   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      -1.334  -0.770   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      -4.001  -2.310   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      -5.335  -4.620   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0      -2.667  -4.620   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0      -5.335  -3.080   0.000  0.00  0.00           C+0
HETATM   17  N   UNK     0      -5.861  -1.633   0.000  0.00  0.00           N+0
HETATM   18  N   UNK     0      -4.001  -0.770   0.000  0.00  0.00           N+0
HETATM   19  N   UNK     0      -2.667  -3.080   0.000  0.00  0.00           N+0
HETATM   20  N   UNK     0      -4.001  -5.390   0.000  0.00  0.00           N+0
HETATM   21  O   UNK     0       4.001  -0.770   0.000  0.00  0.00           O+0
HETATM   22  O   UNK     0     -10.811   1.371   0.000  0.00  0.00           O+0
HETATM   23  O   UNK     0      -1.334  -2.310   0.000  0.00  0.00           O+0
HETATM   24  O   UNK     0       1.334  -2.310   0.000  0.00  0.00           O+0
HETATM   25  O   UNK     0       0.000   1.540   0.000  0.00  0.00           O+0
HETATM   26  O   UNK     0      -6.668  -5.390   0.000  0.00  0.00           O+0
HETATM   27  O   UNK     0      -1.334  -5.390   0.000  0.00  0.00           O+0
HETATM   28  H   UNK     0      -1.334   0.770   0.000  0.00  0.00           H+0
HETATM   29  H   UNK     0       1.334   0.770   0.000  0.00  0.00           H+0
HETATM   30  H   UNK     0       0.000  -1.540   0.000  0.00  0.00           H+0
CONECT    1    3    8                                                       
CONECT    2    4    8                                                       
CONECT    3    1    9                                                       
CONECT    4    2    9                                                       
CONECT    5    8   16                                                       
CONECT    6   10   18                                                       
CONECT    7   11   21                                                       
CONECT    8    1    2    5                                                  
CONECT    9    3    4   22                                                  
CONECT   10    6   12   23   28                                             
CONECT   11    7   12   24   29                                             
CONECT   12   10   11   25   30                                             
CONECT   13   16   18   19                                                  
CONECT   14   16   20   26                                                  
CONECT   15   19   20   27                                                  
CONECT   16    5   13   14   17                                             
CONECT   17   16                                                            
CONECT   18    6   13                                                       
CONECT   19   13   15                                                       
CONECT   20   14   15                                                       
CONECT   21    7                                                            
CONECT   22    9                                                            
CONECT   23   10                                                            
CONECT   24   11                                                            
CONECT   25   12                                                            
CONECT   26   14                                                            
CONECT   27   15                                                            
CONECT   28   10                                                            
CONECT   29   11                                                            
CONECT   30   12                                                            
MASTER        0    0    0    0    0    0    0    0   30    0   62    0
END

Synonyms

Value	Source
5-Amino-5-(4-hydroxybenzyl)-6-((2,3,4,5-tetrahydroxypentyl)amino)dihydropyrimidine-2,4-dione	ChEBI

Chemical Formula

C₁₆H₂₂N₄O₇

Average Molecular Weight

382.373

Monoisotopic Molecular Weight

382.148849064

IUPAC Name

(2R,3S,4S)-5-({5-amino-2,6-dihydroxy-5-[(4-hydroxyphenyl)methyl]-4,5-dihydropyrimidin-4-ylidene}amino)pentane-1,2,3,4-tetrol

Traditional Name

(2R,3S,4S)-5-({5-amino-2,6-dihydroxy-5-[(4-hydroxyphenyl)methyl]pyrimidin-4-ylidene}amino)pentane-1,2,3,4-tetrol

CAS Registry Number

Not Available

SMILES

[H][C@@](O)(CO)[C@@]([H])(O)[C@@]([H])(O)CN=C1N=C(O)N=C(O)C1(N)CC1=CC=C(O)C=C1

InChI Identifier

InChI=1S/C16H22N4O7/c17-16(5-8-1-3-9(22)4-2-8)13(19-15(27)20-14(16)26)18-6-10(23)12(25)11(24)7-21/h1-4,10-12,21-25H,5-7,17H2,(H2,18,19,20,26,27)/t10-,11+,12-,16?/m0/s1

InChI Key

XETIGMNRSOUDLK-USDBNLMRSA-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

Alpha-amino acid or derivatives
Pentose monosaccharide
1-hydroxy-2-unsubstituted benzenoid
Aralkylamine
Phenol
Pyrimidone
Monocyclic benzene moiety
Hydropyrimidine
1,2,5,6-tetrahydropyrimidine
Benzenoid
Pyrimidine
Dicarboximide
Amino acid or derivatives
Carbonic acid derivative
Secondary alcohol
Amidine
Carboxylic acid amidine
Carboxylic acid derivative
Azacycle
Organoheterocyclic compound
Organic 1,3-dipolar compound
Propargyl-type 1,3-dipolar organic compound
Carboximidamide
Polyol
Amine
Hydrocarbon derivative
Alcohol
Organopnictogen compound
Primary aliphatic amine
Organonitrogen compound
Organic oxide
Carbonyl group
Organic nitrogen compound
Primary alcohol
Primary amine
Aromatic heteromonocyclic compound

Molecular Framework

Aromatic heteromonocyclic compounds

External Descriptors

phenols (CHEBI:85936 )
pyrimidone (CHEBI:85936 )
primary amino compound (CHEBI:85936 )

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
logP	-4.2	ChemAxon
pKa (Strongest Acidic)	1.64	ChemAxon
pKa (Strongest Basic)	8.25	ChemAxon
Physiological Charge	1	ChemAxon
Hydrogen Acceptor Count	11	ChemAxon
Hydrogen Donor Count	8	ChemAxon
Polar Surface Area	204.71 Å²	ChemAxon
Rotatable Bond Count	7	ChemAxon
Refractivity	92.46 m³·mol⁻¹	ChemAxon
Polarizability	36.4 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_21) - 70eV, Positive	Not Available	2022-08-08	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	Not Available	2022-08-09	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	Not Available	2022-08-09	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	Not Available	2022-08-09	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	Not Available	2022-08-09	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	Not Available	2022-08-09	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	Not Available	2022-08-09	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

Proteins

Human Pathways

Pathways

Name	SMPDB/PathBank

Metabolic Reactions

Reaction ID	Precursor	Product	Enzyme	Reaction Type	Data Source	Reference

Health Effects and Bioactivity

Health Outcome/Bioactivity	Metabolite Response/Effect	Related Health Condition	Evidence Type	Measured in Matrix	Data Source	Reference

Microbial Sources

Kingdom	Phylum	Total species	Hosts and Body Sites
Archaea	Euryarchaeota	23
	Cyanobacteria	10	Human
		1
	Actinobacteria	8	Cattle ; Human
	Euryarchaeota	1	Human Feces

Exposure Sources

Source Type	Source Sub-type	Species	Data Source	Reference	Details

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

34999856

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

91825633

PDB ID

Not Available

ChEBI ID

85936

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 5-amino-5-(4-hydroxybenzyl)-6-(D-ribitylimino)-5,6-dihydrouracil (MMDBc0055551)

MOL for #<Metabolite:0x00007f09200c0870>

3D MOL for #<Metabolite:0x00007f09200c0870>

3D SDF for #<Metabolite:0x00007f09200c0870>

3D-SDF for #<Metabolite:0x00007f09200c0870>

PDB for #<Metabolite:0x00007f09200c0870>

3D PDB for #<Metabolite:0x00007f09200c0870>

SMILES for #<Metabolite:0x00007f09200c0870>

INCHI for #<Metabolite:0x00007f09200c0870>

Structure for #<Metabolite:0x00007f09200c0870>

3D Structure for #<Metabolite:0x00007f09200c0870>