MiMeDB: Showing metabocard for 6,7-Dimethyl-8-(1-D-ribityl)lumazine (MMDBc0029731)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2021-11-17 23:39:22 UTC

Update Date

2022-08-31 17:16:10 UTC

Metabolite ID

MMDBc0029731

Metabolite Identification

Common Name

6,7-Dimethyl-8-(1-D-ribityl)lumazine

Description

6,7-Dimethyl-8-(1-D-ribityl)lumazine is an intermediate in riboflavin metabolism. 6,7-Dimethyl-8-(1-D-ribityl)lumazine is the second to last step in the synthesis of ribitol and is converted from 4-(1-D-ribitylamino)-5-amino-2,6-dihydroxypyrimidine via the enzyme riboflavin synthase beta chain. It is then

Structure

MOL SDF PDB SMILES InChI


  Mrv0541 02231219472D          

 23 24  0  0  0  0            999 V2000
    4.5503  -11.0998    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.2765  -11.5175    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.5503  -10.2684    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.8275  -11.5211    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    5.9814  -11.0928    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.2731  -12.3422    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.2696   -9.8479    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.8275   -9.8583    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1116  -11.0998    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.9959  -10.2615    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.7111  -11.5141    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.9890  -12.7522    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1116  -10.2684    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.8240   -9.0372    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.4033  -11.5106    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.7042   -9.8513    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.9814  -13.5733    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.6973  -12.3422    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.6938  -13.9876    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.2731  -13.9876    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.6938  -14.8121    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.4097  -13.5767    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.4062  -15.2222    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  2  0  0  0  0
  2  5  1  0  0  0  0
  2  6  1  0  0  0  0
  3  7  2  0  0  0  0
  3  8  1  0  0  0  0
  4  9  1  0  0  0  0
  5 10  2  0  0  0  0
  5 11  1  0  0  0  0
  6 12  1  0  0  0  0
  8 13  1  0  0  0  0
  8 14  2  0  0  0  0
  9 15  2  0  0  0  0
 10 16  1  0  0  0  0
 12 17  1  0  0  0  0
 12 18  1  0  0  0  0
 17 19  1  0  0  0  0
 17 20  1  0  0  0  0
 19 21  1  0  0  0  0
 19 22  1  0  0  0  0
 21 23  1  0  0  0  0
  7 10  1  0  0  0  0
  9 13  1  0  0  0  0
M  END
> <DATABASE_ID>
MMDBc0029731

> <DATABASE_NAME>
MIME

> <SMILES>
CC1=C(C)N(CC(O)C(O)C(O)CO)C2=NC(=O)NC(=O)C2=N1

> <INCHI_IDENTIFIER>
InChI=1S/C13H18N4O6/c1-5-6(2)17(3-7(19)10(21)8(20)4-18)11-9(14-5)12(22)16-13(23)15-11/h7-8,10,18-21H,3-4H2,1-2H3,(H,16,22,23)

> <INCHI_KEY>
SXDXRJZUAJBNFL-UHFFFAOYSA-N

> <FORMULA>
C13H18N4O6

> <MOLECULAR_WEIGHT>
326.3052

> <EXACT_MASS>
326.122634328

> <JCHEM_ACCEPTOR_COUNT>
9

> <JCHEM_AVERAGE_POLARIZABILITY>
31.534559181039732

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
5

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
6,7-dimethyl-8-(2,3,4,5-tetrahydroxypentyl)-2,3,4,8-tetrahydropteridine-2,4-dione

> <ALOGPS_LOGP>
-1.84

> <JCHEM_LOGP>
-2.7431980236666673

> <ALOGPS_LOGS>
-2.42

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
12.85292135903515

> <JCHEM_PKA_STRONGEST_ACIDIC>
6.971683098603213

> <JCHEM_PKA_STRONGEST_BASIC>
-1.2052339987764387

> <JCHEM_POLAR_SURFACE_AREA>
155.04999999999998

> <JCHEM_REFRACTIVITY>
79.00049999999999

> <JCHEM_ROTATABLE_BOND_COUNT>
5

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.23e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
6,7-dimethyl-8-(2,3,4,5-tetrahydroxypentyl)-3H-pteridine-2,4-dione

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 23-FEB-12   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   23-FEB-12         0                                  
HETATM    1  C   UNK     0       8.494 -20.720   0.000  0.00  0.00           C+0
HETATM    2  N   UNK     0       9.849 -21.499   0.000  0.00  0.00           N+0
HETATM    3  C   UNK     0       8.494 -19.168   0.000  0.00  0.00           C+0
HETATM    4  N   UNK     0       7.145 -21.506   0.000  0.00  0.00           N+0
HETATM    5  C   UNK     0      11.165 -20.707   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       9.843 -23.039   0.000  0.00  0.00           C+0
HETATM    7  N   UNK     0       9.837 -18.383   0.000  0.00  0.00           N+0
HETATM    8  C   UNK     0       7.145 -18.402   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       5.808 -20.720   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      11.192 -19.155   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      12.527 -21.493   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      11.179 -23.804   0.000  0.00  0.00           C+0
HETATM   13  N   UNK     0       5.808 -19.168   0.000  0.00  0.00           N+0
HETATM   14  O   UNK     0       7.138 -16.869   0.000  0.00  0.00           O+0
HETATM   15  O   UNK     0       4.486 -21.486   0.000  0.00  0.00           O+0
HETATM   16  C   UNK     0      12.515 -18.389   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0      11.165 -25.337   0.000  0.00  0.00           C+0
HETATM   18  O   UNK     0      12.502 -23.039   0.000  0.00  0.00           O+0
HETATM   19  C   UNK     0      12.495 -26.110   0.000  0.00  0.00           C+0
HETATM   20  O   UNK     0       9.843 -26.110   0.000  0.00  0.00           O+0
HETATM   21  C   UNK     0      12.495 -27.649   0.000  0.00  0.00           C+0
HETATM   22  O   UNK     0      13.831 -25.343   0.000  0.00  0.00           O+0
HETATM   23  O   UNK     0      13.825 -28.415   0.000  0.00  0.00           O+0
CONECT    1    2    3    4                                                  
CONECT    2    1    5    6                                                  
CONECT    3    1    7    8                                                  
CONECT    4    1    9                                                       
CONECT    5    2   10   11                                                  
CONECT    6    2   12                                                       
CONECT    7    3   10                                                       
CONECT    8    3   13   14                                                  
CONECT    9    4   15   13                                                  
CONECT   10    5   16    7                                                  
CONECT   11    5                                                            
CONECT   12    6   17   18                                                  
CONECT   13    8    9                                                       
CONECT   14    8                                                            
CONECT   15    9                                                            
CONECT   16   10                                                            
CONECT   17   12   19   20                                                  
CONECT   18   12                                                            
CONECT   19   17   21   22                                                  
CONECT   20   17                                                            
CONECT   21   19   23                                                       
CONECT   22   19                                                            
CONECT   23   21                                                            
MASTER        0    0    0    0    0    0    0    0   23    0   48    0
END

Synonyms

Value	Source
1-Deoxy-1-(3,4-dihydro-6,7-dimethyl-2,4-dioxo-8(2H)-pteridinyl)-ribitol	HMDB
1-Deoxy-1-[6,7-dimethyl-2,4-dioxo-3,4-dihydropteridin-8(2H)-yl]-D-ribitol	HMDB
6,7-Dimethyl-8-(1'-D-ribityl)lumazine	HMDB
6,7-Dimethyl-8-ribityllumazine	HMDB
6,7-Dimethyl-8-[(2S,3S,4R)-2,3,4,5-tetrahydroxypentyl]pteridine-2,4-dione	HMDB
DMDRL	HMDB

Molecular Formula

C₁₃H₁₈N₄O₆

Average Mass

326.3052

Monoisotopic Mass

326.122634328

IUPAC Name

6,7-dimethyl-8-(2,3,4,5-tetrahydroxypentyl)-2,3,4,8-tetrahydropteridine-2,4-dione

Traditional Name

6,7-dimethyl-8-(2,3,4,5-tetrahydroxypentyl)-3H-pteridine-2,4-dione

CAS Registry Number

5118-16-1

SMILES

CC1=C(C)N(CC(O)C(O)C(O)CO)C2=NC(=O)NC(=O)C2=N1

InChI Identifier

InChI=1S/C13H18N4O6/c1-5-6(2)17(3-7(19)10(21)8(20)4-18)11-9(14-5)12(22)16-13(23)15-11/h7-8,10,18-21H,3-4H2,1-2H3,(H,16,22,23)

InChI Key

SXDXRJZUAJBNFL-UHFFFAOYSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as pteridines and derivatives. These are polycyclic aromatic compounds containing a pteridine moiety, which consists of a pyrimidine fused to a pyrazine ring to form pyrimido(4,5-b)pyrazine.

Kingdom

Organic compounds

Super Class

Organoheterocyclic compounds

Class

Pteridines and derivatives

Sub Class

Not Available

Direct Parent

Pteridines and derivatives

Alternative Parents

Substituents

Pteridine
Pyrimidone
Pyrazine
Pyrimidine
Heteroaromatic compound
Vinylogous amide
Lactam
Secondary alcohol
Polyol
Azacycle
Organic oxide
Organopnictogen compound
Organic oxygen compound
Primary alcohol
Alcohol
Organooxygen compound
Organonitrogen compound
Organic nitrogen compound
Hydrocarbon derivative
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic heteropolycyclic compounds

External Descriptors

Not Available

Functional Ontology

Not Available

Physical Properties

State

Solid

Predicted Properties

Property	Value	Source
Water Solubility	1.23 g/L	ALOGPS
logP	-1.8	ALOGPS
logP	-2.7	ChemAxon
logS	-2.4	ALOGPS
pKa (Strongest Acidic)	6.97	ChemAxon
pKa (Strongest Basic)	-1.2	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	9	ChemAxon
Hydrogen Donor Count	5	ChemAxon
Polar Surface Area	155.05 Å²	ChemAxon
Rotatable Bond Count	5	ChemAxon
Refractivity	79 m³·mol⁻¹	ChemAxon
Polarizability	31.53 Å³	ChemAxon
Number of Rings	2	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

Biological Properties

Cellular Locations

Not Available

Biospecimen Locations

Feces

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

Reactions

Reaction ID	Precursor	Product	Enzyme	Reaction Type	Data Source	Reference
MMDBr0019052	5-Amino-6-ribitylamino uracil	6,7-Dimethyl-8-(1-D-ribityl)lumazine	Riboflavin synthase	Synthesis	PathBank	31602464
MMDBr0019058	6,7-Dimethyl-8-(1-D-ribityl)lumazine	Riboflavin	Riboflavin synthase	Synthesis	PathBank	31602464
MMDBr0019171	3,4-Dihydroxy-2-butanone-4-P	6,7-Dimethyl-8-(1-D-ribityl)lumazine	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/Eubacteria	Proteobacteria	306	Human ; Human feces; Human feces; pleural fluid plaque; bal; Human stool; Pig ; Cattle ; Rat ; Sheep ; Lion ; Chicken	Unknown
Bacteria/Eubacteria	Aquificae	4
Bacteria/Eubacteria	Firmicutes	105	Human ; Human feces; Cattle ; Human subgingival plaque; Human saliva
Bacteria/Eubacteria	Chlamydiae	10	Human ; Sheep ; Cat
Bacteria/Eubacteria	Actinobacteria	48	Cattle ; Human ; Human feces
Bacteria	Proteobacteria	8	Human ; Human feces; Human feces; pleural fluid plaque; bal; Human stool; Pig ; Cattle ; Rat ; Sheep ; Lion ; Chicken	Unknown
Eukaryota/Fungi	Ascomycota	5	Human feces; Human saliva	Unknown
Archaea/Archaea	Crenarchaeota	15
Archaea/Archaea	Euryarchaeota	24
Bacteria/Eubacteria	Bacteroidetes	11	Human ; Human feces
Bacteria/Eubacteria	Spirochaetes	7	Pig ; Human
Bacteria/Eubacteria	Chloroflexi	6
Bacteria/Eubacteria	Chlorobi	11
Bacteria/Eubacteria	Cyanobacteria	27	Human
Bacteria/Eubacteria	Deinococcus-thermus	5
Bacteria/Eubacteria	Elusimicrobia	1
Bacteria/Eubacteria	Fusobacteria	1	Human ; Human feces
Bacteria/Eubacteria	Gemmatimonadetes	1
Bacteria/Eubacteria	Thermotogae	5
Archaea	Euryarchaeota	1
Bacteria/Eubacteria	Planctomycetes	1
Archaea	Crenarchaeota	1
Bacteria/Eubacteria	Acidobacteria	1
Bacteria	nah	1
Bacteria/Eubacteria	Nitrospirae	1

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
Human Feces	Detected but not Quantified									HMDB

External Links

HMDB ID

HMDB0003826

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

FDB023230

KNApSAcK ID

Not Available

Chemspider ID

652

KEGG Compound ID

C04332

BioCyc ID

DIMETHYL-D-RIBITYL-LUMAZINE

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

672

PDB ID

Not Available

ChEBI ID

17601

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 ]
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 6,7-Dimethyl-8-(1-D-ribityl)lumazine (MMDBc0029731)

MOL for #<Metabolite:0x00007f9207f90600>

3D MOL for #<Metabolite:0x00007f9207f90600>

3D SDF for #<Metabolite:0x00007f9207f90600>

3D-SDF for #<Metabolite:0x00007f9207f90600>

PDB for #<Metabolite:0x00007f9207f90600>

3D PDB for #<Metabolite:0x00007f9207f90600>

SMILES for #<Metabolite:0x00007f9207f90600>

INCHI for #<Metabolite:0x00007f9207f90600>

Structure for #<Metabolite:0x00007f9207f90600>

3D Structure for #<Metabolite:0x00007f9207f90600>