MiMeDB: Showing metabocard for 7,8-didemethyl-8-hydroxy-5-deazariboflavin (MMDBc0055627)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2022-06-17 20:00:47 UTC

Update Date

2022-08-12 20:09:26 UTC

Metabolite ID

MMDBc0055627

Metabolite Identification

Common Name

7,8-didemethyl-8-hydroxy-5-deazariboflavin

Description

7,8-didemethyl-8-hydroxy-5-deazariboflavin(1-) belongs to the class of organic compounds known as quinolines and derivatives. Quinolines and derivatives are compounds containing a quinoline moiety, which consists of a benzene ring fused to a pyrimidine ring to form benzo[b]azabenzene. Based on a literature review a significant number of articles have been published on 7,8-didemethyl-8-hydroxy-5-deazariboflavin(1-).

Structure

MOL SDF PDB SMILES InChI


  Mrv1652306172222002D          

 29 31  0  0  1  0            999 V2000
   -1.4289   -1.6500    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
   -0.7145   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000   -2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2868   -1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145   -1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145   -2.8875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000   -1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -1.2375    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    3.5724   -1.2375    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.8579   -1.6500    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.7145   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.0000    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    1.2375    0.0000 N   0  5  0  0  0  0  0  0  0  0  0  0
    0.7145   -1.2375    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    5.0013   -1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145   -3.7125    0.0000 O   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
    3.5724   -0.4125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579   -2.4750    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
    2.1434    1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -2.0625    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724   -2.0625    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579   -0.8250    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  2  0  0  0  0
  7  1  1  0  0  0  0
  7  3  2  0  0  0  0
  8  2  1  0  0  0  0
  8  4  1  0  0  0  0
  9  3  1  0  0  0  0
 10  4  2  0  0  0  0
 10  7  1  0  0  0  0
 11  5  1  0  0  0  0
 12  6  1  0  0  0  0
 13 11  1  0  0  0  0
 13 12  1  0  0  0  0
 14  9  2  0  0  0  0
 15  9  1  0  0  0  0
 17 14  1  0  0  0  0
 17 16  2  0  0  0  0
 18 15  1  0  0  0  0
 18 16  1  0  0  0  0
 19  5  1  0  0  0  0
 19 10  1  0  0  0  0
 19 14  1  0  0  0  0
 20  6  1  0  0  0  0
 21  8  2  0  0  0  0
 11 22  1  1  0  0  0
 12 23  1  1  0  0  0
 13 24  1  6  0  0  0
 25 15  2  0  0  0  0
 26 16  1  0  0  0  0
 11 27  1  1  0  0  0
 12 28  1  1  0  0  0
 13 29  1  6  0  0  0
M  CHG  1  18  -1
M  END


  Mrv1652306172222002D          

 29 31  0  0  1  0            999 V2000
   -1.4289   -1.6500    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
   -0.7145   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000   -2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2868   -1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145   -1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145   -2.8875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000   -1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -1.2375    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    3.5724   -1.2375    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.8579   -1.6500    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.7145   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.0000    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    1.2375    0.0000 N   0  5  0  0  0  0  0  0  0  0  0  0
    0.7145   -1.2375    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    5.0013   -1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145   -3.7125    0.0000 O   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
    3.5724   -0.4125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579   -2.4750    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
    2.1434    1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -2.0625    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724   -2.0625    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579   -0.8250    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  2  0  0  0  0
  7  1  1  0  0  0  0
  7  3  2  0  0  0  0
  8  2  1  0  0  0  0
  8  4  1  0  0  0  0
  9  3  1  0  0  0  0
 10  4  2  0  0  0  0
 10  7  1  0  0  0  0
 11  5  1  0  0  0  0
 12  6  1  0  0  0  0
 13 11  1  0  0  0  0
 13 12  1  0  0  0  0
 14  9  2  0  0  0  0
 15  9  1  0  0  0  0
 17 14  1  0  0  0  0
 17 16  2  0  0  0  0
 18 15  1  0  0  0  0
 18 16  1  0  0  0  0
 19  5  1  0  0  0  0
 19 10  1  0  0  0  0
 19 14  1  0  0  0  0
 20  6  1  0  0  0  0
 21  8  2  0  0  0  0
 11 22  1  1  0  0  0
 12 23  1  1  0  0  0
 13 24  1  6  0  0  0
 25 15  2  0  0  0  0
 26 16  1  0  0  0  0
 11 27  1  1  0  0  0
 12 28  1  1  0  0  0
 13 29  1  6  0  0  0
M  CHG  1  18  -1
M  END
> <DATABASE_ID>
MMDBc0055627

> <DATABASE_NAME>
MIME

> <SMILES>
[H][C@@](O)(CO)[C@@]([H])(O)[C@@]([H])(O)CN1C2=CC(=O)C=CC2=CC2=C1N=C(O)[N-]C2=O

> <INCHI_IDENTIFIER>
InChI=1S/C16H17N3O7/c20-6-12(23)13(24)11(22)5-19-10-4-8(21)2-1-7(10)3-9-14(19)17-16(26)18-15(9)25/h1-4,11-13,20,22-24H,5-6H2,(H2,17,18,21,25,26)/p-1/t11-,12+,13-/m0/s1

> <INCHI_KEY>
YUTUUCYDXGWRNU-XQQFMLRXSA-M

> <FORMULA>
C16H16N3O7

> <MOLECULAR_WEIGHT>
362.319

> <EXACT_MASS>
362.099373447

> <JCHEM_ACCEPTOR_COUNT>
10

> <JCHEM_ATOM_COUNT>
42

> <JCHEM_AVERAGE_POLARIZABILITY>
34.17827664591092

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
5

> <JCHEM_FORMAL_CHARGE>
-1

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
2-hydroxy-4,8-dioxo-10-[(2S,3S,4R)-2,3,4,5-tetrahydroxypentyl]-3H,4H,8H,10H-pyrimido[4,5-b]quinolin-3-ide

> <JCHEM_LOGP>
-2.0927302209999996

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
9.069878094906116

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.707098897734296

> <JCHEM_PKA_STRONGEST_BASIC>
-0.13560240391066103

> <JCHEM_POLAR_SURFACE_AREA>
160.12

> <JCHEM_REFRACTIVITY>
100.29359999999998

> <JCHEM_ROTATABLE_BOND_COUNT>
5

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
2-hydroxy-4,8-dioxo-10-[(2S,3S,4R)-2,3,4,5-tetrahydroxypentyl]-3H-pyrimido[4,5-b]quinolin-3-ide

> <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      -2.667  -3.080   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -2.667  -4.620   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -1.334  -0.770   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       0.000  -4.620   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       2.667  -3.080   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       8.002  -3.080   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      -1.334  -2.310   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      -1.334  -5.390   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       0.000  -3.080   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       4.001  -2.310   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       6.668  -2.310   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       5.335  -3.080   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       0.000   1.540   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       2.667   1.540   0.000  0.00  0.00           C+0
HETATM   17  N   UNK     0       2.667   0.000   0.000  0.00  0.00           N+0
HETATM   18  N   UNK     0       1.334   2.310   0.000  0.00  0.00           N-1
HETATM   19  N   UNK     0       1.334  -2.310   0.000  0.00  0.00           N+0
HETATM   20  O   UNK     0       9.336  -2.310   0.000  0.00  0.00           O+0
HETATM   21  O   UNK     0      -1.334  -6.930   0.000  0.00  0.00           O+0
HETATM   22  O   UNK     0       4.001  -0.770   0.000  0.00  0.00           O+0
HETATM   23  O   UNK     0       6.668  -0.770   0.000  0.00  0.00           O+0
HETATM   24  O   UNK     0       5.335  -4.620   0.000  0.00  0.00           O+0
HETATM   25  O   UNK     0      -1.334   2.310   0.000  0.00  0.00           O+0
HETATM   26  O   UNK     0       4.001   2.310   0.000  0.00  0.00           O+0
HETATM   27  H   UNK     0       4.001  -3.850   0.000  0.00  0.00           H+0
HETATM   28  H   UNK     0       6.668  -3.850   0.000  0.00  0.00           H+0
HETATM   29  H   UNK     0       5.335  -1.540   0.000  0.00  0.00           H+0
CONECT    1    2    7                                                       
CONECT    2    1    8                                                       
CONECT    3    7    9                                                       
CONECT    4    8   10                                                       
CONECT    5   11   19                                                       
CONECT    6   12   20                                                       
CONECT    7    1    3   10                                                  
CONECT    8    2    4   21                                                  
CONECT    9    3   14   15                                                  
CONECT   10    4    7   19                                                  
CONECT   11    5   13   22   27                                             
CONECT   12    6   13   23   28                                             
CONECT   13   11   12   24   29                                             
CONECT   14    9   17   19                                                  
CONECT   15    9   18   25                                                  
CONECT   16   17   18   26                                                  
CONECT   17   14   16                                                       
CONECT   18   15   16                                                       
CONECT   19    5   10   14                                                  
CONECT   20    6                                                            
CONECT   21    8                                                            
CONECT   22   11                                                            
CONECT   23   12                                                            
CONECT   24   13                                                            
CONECT   25   15                                                            
CONECT   26   16                                                            
CONECT   27   11                                                            
CONECT   28   12                                                            
CONECT   29   13                                                            
MASTER        0    0    0    0    0    0    0    0   29    0   62    0
END

Synonyms

Value	Source
7,8-Didemethyl-8-hydroxy-5-deazariboflavin	ChEBI
7,8-Didemethyl-8-hydroxy-5-deazariboflavin anion	ChEBI
7,8-Didemethyl-8-hydroxy-5-deazariboflavin-3-ide	ChEBI

Molecular Formula

C₁₆H₁₆N₃O₇

Average Mass

362.319

Monoisotopic Mass

362.099373447

IUPAC Name

2-hydroxy-4,8-dioxo-10-[(2S,3S,4R)-2,3,4,5-tetrahydroxypentyl]-3H,4H,8H,10H-pyrimido[4,5-b]quinolin-3-ide

Traditional Name

2-hydroxy-4,8-dioxo-10-[(2S,3S,4R)-2,3,4,5-tetrahydroxypentyl]-3H-pyrimido[4,5-b]quinolin-3-ide

CAS Registry Number

Not Available

SMILES

[H][C@@](O)(CO)[C@@]([H])(O)[C@@]([H])(O)CN1C2=CC(=O)C=CC2=CC2=C1N=C(O)[N-]C2=O

InChI Identifier

InChI=1S/C16H17N3O7/c20-6-12(23)13(24)11(22)5-19-10-4-8(21)2-1-7(10)3-9-14(19)17-16(26)18-15(9)25/h1-4,11-13,20,22-24H,5-6H2,(H2,17,18,21,25,26)/p-1/t11-,12+,13-/m0/s1

InChI Key

YUTUUCYDXGWRNU-XQQFMLRXSA-M

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as quinolines and derivatives. Quinolines and derivatives are compounds containing a quinoline moiety, which consists of a benzene ring fused to a pyrimidine ring to form benzo[b]azabenzene.

Kingdom

Organic compounds

Super Class

Organoheterocyclic compounds

Class

Quinolines and derivatives

Sub Class

Not Available

Direct Parent

Quinolines and derivatives

Alternative Parents

Substituents

Pyridopyrimidine
Pyrido[2,3-d]pyrimidine
Quinoline
Pyrimidone
Hydroxypyrimidine
Pyridine
Pyrimidine
Benzenoid
Heteroaromatic compound
Vinylogous amide
Secondary alcohol
Cyclic ketone
Polyol
Azacycle
Alcohol
Hydrocarbon derivative
Organic oxide
Organopnictogen compound
Organic oxygen compound
Organic nitrogen compound
Primary alcohol
Organooxygen compound
Organonitrogen compound
Organic anion
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic heteropolycyclic compounds

External Descriptors

organic anion (CHEBI:59904 )

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
logP	-2.1	ChemAxon
pKa (Strongest Acidic)	3.71	ChemAxon
pKa (Strongest Basic)	-0.14	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	10	ChemAxon
Hydrogen Donor Count	5	ChemAxon
Polar Surface Area	160.12 Å²	ChemAxon
Rotatable Bond Count	5	ChemAxon
Refractivity	100.29 m³·mol⁻¹	ChemAxon
Polarizability	34.18 Å³	ChemAxon
Number of Rings	3	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

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

Reactions

Reaction ID	Precursor	Product	Enzyme	Reaction Type	Data Source	Reference

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
Bacteria	Actinobacteria	21	Human ; Cattle
Archaea/Archaea	Euryarchaeota	24
Bacteria	Cyanobacteria	7
Archaea	Euryarchaeota	1
Bacteria	nah	1

Exposure Sources

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

26331748

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

59904

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 7,8-didemethyl-8-hydroxy-5-deazariboflavin (MMDBc0055627)

MOL for #<Metabolite:0x00007fdb59459b88>

3D MOL for #<Metabolite:0x00007fdb59459b88>

3D SDF for #<Metabolite:0x00007fdb59459b88>

3D-SDF for #<Metabolite:0x00007fdb59459b88>

PDB for #<Metabolite:0x00007fdb59459b88>

3D PDB for #<Metabolite:0x00007fdb59459b88>

SMILES for #<Metabolite:0x00007fdb59459b88>

INCHI for #<Metabolite:0x00007fdb59459b88>

Structure for #<Metabolite:0x00007fdb59459b88>

3D Structure for #<Metabolite:0x00007fdb59459b88>