MiMeDB: Showing metabocard for Leucocyanidin (MMDBc0033665)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2021-11-19 04:58:05 UTC

Update Date

2024-09-27 20:59:19 UTC

Metabolite ID

MMDBc0033665

Metabolite Identification

Common Name

Leucocyanidin

Description

Structure

MOL SDF PDB SMILES InChI


  Mrv1652303082008142D          

 22 24  0  0  1  0            999 V2000
    0.0000   -2.4750    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
   -1.4289   -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
   -0.7145   -1.2375    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
    0.7145   -1.2375    0.0000 C   0  0  2  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
    1.4289    0.0000    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.1434   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724   -1.2375    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
    2.1434   -1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -1.6500    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.2868   -1.6500    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579    0.8250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.8250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    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   -2.8875    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  2  0  0  0  0
  4  5  1  0  0  0  0
  5  6  2  0  0  0  0
  1  6  1  0  0  0  0
  7  6  1  6  0  0  0
  7  8  1  0  0  0  0
  8  9  1  0  0  0  0
  9 10  1  0  0  0  0
 10 11  2  0  0  0  0
 11 12  1  0  0  0  0
 12 13  2  0  0  0  0
 13 14  1  0  0  0  0
 14 15  2  0  0  0  0
 10 15  1  0  0  0  0
 15 16  1  0  0  0  0
  7 16  1  0  0  0  0
 13 17  1  0  0  0  0
 11 18  1  0  0  0  0
  9 19  1  1  0  0  0
  8 20  1  1  0  0  0
  4 21  1  0  0  0  0
  3 22  1  0  0  0  0
M  END
> <DATABASE_ID>
MMDBc0033665

> <DATABASE_NAME>
MIME

> <SMILES>
O[C@H]1[C@@H](O)C2=C(O)C=C(O)C=C2O[C@@H]1C1=CC(O)=C(O)C=C1

> <INCHI_IDENTIFIER>
InChI=1S/C15H14O7/c16-7-4-10(19)12-11(5-7)22-15(14(21)13(12)20)6-1-2-8(17)9(18)3-6/h1-5,13-21H/t13-,14-,15+/m0/s1

> <INCHI_KEY>
SBZWTSHAFILOTE-SOUVJXGZSA-N

> <FORMULA>
C15H14O7

> <MOLECULAR_WEIGHT>
306.2675

> <EXACT_MASS>
306.073952802

> <JCHEM_ACCEPTOR_COUNT>
7

> <JCHEM_ATOM_COUNT>
36

> <JCHEM_AVERAGE_POLARIZABILITY>
29.36523193147382

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
6

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
(2R,3S,4S)-2-(3,4-dihydroxyphenyl)-3,4-dihydro-2H-1-benzopyran-3,4,5,7-tetrol

> <ALOGPS_LOGP>
0.44

> <JCHEM_LOGP>
0.8761108683333332

> <ALOGPS_LOGS>
-2.14

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
9.54750159896668

> <JCHEM_PKA_STRONGEST_ACIDIC>
8.950550452291846

> <JCHEM_PKA_STRONGEST_BASIC>
-3.6966922314631683

> <JCHEM_POLAR_SURFACE_AREA>
130.61

> <JCHEM_REFRACTIVITY>
75.20720000000001

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
2.22e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
procyanidol

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 08-MAR-20   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   08-MAR-20         0                                  
HETATM    1  C   UNK     0       0.000  -4.620   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -1.334  -5.390   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -2.667  -4.620   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -2.667  -3.080   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      -1.334  -2.310   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       0.000  -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  -0.770   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       2.667   0.000   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       4.001  -0.770   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       5.335   0.000   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       6.668  -0.770   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       6.668  -2.310   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       5.335  -3.080   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       4.001  -2.310   0.000  0.00  0.00           C+0
HETATM   16  O   UNK     0       2.667  -3.080   0.000  0.00  0.00           O+0
HETATM   17  O   UNK     0       8.002  -3.080   0.000  0.00  0.00           O+0
HETATM   18  O   UNK     0       5.335   1.540   0.000  0.00  0.00           O+0
HETATM   19  O   UNK     0       2.667   1.540   0.000  0.00  0.00           O+0
HETATM   20  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   21  O   UNK     0      -4.001  -2.310   0.000  0.00  0.00           O+0
HETATM   22  O   UNK     0      -4.001  -5.390   0.000  0.00  0.00           O+0
CONECT    1    2    6                                                       
CONECT    2    1    3                                                       
CONECT    3    2    4   22                                                  
CONECT    4    3    5   21                                                  
CONECT    5    4    6                                                       
CONECT    6    5    1    7                                                  
CONECT    7    6    8   16                                                  
CONECT    8    7    9   20                                                  
CONECT    9    8   10   19                                                  
CONECT   10    9   11   15                                                  
CONECT   11   10   12   18                                                  
CONECT   12   11   13                                                       
CONECT   13   12   14   17                                                  
CONECT   14   13   15                                                       
CONECT   15   14   10   16                                                  
CONECT   16   15    7                                                       
CONECT   17   13                                                            
CONECT   18   11                                                            
CONECT   19    9                                                            
CONECT   20    8                                                            
CONECT   21    4                                                            
CONECT   22    3                                                            
MASTER        0    0    0    0    0    0    0    0   22    0   48    0
END

Synonyms

Value	Source
2,3-trans-3,4-cis-Leucocyanidin	ChEBI
2-(3,4-Dihydroxyphenyl)-3,4-dihydro-2H-1-benzopyran-3,4,5,7-tetrol	ChEBI
3,3',4,4',5,7-Flavanhexol	ChEBI
3,4-Cyanidiol	ChEBI
Leucoanthocyanidol	ChEBI
Leucocianidol	ChEBI
Leucocyanidol	ChEBI
Leukocyanidine	ChEBI
Procyanidol	ChEBI
Resivit	ChEBI
Flavan	Kegg

Molecular Formula

C₁₅H₁₄O₇

Average Mass

306.2675

Monoisotopic Mass

306.073952802

IUPAC Name

(2R,3S,4S)-2-(3,4-dihydroxyphenyl)-3,4-dihydro-2H-1-benzopyran-3,4,5,7-tetrol

Traditional Name

procyanidol

CAS Registry Number

480-17-1

SMILES

O[C@H]1[C@@H](O)C2=C(O)C=C(O)C=C2O[C@@H]1C1=CC(O)=C(O)C=C1

InChI Identifier

InChI=1S/C15H14O7/c16-7-4-10(19)12-11(5-7)22-15(14(21)13(12)20)6-1-2-8(17)9(18)3-6/h1-5,13-21H/t13-,14-,15+/m0/s1

InChI Key

SBZWTSHAFILOTE-SOUVJXGZSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as catechins. Catechins are compounds containing a catechin moiety, which is a 3,4-dihydro-2-chromene-3,5.7-Tiol.

Kingdom

Organic compounds

Super Class

Phenylpropanoids and polyketides

Class

Flavonoids

Sub Class

Flavans

Direct Parent

Catechins

Alternative Parents

Substituents

Catechin
Leucoanthocyanidin-skeleton
3'-hydroxyflavonoid
3-hydroxyflavonoid
4'-hydroxyflavonoid
7-hydroxyflavonoid
Hydroxyflavonoid
4-hydroxyflavonoid
5-hydroxyflavonoid
Chromane
Benzopyran
1-benzopyran
Catechol
Alkyl aryl ether
1-hydroxy-2-unsubstituted benzenoid
1-hydroxy-4-unsubstituted benzenoid
Phenol
Benzenoid
Monocyclic benzene moiety
Secondary alcohol
1,2-diol
Oxacycle
Organoheterocyclic compound
Polyol
Ether
Organic oxygen compound
Organooxygen compound
Hydrocarbon derivative
Alcohol
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic heteropolycyclic compounds

External Descriptors

leucocyanidin (CHEBI:11412 )
Flavans, Flavanols and Leucoanthocyanidins (C05906 )
Flavan 3,4-diols (C05906 )
Flavans, Flavanols and Leucoanthocyanidins (LMPK12020203 )

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
Water Solubility	2.22 g/L	ALOGPS
logP	0.44	ALOGPS
logP	0.88	ChemAxon
logS	-2.1	ALOGPS
pKa (Strongest Acidic)	8.95	ChemAxon
pKa (Strongest Basic)	-3.7	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	7	ChemAxon
Hydrogen Donor Count	6	ChemAxon
Polar Surface Area	130.61 Å²	ChemAxon
Rotatable Bond Count	1	ChemAxon
Refractivity	75.21 m³·mol⁻¹	ChemAxon
Polarizability	29.37 Å³	ChemAxon
Number of Rings	3	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	No	ChemAxon
Ghose Filter	Yes	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_2_1) - 70eV, Positive	Not Available	2022-08-08	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - ESI-TOF 10V, Negative	splash10-004r-0791000000-10ab351997f48e512657	2017-08-03	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - ESI-TOF 10V, Negative	splash10-0udi-0009000000-003cf3d9205115931541	2017-08-14	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - ESI-TOF 30V, Negative	splash10-0fb9-0900000000-6485766e32e558575478	2017-08-14	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - ESI-TOF 20V, Negative	splash10-0fb9-0930000000-f55130580bbd8b0b45e4	2017-08-14	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - ESI-TOF 10V, Negative	splash10-004r-0791000000-10ab351997f48e512657	2017-08-14	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-0a4i-0229000000-7b12cfd90f26ce654a82	2016-09-12	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-0a4r-0931000000-86ef21dc0c7f73f0a208	2016-09-12	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-052r-2900000000-21b061fd42eb9d16646c	2016-09-12	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-0a4i-0309000000-88b0e7c6fd6279325ca3	2016-09-12	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-0pbi-0933000000-f4c60b32f791e72758fe	2016-09-12	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-0a6r-3910000000-468d3b91f46d02a3398b	2016-09-12	View Spectrum
MS	Mass Spectrum (Electron Ionization)	Not Available	2022-08-06	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

Not Available

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
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

C00008991

Chemspider ID

Not Available

KEGG Compound ID

C05906

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

440833

PDB ID

Not Available

ChEBI ID

11412

Food Biomarker Ontology

Not Available

References

Synthesis Reference

Not Available

General References

Ramirez-Gaona M, Marcu A, Pon A, Guo AC, Sajed T, Wishart NA, Karu N, Djoumbou Feunang Y, Arndt D, Wishart DS: YMDB 2.0: a significantly expanded version of the yeast metabolome database. Nucleic Acids Res. 2017 Jan 4;45(D1):D440-D445. doi: 10.1093/nar/gkw1058. Epub 2016 Nov 28. [PubMed:27899612 ]

Showing metabocard for Leucocyanidin (MMDBc0033665)

MOL for #<Metabolite:0x00007f46e4311050>

3D MOL for #<Metabolite:0x00007f46e4311050>

3D SDF for #<Metabolite:0x00007f46e4311050>

3D-SDF for #<Metabolite:0x00007f46e4311050>

PDB for #<Metabolite:0x00007f46e4311050>

3D PDB for #<Metabolite:0x00007f46e4311050>

SMILES for #<Metabolite:0x00007f46e4311050>

INCHI for #<Metabolite:0x00007f46e4311050>

Structure for #<Metabolite:0x00007f46e4311050>

3D Structure for #<Metabolite:0x00007f46e4311050>