NP-MRD: Showing NP-Card for (-)-Dioxibrassinin (NP0049181)

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Record Information

Version

2.0

Created at

2022-03-17 21:08:23 UTC

Updated at

2022-03-17 21:08:24 UTC

NP-MRD ID

NP0049181

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(-)-Dioxibrassinin

Description

(-)-Dioxibrassinin belongs to the class of organic compounds known as beta amino acids and derivatives. These are amino acids having a (-NH2) group attached to the beta carbon atom (-)-Dioxibrassinin is an extremely weak basic (essentially neutral) compound (based on its pKa). Outside of the human body, (-)-Dioxibrassinin has been detected, but not quantified in, brassicas and cauliflowers. (-)-Dioxibrassinin is found in Brassica oleracea and Pseudomonas cichorii. This could make (-)-dioxibrassinin a potential biomarker for the consumption of these foods.

Structure

MOL SDF PDB SMILES InChI


  Mrv0541 02241208532D          

 17 18  0  0  0  0            999 V2000
   -1.5780   -0.8563    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7896   -0.6156    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1856   -1.1796    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3714   -1.9832    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1597   -2.2239    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7637   -1.6625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1637    1.3255    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
    0.9438    1.0559    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1033    0.2442    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.4787   -0.2965    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6383   -1.1068    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4266   -0.8660    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.5670    1.5965    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
    1.4102    2.4068    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7637   -2.0519    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.9588   -1.8662    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3356   -2.4068    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0  0  0  0
  1  6  1  0  0  0  0
  2  3  1  0  0  0  0
  3  4  2  0  0  0  0
  3 11  1  0  0  0  0
  4  5  1  0  0  0  0
  4 17  1  0  0  0  0
  5  6  2  0  0  0  0
  7  8  2  0  0  0  0
  8  9  1  0  0  0  0
  8 13  1  0  0  0  0
  9 10  1  0  0  0  0
 10 11  1  0  0  0  0
 11 12  1  0  0  0  0
 11 16  1  0  0  0  0
 13 14  1  0  0  0  0
 15 16  2  0  0  0  0
 16 17  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0049181

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CSC(=S)NCC1(O)C(=O)NC2=C1C=CC=C2

> <INCHI_IDENTIFIER>
InChI=1S/C11H12N2O2S2/c1-17-10(16)12-6-11(15)7-4-2-3-5-8(7)13-9(11)14/h2-5,15H,6H2,1H3,(H,12,16)(H,13,14)

> <INCHI_KEY>
DXLDPLVGKCAHPY-UHFFFAOYSA-N

> <FORMULA>
C11H12N2O2S2

> <MOLECULAR_WEIGHT>
268.355

> <EXACT_MASS>
268.034019018

> <JCHEM_ACCEPTOR_COUNT>
2

> <JCHEM_AVERAGE_POLARIZABILITY>
27.125562145349427

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
N-[(3-hydroxy-2-oxo-2,3-dihydro-1H-indol-3-yl)methyl](methylsulfanyl)carbothioamide

> <ALOGPS_LOGP>
0.95

> <JCHEM_LOGP>
1.7185026793333338

> <ALOGPS_LOGS>
-3.63

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
11.395969186048633

> <JCHEM_PKA_STRONGEST_ACIDIC>
7.502335224850136

> <JCHEM_PKA_STRONGEST_BASIC>
-4.315764748461464

> <JCHEM_POLAR_SURFACE_AREA>
61.36

> <JCHEM_REFRACTIVITY>
74.19159999999998

> <JCHEM_ROTATABLE_BOND_COUNT>
3

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
6.32e-02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
N-[(3-hydroxy-2-oxo-1H-indol-3-yl)methyl]methylsulfanylcarbothioamide

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 24-FEB-12   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   24-FEB-12         0                                  
HETATM    1  C   UNK     0      -2.946  -1.598   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -1.474  -1.149   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -0.346  -2.202   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -0.693  -3.702   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      -2.165  -4.151   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      -3.292  -3.103   0.000  0.00  0.00           C+0
HETATM    7  S   UNK     0       0.306   2.474   0.000  0.00  0.00           S+0
HETATM    8  C   UNK     0       1.762   1.971   0.000  0.00  0.00           C+0
HETATM    9  N   UNK     0       2.059   0.456   0.000  0.00  0.00           N+0
HETATM   10  C   UNK     0       0.894  -0.553   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       1.191  -2.066   0.000  0.00  0.00           C+0
HETATM   12  O   UNK     0       2.663  -1.617   0.000  0.00  0.00           O+0
HETATM   13  S   UNK     0       2.925   2.980   0.000  0.00  0.00           S+0
HETATM   14  C   UNK     0       2.632   4.493   0.000  0.00  0.00           C+0
HETATM   15  O   UNK     0       3.292  -3.830   0.000  0.00  0.00           O+0
HETATM   16  C   UNK     0       1.790  -3.484   0.000  0.00  0.00           C+0
HETATM   17  N   UNK     0       0.626  -4.493   0.000  0.00  0.00           N+0
CONECT    1    2    6                                                       
CONECT    2    1    3                                                       
CONECT    3    2    4   11                                                  
CONECT    4    3    5   17                                                  
CONECT    5    4    6                                                       
CONECT    6    1    5                                                       
CONECT    7    8                                                            
CONECT    8    7    9   13                                                  
CONECT    9    8   10                                                       
CONECT   10    9   11                                                       
CONECT   11    3   10   12   16                                             
CONECT   12   11                                                            
CONECT   13    8   14                                                       
CONECT   14   13                                                            
CONECT   15   16                                                            
CONECT   16   11   15   17                                                  
CONECT   17    4   16                                                       
MASTER        0    0    0    0    0    0    0    0   17    0   36    0
END

View in JSmol

Synonyms

Value	Source
Dioxibrassinin	HMDB
N-[(2,3-Dihydroxy-3H-indol-3-yl)methyl](methylsulfanyl)carboimidothioate	Generator
N-[(2,3-Dihydroxy-3H-indol-3-yl)methyl](methylsulphanyl)carboimidothioate	Generator
N-[(2,3-Dihydroxy-3H-indol-3-yl)methyl](methylsulphanyl)carboimidothioic acid	Generator

Chemical Formula

C₁₁H₁₂N₂O₂S₂

Average Mass

268.3550 Da

Monoisotopic Mass

268.03402 Da

IUPAC Name

N-[(3-hydroxy-2-oxo-2,3-dihydro-1H-indol-3-yl)methyl](methylsulfanyl)carbothioamide

Traditional Name

N-[(3-hydroxy-2-oxo-1H-indol-3-yl)methyl]methylsulfanylcarbothioamide

CAS Registry Number

133761-64-5

SMILES

CSC(=S)NCC1(O)C(=O)NC2=C1C=CC=C2

InChI Identifier

InChI=1S/C11H12N2O2S2/c1-17-10(16)12-6-11(15)7-4-2-3-5-8(7)13-9(11)14/h2-5,15H,6H2,1H3,(H,12,16)(H,13,14)

InChI Key

DXLDPLVGKCAHPY-UHFFFAOYSA-N

Experimental Spectra

Not Available

Predicted Spectra

Not Available

Chemical Shift Submissions

Not Available

Species

Species of Origin

Species Name	Source	Reference
Brassica oleracea	Plant	KNApSAcK
Brassica oleracea var. botrytis	FooDB	KNAPSACK
Pseudomonas cichorii	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as beta amino acids and derivatives. These are amino acids having a (-NH2) group attached to the beta carbon atom.

Kingdom

Organic compounds

Super Class

Organic acids and derivatives

Class

Carboxylic acids and derivatives

Sub Class

Amino acids, peptides, and analogues

Direct Parent

Beta amino acids and derivatives

Alternative Parents

Substituents

Beta amino acid or derivatives
Indole or derivatives
Dihydroindole
Benzenoid
Tertiary alcohol
Dithiocarbamic acid ester
Carboxamide group
Lactam
Secondary carboxylic acid amide
Azacycle
Organoheterocyclic compound
Sulfenyl compound
Hydrocarbon derivative
Organosulfur compound
Organooxygen compound
Organonitrogen compound
Alcohol
Organopnictogen compound
Organic oxygen compound
Organic oxide
Carbonyl group
Organic nitrogen compound
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic heteropolycyclic compounds

External Descriptors

Not Available

Physical Properties

State

Not Available

Experimental Properties

Property	Value	Reference
Melting Point	Not Available	Not Available
Boiling Point	Not Available	Not Available
Water Solubility	Not Available	Not Available
LogP	Not Available	Not Available

Predicted Properties

Property	Value	Source
logP	0.95	ALOGPS
logP	1.72	ChemAxon
logS	-3.6	ALOGPS
pKa (Strongest Acidic)	7.5	ChemAxon
pKa (Strongest Basic)	-4.3	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	2	ChemAxon
Hydrogen Donor Count	3	ChemAxon
Polar Surface Area	61.36 Å²	ChemAxon
Rotatable Bond Count	3	ChemAxon
Refractivity	74.19 m³·mol⁻¹	ChemAxon
Polarizability	27.13 Å³	ChemAxon
Number of Rings	2	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

External Links

HMDB ID

HMDB0038634

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

FDB018029

KNApSAcK ID

C00037061

Chemspider ID

9982363

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

11807698

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Not Available

Showing NP-Card for (-)-Dioxibrassinin (NP0049181)

MOL for NP0049181 ((-)-Dioxibrassinin)

3D MOL for NP0049181 ((-)-Dioxibrassinin)

3D SDF for NP0049181 ((-)-Dioxibrassinin)

3D-SDF for NP0049181 ((-)-Dioxibrassinin)

PDB for NP0049181 ((-)-Dioxibrassinin)

3D PDB for NP0049181 ((-)-Dioxibrassinin)

SMILES for NP0049181 ((-)-Dioxibrassinin)

INCHI for NP0049181 ((-)-Dioxibrassinin)

Structure for NP0049181 ((-)-Dioxibrassinin)

3D Structure for NP0049181 ((-)-Dioxibrassinin)