NP-MRD: Showing NP-Card for 3-[(1,2,4-trihydroxy-3,3-dimethylbutylidene)amino]propanoic acid (NP0282271)

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Record Information

Version

2.0

Created at

2022-09-09 09:02:19 UTC

Updated at

2022-09-09 09:02:19 UTC

NP-MRD ID

NP0282271

Secondary Accession Numbers

None

Natural Product Identification

Common Name

3-[(1,2,4-trihydroxy-3,3-dimethylbutylidene)amino]propanoic acid

Description

Pantothenic acid, also known as pantothenate, 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. Net microbial synthesis of pantothenic acid in the rumen of steer calves has been estimated to be 2.2 Mg/kg of digestible organic matter consumed per day. Pantothenic acid is an extremely weak basic (essentially neutral) compound (based on its pKa). In humans, pantothenic acid is involved in the metabolic disorder called the gaba-transaminase deficiency pathway. Outside of the human body, Pantothenic acid is found, on average, in the highest concentration within a few different foods, such as jew's ears, shiitakes, and snack bars and in a lower concentration in common buckwheats, enokitakes, and cheeses. Pantothenic acid has also been detected, but not quantified in, several different foods, such as tallows, other cereal products, gadiformes, cinnamons, and charrs. 3-[(1,2,4-trihydroxy-3,3-dimethylbutylidene)amino]propanoic acid is found in Apis cerana, Arabidopsis thaliana, Daphnia pulex, Homo sapiens, Litoria verreauxii, Salmonella enterica and Trypanosoma brucei. 3-[(1,2,4-trihydroxy-3,3-dimethylbutylidene)amino]propanoic acid was first documented in 2014 (PMID: 24727172). This could make pantothenic acid a potential biomarker for the consumption of these foods.

Structure

MOL 3D MOL SDF PDB SMILES InChI

     RDKit          3D

 32 31  0  0  0  0  0  0  0  0999 V2000
   -2.3870    0.5905   -1.0067 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5656    0.8822    0.2489 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5302    1.9063   -0.0878 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5622    1.4669    1.2321 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5418    0.4793    1.4278 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9854   -0.4016    0.7778 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.0896   -1.2360    1.0706 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0332   -1.0395   -0.1205 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4258   -1.4521   -1.3794 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.1851   -1.2342    0.2294 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.1741   -1.8594   -0.6144 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5541   -1.3829   -0.2122 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6247    0.0916   -0.3710 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.8432    0.5705   -1.5086 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.4592    0.9501    0.6822 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8279   -0.4285   -0.8278 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2631    1.2766   -1.0745 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7751    0.5537   -1.9119 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3901    1.8380    0.5243 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2611    1.8738   -1.1695 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9960    2.9110    0.0722 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0917    2.2796    0.6664 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1190    1.8171    2.1615 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5591    0.2271    2.3868 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4864   -0.1694    1.7398 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9778   -2.0242    0.4853 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0808   -2.1035   -1.9626 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.1008   -2.9617   -0.4855 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0426   -1.6416   -1.6932 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.2938   -1.8785   -0.8778 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.7049   -1.6895    0.8419 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.0245    1.7881    0.7563 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  2  4  1  0
  4  5  1  0
  2  6  1  0
  6  7  1  0
  6  8  1  0
  8  9  1  0
  8 10  2  0
 10 11  1  0
 11 12  1  0
 12 13  1  0
 13 15  1  0
 13 14  2  0
  1 16  1  0
  1 17  1  0
  1 18  1  0
  3 19  1  0
  3 20  1  0
  3 21  1  0
  4 22  1  0
  4 23  1  0
  5 24  1  0
  6 25  1  1
  7 26  1  0
  9 27  1  0
 11 28  1  0
 11 29  1  0
 12 30  1  0
 12 31  1  0
 15 32  1  0
M  END


  Mrv1652305221920132D          

 15 14  0  0  0  0            999 V2000
    2.0625    1.5395    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0625   -0.1105    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000   -1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4125   -0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8875    0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4125   -2.1434    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2375    0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8250    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0625    0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.3000    1.4289    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000   -2.8579    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2375   -2.1434    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.8250    1.4289    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.2375   -0.7145    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  4  3  1  0  0  0  0
  6  3  1  0  0  0  0
  8  7  1  0  0  0  0
  9  1  1  0  0  0  0
  9  2  1  0  0  0  0
  9  5  1  0  0  0  0
  9  7  1  0  0  0  0
 10  4  1  4  0  0  0
 10  8  2  0  0  0  0
 11  5  1  0  0  0  0
 12  6  2  0  0  0  0
 13  6  1  0  0  0  0
 14  7  1  0  0  0  0
 15  8  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0282271

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CC(C)(CO)C(O)C(O)=NCCC(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C9H17NO5/c1-9(2,5-11)7(14)8(15)10-4-3-6(12)13/h7,11,14H,3-5H2,1-2H3,(H,10,15)(H,12,13)

> <INCHI_KEY>
GHOKWGTUZJEAQD-UHFFFAOYSA-N

> <FORMULA>
C9H17NO5

> <MOLECULAR_WEIGHT>
219.235

> <EXACT_MASS>
219.110672659

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_ATOM_COUNT>
32

> <JCHEM_AVERAGE_POLARIZABILITY>
21.9153556291201

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
3-(2,4-dihydroxy-3,3-dimethylbutanamido)propanoic acid

> <ALOGPS_LOGP>
-0.83

> <JCHEM_LOGP>
-1.3553751066666662

> <ALOGPS_LOGS>
-1.71

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
12.685728183953426

> <JCHEM_PKA_STRONGEST_ACIDIC>
4.3547414254714205

> <JCHEM_PKA_STRONGEST_BASIC>
-2.7860052632571373

> <JCHEM_POLAR_SURFACE_AREA>
106.86

> <JCHEM_REFRACTIVITY>
51.5111

> <JCHEM_ROTATABLE_BOND_COUNT>
6

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
4.23e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
pantothenic acid

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 22-MAY-19   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   22-MAY-19         0                                  
HETATM    1  C   UNK     0       3.850   2.874   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       3.850  -0.206   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       0.000  -2.667   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -0.770  -1.334   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       5.390   1.334   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      -0.770  -4.001   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       2.310   1.334   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       1.540   0.000   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       3.850   1.334   0.000  0.00  0.00           C+0
HETATM   10  N   UNK     0       0.000   0.000   0.000  0.00  0.00           N+0
HETATM   11  O   UNK     0       6.160   2.667   0.000  0.00  0.00           O+0
HETATM   12  O   UNK     0       0.000  -5.335   0.000  0.00  0.00           O+0
HETATM   13  O   UNK     0      -2.310  -4.001   0.000  0.00  0.00           O+0
HETATM   14  O   UNK     0       1.540   2.667   0.000  0.00  0.00           O+0
HETATM   15  O   UNK     0       2.310  -1.334   0.000  0.00  0.00           O+0
CONECT    1    9                                                            
CONECT    2    9                                                            
CONECT    3    4    6                                                       
CONECT    4    3   10                                                       
CONECT    5    9   11                                                       
CONECT    6    3   12   13                                                  
CONECT    7    8    9   14                                                  
CONECT    8    7   10   15                                                  
CONECT    9    1    2    5    7                                             
CONECT   10    4    8                                                       
CONECT   11    5                                                            
CONECT   12    6                                                            
CONECT   13    6                                                            
CONECT   14    7                                                            
CONECT   15    8                                                            
MASTER        0    0    0    0    0    0    0    0   15    0   28    0
END

View in JSmol

Synonyms

Value	Source
N-(2,4-Dihydroxy-3,3-dimethylbutanoyl)-beta-alanine	ChEBI
N-(2,4-Dihydroxy-3,3-dimethylbutanoyl)-b-alanine	Generator
N-(2,4-Dihydroxy-3,3-dimethylbutanoyl)-β-alanine	Generator
Pantothenate	Generator
(+)-Pantothenate	HMDB
(+)-Pantothenic acid	HMDB
(D)-(+)-Pantothenate	HMDB
(D)-(+)-Pantothenic acid	HMDB
(R)-Pantothenate	HMDB
Chick antidermatitis factor	HMDB
D(+)-N-(2,4-Dihydroxy-3,3-dimethylbutyryl)-b-alanine	HMDB
D(+)-N-(2,4-Dihydroxy-3,3-dimethylbutyryl)-beta-alanine	HMDB
D-Pantothenate	HMDB
D-Pantothenic acid	HMDB
delta-Pantothenate	HMDB
delta-Pantothenic acid	HMDB
Vitamin b5	HMDB
DL-Pantothenate	Generator

Chemical Formula

C₉H₁₇NO₅

Average Mass

219.2350 Da

Monoisotopic Mass

219.11067 Da

IUPAC Name

3-(2,4-dihydroxy-3,3-dimethylbutanamido)propanoic acid

Traditional Name

pantothenic acid

CAS Registry Number

Not Available

SMILES

CC(C)(CO)C(O)C(O)=NCCC(O)=O

InChI Identifier

InChI=1S/C9H17NO5/c1-9(2,5-11)7(14)8(15)10-4-3-6(12)13/h7,11,14H,3-5H2,1-2H3,(H,10,15)(H,12,13)

InChI Key

GHOKWGTUZJEAQD-UHFFFAOYSA-N

Experimental Spectra

Spectrum Type	Description	Depositor Email	Depositor Organization	Depositor	Deposition Date	View
1D NMR	¹H NMR Spectrum (1D, 600 MHz, H₂O, experimental)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
2D NMR	[¹H, ¹H]-TOCSY 2D NMR Spectrum (experimental)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
2D NMR	[¹H, ¹³C]-HSQC NMR Spectrum (2D, 600 MHz, H₂O, experimental)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum

Predicted Spectra

Spectrum Type	Description	Depositor ID	Depositor Organization	Depositor	Deposition Date	View
1D NMR	¹³C NMR Spectrum (1D, 25 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 252 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 50 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 75 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 101 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 126 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 151 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 176 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 201 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 226 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum

Chemical Shift Submissions

Not Available

Species

Species of Origin

Species Name	Source	Reference
Apis cerana	LOTUS Database	35616633
Arabidopsis thaliana	LOTUS Database	35616633
Daphnia pulex	LOTUS Database	35616633
Homo sapiens	LOTUS Database	35616633
Litoria verreauxii	LOTUS Database	35616633
Salmonella enterica	LOTUS Database	35616633
Trypanosoma brucei	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
Fatty amide
Monosaccharide
N-acyl-amine
Fatty acyl
Carboxamide group
Secondary carboxylic acid amide
Secondary alcohol
Carboxylic acid
Monocarboxylic acid or derivatives
Organonitrogen compound
Hydrocarbon derivative
Organic oxide
Organopnictogen compound
Alcohol
Organic oxygen compound
Carbonyl group
Organic nitrogen compound
Organooxygen compound
Primary alcohol
Aliphatic acyclic compound

Molecular Framework

Aliphatic acyclic compounds

External Descriptors

pantothenic acids (CHEBI:7916 )

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	-0.83	ALOGPS
logP	-1.4	ChemAxon
logS	-1.7	ALOGPS
pKa (Strongest Acidic)	4.35	ChemAxon
pKa (Strongest Basic)	-2.8	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	5	ChemAxon
Hydrogen Donor Count	4	ChemAxon
Polar Surface Area	106.86 Å²	ChemAxon
Rotatable Bond Count	6	ChemAxon
Refractivity	51.51 m³·mol⁻¹	ChemAxon
Polarizability	21.92 Å³	ChemAxon
Number of Rings	0	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

External Links

HMDB ID

Not Available

DrugBank ID

DB01783

Phenol Explorer Compound ID

Not Available

FoodDB ID

FDB008322

KNApSAcK ID

Not Available

Chemspider ID

Not Available

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Pantothenic_acid

METLIN ID

Not Available

PubChem Compound

988

PDB ID

Not Available

ChEBI ID

7916

Good Scents ID

Not Available

References

General References

Srivastava M, Singh NP, Yadav RA: Experimental Raman and IR spectral and theoretical studies of vibrational spectrum and molecular structure of Pantothenic acid (vitamin B5). Spectrochim Acta A Mol Biomol Spectrosc. 2014 Aug 14;129:131-42. doi: 10.1016/j.saa.2014.02.121. Epub 2014 Mar 24. [PubMed:24727172 ]
LOTUS database [Link]

Showing NP-Card for 3-[(1,2,4-trihydroxy-3,3-dimethylbutylidene)amino]propanoic acid (NP0282271)

MOL for NP0282271 (3-[(1,2,4-trihydroxy-3,3-dimethylbutylidene)amino]propanoic acid)

3D MOL for NP0282271 (3-[(1,2,4-trihydroxy-3,3-dimethylbutylidene)amino]propanoic acid)

3D SDF for NP0282271 (3-[(1,2,4-trihydroxy-3,3-dimethylbutylidene)amino]propanoic acid)

3D-SDF for NP0282271 (3-[(1,2,4-trihydroxy-3,3-dimethylbutylidene)amino]propanoic acid)

PDB for NP0282271 (3-[(1,2,4-trihydroxy-3,3-dimethylbutylidene)amino]propanoic acid)

3D PDB for NP0282271 (3-[(1,2,4-trihydroxy-3,3-dimethylbutylidene)amino]propanoic acid)

SMILES for NP0282271 (3-[(1,2,4-trihydroxy-3,3-dimethylbutylidene)amino]propanoic acid)

INCHI for NP0282271 (3-[(1,2,4-trihydroxy-3,3-dimethylbutylidene)amino]propanoic acid)

Structure for NP0282271 (3-[(1,2,4-trihydroxy-3,3-dimethylbutylidene)amino]propanoic acid)

3D Structure for NP0282271 (3-[(1,2,4-trihydroxy-3,3-dimethylbutylidene)amino]propanoic acid)