NP-MRD: Showing NP-Card for (R)-3-Hydroxydecanoic acid (NP0091117)

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Record Information

Version

2.0

Created at

2022-05-11 18:31:10 UTC

Updated at

2022-05-11 18:31:10 UTC

NP-MRD ID

NP0091117

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(R)-3-Hydroxydecanoic acid

Description

(R)-3-Hydroxydecanoic acid, also known as 3-HDA or myrmicacin, belongs to the class of organic compounds known as medium-chain hydroxy acids and derivatives. These are hydroxy acids with a 6 to 12 carbon atoms long side chain (R)-3-Hydroxydecanoic acid is a very hydrophobic molecule, practically insoluble (in water), and relatively neutral (R)-3-Hydroxydecanoic acid exists in all eukaryotes, ranging from yeast to humans. Within humans, (R)-3-hydroxydecanoic acid participates in a number of enzymatic reactions. In particular, (R)-3-hydroxydecanoic acid can be biosynthesized from 3-oxodecanoic acid; which is mediated by the enzyme fatty acid synthase. Beta ketoacyl synthase domain. In addition, (R)-3-hydroxydecanoic acid can be converted into trans-dec-2-enoic acid; which is catalyzed by the enzyme fatty acid synthase. Dyhydrase domain. (R)-3-Hydroxydecanoic acid is found in Apis mellifera. In humans, (R)-3-hydroxydecanoic acid is involved in fatty acid biosynthesis.

Structure

MOL 3D MOL SDF PDB SMILES InChI

     RDKit          3D

 33 32  0  0  0  0  0  0  0  0999 V2000
    4.7228   -0.6343    0.7906 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5582    0.1078    0.1335 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4021   -0.0154    1.0743 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2017    0.7106    0.5355 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8025    0.1135   -0.7829 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3940    0.7947   -1.3312 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5895    0.7214   -0.4459 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0725   -0.6554   -0.1761 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.0907   -1.4104    0.4725 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3282   -0.6574    0.6562 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4501    0.0738    0.0762 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5002    0.6243   -1.0331 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.6389    0.1893    0.8406 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.5134   -0.8140    0.0514 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.3254   -1.5373    1.2556 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.1401    0.0472    1.5562 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.8740    1.1405   -0.0427 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.4030   -0.3787   -0.8495 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.1055   -1.1047    1.1136 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.6633    0.3319    2.0991 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3689    0.7337    1.2653 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5374    1.7699    0.3003 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6823   -0.9649   -0.6833 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6878    0.2573   -1.4961 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6276    0.3943   -2.3672 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1026    1.8719   -1.5411 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4128    1.2110    0.5510 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4000    1.3731   -0.8959 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3377   -1.1336   -1.1487 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3833   -2.3270    0.6477 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6185   -1.7183    0.8099 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0485   -0.2557    1.6717 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.9936    1.1407    0.9443 H   0  0  0  0  0  0  0  0  0  0  0  0
  8  9  1  0
  8  7  1  0
  7  6  1  0
  6  5  1  0
  5  4  1  0
  4  3  1  0
  3  2  1  0
  2  1  1  0
  8 10  1  0
 10 11  1  0
 11 13  1  0
 11 12  2  0
  8 29  1  6
  9 30  1  0
  7 27  1  0
  7 28  1  0
  6 25  1  0
  6 26  1  0
  5 23  1  0
  5 24  1  0
  4 21  1  0
  4 22  1  0
  3 19  1  0
  3 20  1  0
  2 17  1  0
  2 18  1  0
  1 14  1  0
  1 15  1  0
  1 16  1  0
 10 31  1  0
 10 32  1  0
 13 33  1  0
M  END


  Mrv0541 02241201182D          

 14 13  0  0  1  0            999 V2000
   10.4123   -7.0554    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.1267   -7.4679    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.8413   -7.0554    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.5557   -7.4679    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   13.2702   -7.0554    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   13.9847   -7.4679    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   14.6992   -7.0554    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   15.4136   -7.4679    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   16.1281   -7.0554    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   16.8426   -7.4679    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   16.1281   -6.2304    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   14.1118   -6.4122    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    9.6978   -7.4679    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   15.1578   -6.4462    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  0  0  0  0
  3  2  1  0  0  0  0
  4  3  1  0  0  0  0
  5  4  1  0  0  0  0
  6  5  1  0  0  0  0
  7  6  1  0  0  0  0
  8  7  1  0  0  0  0
  9  8  1  0  0  0  0
 10  9  2  0  0  0  0
 11  9  1  0  0  0  0
  7 12  1  1  0  0  0
  1 13  1  0  0  0  0
  7 14  1  6  0  0  0
M  END
> <DATABASE_ID>
NP0091117

> <DATABASE_NAME>
NP-MRD

> <SMILES>
[H][C@@](O)(CCCCCCC)CC(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C10H20O3/c1-2-3-4-5-6-7-9(11)8-10(12)13/h9,11H,2-8H2,1H3,(H,12,13)/t9-/m1/s1

> <INCHI_KEY>
FYSSBMZUBSBFJL-SECBINFHSA-N

> <FORMULA>
C10H20O3

> <MOLECULAR_WEIGHT>
188.264

> <EXACT_MASS>
188.141244506

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_AVERAGE_POLARIZABILITY>
22.346980006857343

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
(3R)-3-hydroxydecanoic acid

> <ALOGPS_LOGP>
2.60

> <JCHEM_LOGP>
2.358359720666666

> <ALOGPS_LOGS>
-2.03

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
15.288498288675335

> <JCHEM_PKA_STRONGEST_ACIDIC>
4.671850167040888

> <JCHEM_PKA_STRONGEST_BASIC>
-2.7985874263168293

> <JCHEM_POLAR_SURFACE_AREA>
57.53

> <JCHEM_REFRACTIVITY>
50.9931

> <JCHEM_ROTATABLE_BOND_COUNT>
8

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.74e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(R)-3-hydroxydecanoic acid

> <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      19.436 -13.170   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      20.770 -13.940   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      22.104 -13.170   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      23.437 -13.940   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      24.771 -13.170   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      26.105 -13.940   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      27.439 -13.170   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      28.772 -13.940   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      30.106 -13.170   0.000  0.00  0.00           C+0
HETATM   10  O   UNK     0      31.440 -13.940   0.000  0.00  0.00           O+0
HETATM   11  O   UNK     0      30.106 -11.630   0.000  0.00  0.00           O+0
HETATM   12  O   UNK     0      26.342 -11.969   0.000  0.00  0.00           O+0
HETATM   13  C   UNK     0      18.103 -13.940   0.000  0.00  0.00           C+0
HETATM   14  H   UNK     0      28.295 -12.033   0.000  0.00  0.00           H+0
CONECT    1    2   13                                                       
CONECT    2    1    3                                                       
CONECT    3    2    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4    6                                                       
CONECT    6    5    7                                                       
CONECT    7    6    8   12   14                                             
CONECT    8    7    9                                                       
CONECT    9    8   10   11                                                  
CONECT   10    9                                                            
CONECT   11    9                                                            
CONECT   12    7                                                            
CONECT   13    1                                                            
CONECT   14    7                                                            
MASTER        0    0    0    0    0    0    0    0   14    0   26    0
END

View in JSmol

Synonyms

Value	Source
(R)-3-Hydroxydecanoate	Generator
3-HDA	HMDB
3-Hydroxydecanoic acid	HMDB
beta-Hydroxydecanoic acid	HMDB
Myrmicacin, (+-)-isomer	HMDB
Myrmicacin monosodium (+-)-isomer	HMDB
3-Hydroxy-decanoic acid	HMDB
Myrmicacin, (R)-isomer	HMDB
Myrmicacin	HMDB

Chemical Formula

C₁₀H₂₀O₃

Average Mass

188.2640 Da

Monoisotopic Mass

188.14124 Da

IUPAC Name

(3R)-3-hydroxydecanoic acid

Traditional Name

(R)-3-hydroxydecanoic acid

CAS Registry Number

Not Available

SMILES

[H][C@@](O)(CCCCCCC)CC(O)=O

InChI Identifier

InChI=1S/C10H20O3/c1-2-3-4-5-6-7-9(11)8-10(12)13/h9,11H,2-8H2,1H3,(H,12,13)/t9-/m1/s1

InChI Key

FYSSBMZUBSBFJL-SECBINFHSA-N

Experimental Spectra

Not Available

Predicted Spectra

Spectrum Type	Description	Depositor ID	Depositor Organization	Depositor	Deposition Date	View
1D NMR	¹³C NMR Spectrum (1D, 25 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 252 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 50 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 75 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 101 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 126 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 151 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 176 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 201 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 226 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, 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
Anas platyrhynchos	FooDB	FooDB
Anatidae	FooDB	FooDB
Anser anser	FooDB	FooDB
Apis mellifera	LOTUS Database	35616633
Bison bison	FooDB	FooDB
Bos taurus	FooDB	FooDB
Bos taurus X Bison bison	FooDB	FooDB
Bubalus bubalis	FooDB	FooDB
Capra aegagrus hircus	FooDB	FooDB
Cervidae	FooDB	FooDB
Cervus canadensis	FooDB	FooDB
Columba	FooDB	FooDB
Columbidae	FooDB	FooDB
Dromaius novaehollandiae	FooDB	FooDB
Equus caballus	FooDB	FooDB
Gallus gallus	FooDB	FooDB
Lagopus muta	FooDB	FooDB
Leporidae	FooDB	FooDB
Lepus timidus	FooDB	FooDB
Melanitta fusca	FooDB	FooDB
Meleagris gallopavo	FooDB	FooDB
Numida meleagris	FooDB	FooDB
Odocoileus	FooDB	FooDB
Oryctolagus	FooDB	FooDB
Ovis aries	FooDB	FooDB
Phasianidae	FooDB	FooDB
Phasianus colchicus	FooDB	FooDB
Struthio camelus	FooDB	FooDB
Sus scrofa	FooDB	FooDB
Sus scrofa domestica	FooDB	FooDB

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as medium-chain hydroxy acids and derivatives. These are hydroxy acids with a 6 to 12 carbon atoms long side chain.

Kingdom

Organic compounds

Super Class

Organic acids and derivatives

Class

Hydroxy acids and derivatives

Sub Class

Medium-chain hydroxy acids and derivatives

Direct Parent

Medium-chain hydroxy acids and derivatives

Alternative Parents

Substituents

Medium-chain hydroxy acid
Medium-chain fatty acid
Beta-hydroxy acid
Hydroxy fatty acid
Fatty acyl
Fatty acid
Secondary alcohol
Carboxylic acid derivative
Carboxylic acid
Monocarboxylic acid or derivatives
Organic oxide
Alcohol
Carbonyl group
Hydrocarbon derivative
Organic oxygen compound
Organooxygen compound
Aliphatic acyclic compound

Molecular Framework

Aliphatic acyclic compounds

External Descriptors

Hydroxy fatty acids (LMFA01050245 )

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	2.6	ALOGPS
logP	2.36	ChemAxon
logS	-2	ALOGPS
pKa (Strongest Acidic)	4.67	ChemAxon
pKa (Strongest Basic)	-2.8	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	3	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	57.53 Å²	ChemAxon
Rotatable Bond Count	8	ChemAxon
Refractivity	50.99 m³·mol⁻¹	ChemAxon
Polarizability	22.35 Å³	ChemAxon
Number of Rings	0	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

HMDB0010725

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

FDB027873

KNApSAcK ID

Not Available

Chemspider ID

4472223

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

5312798

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Not Available

Showing NP-Card for (R)-3-Hydroxydecanoic acid (NP0091117)

MOL for NP0091117 ((R)-3-Hydroxydecanoic acid)

3D MOL for NP0091117 ((R)-3-Hydroxydecanoic acid)

3D SDF for NP0091117 ((R)-3-Hydroxydecanoic acid)

3D-SDF for NP0091117 ((R)-3-Hydroxydecanoic acid)

PDB for NP0091117 ((R)-3-Hydroxydecanoic acid)

3D PDB for NP0091117 ((R)-3-Hydroxydecanoic acid)

SMILES for NP0091117 ((R)-3-Hydroxydecanoic acid)

INCHI for NP0091117 ((R)-3-Hydroxydecanoic acid)

Structure for NP0091117 ((R)-3-Hydroxydecanoic acid)

3D Structure for NP0091117 ((R)-3-Hydroxydecanoic acid)