NP-MRD: Showing NP-Card for (3r,5z)-3-hydroxydodec-5-enoic acid (NP0279670)

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Record Information

Version

2.0

Created at

2022-09-09 05:08:36 UTC

Updated at

2022-09-09 05:08:36 UTC

NP-MRD ID

NP0279670

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(3r,5z)-3-hydroxydodec-5-enoic acid

Description

3R-hydroxy-5z-dodecenoic acid 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. (3r,5z)-3-hydroxydodec-5-enoic acid is found in Globisporangium ultimum. Based on a literature review very few articles have been published on 3r-hydroxy-5z-dodecenoic acid.

Structure

MOL 3D MOL SDF PDB SMILES InChI

     RDKit          3D

 37 36  0  0  0  0  0  0  0  0999 V2000
    4.8009   -0.5762   -0.2109 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4288   -1.1469   -0.0257 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3693   -0.4263   -0.8278 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2418    1.0090   -0.4890 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9128    1.2762    0.9151 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6243    0.8063    1.4884 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3218   -0.6027    1.4999 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7596   -1.0906    0.9129 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7862   -0.3458    0.1881 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1657   -0.4967    0.8067 C   0  0  1  0  0  0  0  0  0  0  0  0
   -3.0910   -0.0111    2.1359 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2053    0.3509    0.1235 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4198    0.0665   -1.2916 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8539   -0.8149   -1.9656 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.3553    0.8454   -2.0086 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.3828   -0.8030    0.7225 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.3789   -1.1032   -1.0242 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.8393    0.5051   -0.3445 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.4485   -2.1981   -0.4055 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.1795   -1.1883    1.0355 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.6218   -0.5786   -1.9272 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4229   -0.9493   -0.7017 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.1712    1.5756   -0.8260 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4650    1.4296   -1.2060 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0273    2.4077    1.0585 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.7594    0.9058    1.5951 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1663    1.4566    1.0434 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6028    1.1281    2.5966 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9835   -1.2978    1.9965 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9211   -2.1907    0.9675 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8693   -0.8316   -0.8354 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6242    0.6985   -0.0205 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5001   -1.5419    0.8673 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9712    0.2639    2.4655 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.1893    0.2163    0.6435 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9721    1.4446    0.2177 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.1324    1.8076   -2.2642 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  1  0
  4  5  1  0
  5  6  1  0
  6  7  1  0
  7  8  2  0
  8  9  1  0
  9 10  1  0
 10 11  1  0
 10 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
  2 19  1  0
  2 20  1  0
  3 21  1  0
  3 22  1  0
  4 23  1  0
  4 24  1  0
  5 25  1  0
  5 26  1  0
  6 27  1  0
  6 28  1  0
  7 29  1  0
  8 30  1  0
  9 31  1  0
  9 32  1  0
 10 33  1  1
 11 34  1  0
 12 35  1  0
 12 36  1  0
 15 37  1  0
M  END


  Mrv1652309092207082D          

 15 14  0  0  1  0            999 V2000
    1.7605   -1.8414    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4750   -1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1895   -1.8414    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9039   -1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.6184   -1.8414    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.3329   -1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.0474   -1.8414    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.7618   -1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.7618   -0.6039    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.4763   -0.1914    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    8.1908   -0.6039    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.4763    0.6336    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.1908    1.0461    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.1908    1.8711    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    8.9052    0.6336    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  1  0  0  0  0
  7  8  2  0  0  0  0
  8  9  1  0  0  0  0
  9 10  1  0  0  0  0
 10 11  1  6  0  0  0
 10 12  1  0  0  0  0
 12 13  1  0  0  0  0
 13 14  2  0  0  0  0
 13 15  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0279670

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CCCCCC\C=C/C[C@@H](O)CC(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C12H22O3/c1-2-3-4-5-6-7-8-9-11(13)10-12(14)15/h7-8,11,13H,2-6,9-10H2,1H3,(H,14,15)/b8-7-/t11-/m1/s1

> <INCHI_KEY>
GZUALOWLHSCENG-SKVAFPRGSA-N

> <FORMULA>
C12H22O3

> <MOLECULAR_WEIGHT>
214.305

> <EXACT_MASS>
214.156894568

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_ATOM_COUNT>
37

> <JCHEM_AVERAGE_POLARIZABILITY>
24.98340694586034

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
(3R,5Z)-3-hydroxydodec-5-enoic acid

> <JCHEM_LOGP>
2.8855753939999995

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
15.232874329026991

> <JCHEM_PKA_STRONGEST_ACIDIC>
4.6098053289732785

> <JCHEM_PKA_STRONGEST_BASIC>
-2.822896326346787

> <JCHEM_POLAR_SURFACE_AREA>
57.53

> <JCHEM_REFRACTIVITY>
61.3117

> <JCHEM_ROTATABLE_BOND_COUNT>
9

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
(3R,5Z)-3-hydroxydodec-5-enoic acid

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 09-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   09-SEP-22         0                                  
HETATM    1  C   UNK     0       3.286  -3.437   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       4.620  -2.667   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       5.954  -3.437   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       7.287  -2.667   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       8.621  -3.437   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       9.955  -2.667   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      11.288  -3.437   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      12.622  -2.667   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      12.622  -1.127   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      13.956  -0.357   0.000  0.00  0.00           C+0
HETATM   11  O   UNK     0      15.289  -1.127   0.000  0.00  0.00           O+0
HETATM   12  C   UNK     0      13.956   1.183   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      15.289   1.953   0.000  0.00  0.00           C+0
HETATM   14  O   UNK     0      15.289   3.493   0.000  0.00  0.00           O+0
HETATM   15  O   UNK     0      16.623   1.183   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4    6                                                       
CONECT    6    5    7                                                       
CONECT    7    6    8                                                       
CONECT    8    7    9                                                       
CONECT    9    8   10                                                       
CONECT   10    9   11   12                                                  
CONECT   11   10                                                            
CONECT   12   10   13                                                       
CONECT   13   12   14   15                                                  
CONECT   14   13                                                            
CONECT   15   13                                                            
MASTER        0    0    0    0    0    0    0    0   15    0   28    0
END

View in JSmol

Synonyms

Value	Source
3R-Hydroxy-5Z-dodecenoate	Generator

Chemical Formula

C₁₂H₂₂O₃

Average Mass

214.3050 Da

Monoisotopic Mass

214.15689 Da

IUPAC Name

(3R,5Z)-3-hydroxydodec-5-enoic acid

Traditional Name

(3R,5Z)-3-hydroxydodec-5-enoic acid

CAS Registry Number

Not Available

SMILES

CCCCCC\C=C/C[C@@H](O)CC(O)=O

InChI Identifier

InChI=1S/C12H22O3/c1-2-3-4-5-6-7-8-9-11(13)10-12(14)15/h7-8,11,13H,2-6,9-10H2,1H3,(H,14,15)/b8-7-/t11-/m1/s1

InChI Key

GZUALOWLHSCENG-SKVAFPRGSA-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, 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
Globisporangium ultimum	LOTUS Database	35616633

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
Unsaturated 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 (LMFA01050254 )

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	2.89	ChemAxon
pKa (Strongest Acidic)	4.61	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	9	ChemAxon
Refractivity	61.31 m³·mol⁻¹	ChemAxon
Polarizability	24.98 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

Not Available

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

Not Available

KNApSAcK ID

Not Available

Chemspider ID

4472232

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

5312807

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

LOTUS database [Link]

Showing NP-Card for (3r,5z)-3-hydroxydodec-5-enoic acid (NP0279670)

MOL for NP0279670 ((3r,5z)-3-hydroxydodec-5-enoic acid)

3D MOL for NP0279670 ((3r,5z)-3-hydroxydodec-5-enoic acid)

3D SDF for NP0279670 ((3r,5z)-3-hydroxydodec-5-enoic acid)

3D-SDF for NP0279670 ((3r,5z)-3-hydroxydodec-5-enoic acid)

PDB for NP0279670 ((3r,5z)-3-hydroxydodec-5-enoic acid)

3D PDB for NP0279670 ((3r,5z)-3-hydroxydodec-5-enoic acid)

SMILES for NP0279670 ((3r,5z)-3-hydroxydodec-5-enoic acid)

INCHI for NP0279670 ((3r,5z)-3-hydroxydodec-5-enoic acid)

Structure for NP0279670 ((3r,5z)-3-hydroxydodec-5-enoic acid)

3D Structure for NP0279670 ((3r,5z)-3-hydroxydodec-5-enoic acid)