NP-MRD: Showing NP-Card for 3-dehydroretinal (NP0269010)

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Record Information

Version

2.0

Created at

2022-09-08 14:19:13 UTC

Updated at

2022-09-08 14:19:13 UTC

NP-MRD ID

NP0269010

Secondary Accession Numbers

None

Natural Product Identification

Common Name

3-dehydroretinal

Description

Vitamin A2 aldehyde, also known as 3-dehydroretinal or alpha-retinene, belongs to the class of organic compounds known as retinoids. These are oxygenated derivatives of 3,7-dimethyl-1-(2,6,6-trimethylcyclohex-1-enyl)nona-1,3,5,7-tetraene and derivatives thereof. Thus, vitamin A2 aldehyde is considered to be an isoprenoid lipid molecule. Vitamin A2 aldehyde is a very hydrophobic molecule, practically insoluble (in water), and relatively neutral. Outside of the human body, Vitamin A2 aldehyde has been detected, but not quantified in, fishes. This could make vitamin A2 aldehyde a potential biomarker for the consumption of these foods. 3-dehydroretinal is found in Watasenia scintillans. A retinal which contains an additional double bond between the 3 and 4 positions of the six-membered ring, and in which all of the double bonds in the side chain have the E-configuration.

Structure

MOL 3D MOL SDF PDB SMILES InChI

     RDKit          3D

 47 47  0  0  0  0  0  0  0  0999 V2000
   -3.2553    2.5444    1.5918 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7726    1.1810    1.2414 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9503    0.2712    0.7540 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5582    0.6880    0.5910 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6199   -0.0904    0.1224 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7510    0.4716    0.0134 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0079    1.8651    0.4298 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7097   -0.2749   -0.4492 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1163    0.1397   -0.6161 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9711   -0.7195   -1.0942 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.3869   -0.3691   -1.2851 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.9647    0.9503   -0.9659 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.2104   -1.3016   -1.7782 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.6126   -1.0783   -2.0067 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.2117   -0.0174   -1.7769 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4124   -1.0640    0.4193 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5929   -2.1263    1.1868 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0978   -1.3355   -1.0750 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8501   -1.3208    0.5838 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.6660   -0.2515    1.1299 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.1852    0.9251    1.4438 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4492    2.4322    2.3521 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7872    3.0392    0.7048 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0552    3.1916    1.9457 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2689    1.6889    0.8663 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7816   -1.1096   -0.1880 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6408    1.9443    1.4912 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2869    2.5234   -0.1362 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0315    2.2099    0.3511 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4419   -1.2861   -0.7334 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.4390    1.1243   -0.3510 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.6241   -1.7165   -1.3563 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.7979    0.8937   -0.2329 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.2142    1.6933   -0.7013 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.4091    1.3413   -1.9333 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.7599   -2.2794   -2.0103 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.1905   -1.9386   -2.4240 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2044   -2.8507    0.4832 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3527   -2.6068    1.8813 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8155   -1.6942    1.8103 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5433   -2.2730   -1.2111 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0973   -1.4665   -1.5829 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5760   -0.5018   -1.5418 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9953   -2.2367    1.2799 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.3237   -1.7440   -0.3660 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.7699   -0.4371    1.2946 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.7971    1.7156    1.8481 H   0  0  0  0  0  0  0  0  0  0  0  0
 12 11  1  0
 11 10  1  0
 10  9  2  0
  9  8  1  0
  8  6  2  0
  6  7  1  0
  6  5  1  0
  5  4  2  0
  4  3  1  0
  3  2  2  0
  2  1  1  0
  2 21  1  0
 21 20  2  0
 20 19  1  0
 19 16  1  0
 16 17  1  0
 16 18  1  0
 11 13  2  0
 13 14  1  0
 14 15  2  0
 16  3  1  0
 12 33  1  0
 12 34  1  0
 12 35  1  0
 10 32  1  0
  9 31  1  0
  8 30  1  0
  7 27  1  0
  7 28  1  0
  7 29  1  0
  5 26  1  0
  4 25  1  0
  1 22  1  0
  1 23  1  0
  1 24  1  0
 21 47  1  0
 20 46  1  0
 19 44  1  0
 19 45  1  0
 17 38  1  0
 17 39  1  0
 17 40  1  0
 18 41  1  0
 18 42  1  0
 18 43  1  0
 13 36  1  0
 14 37  1  0
M  END


  Mrv0541 05061308392D          

 21 21  0  0  0  0            999 V2000
    2.8579    3.3000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.7158    3.3000    0.0000 C   0  0  0  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
    0.1842    1.8695    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2448    1.8695    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2868    2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724    2.0625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0013    2.0625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434    2.0625    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
    6.4302    2.0625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.1447    2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579    2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.7158    2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.8250    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
    7.1447    3.3000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  8  6  1  0  0  0  0
  9  6  2  0  0  0  0
 10  7  2  0  0  0  0
 12 11  2  0  0  0  0
 14  7  1  0  0  0  0
 15 13  1  0  0  0  0
 16  1  1  0  0  0  0
 16  8  2  0  0  0  0
 16 11  1  0  0  0  0
 17  2  1  0  0  0  0
 17  9  1  0  0  0  0
 17 13  2  0  0  0  0
 18  3  1  0  0  0  0
 18 10  1  0  0  0  0
 19 12  1  0  0  0  0
 19 18  2  0  0  0  0
 20  4  1  0  0  0  0
 20  5  1  0  0  0  0
 20 14  1  0  0  0  0
 20 19  1  0  0  0  0
 21 15  2  0  0  0  0
M  END
> <DATABASE_ID>
NP0269010

> <DATABASE_NAME>
NP-MRD

> <SMILES>
C\C(\C=C\C=C(/C)\C=C\C1=C(C)C=CCC1(C)C)=C/C=O

> <INCHI_IDENTIFIER>
InChI=1S/C20H26O/c1-16(8-6-9-17(2)13-15-21)11-12-19-18(3)10-7-14-20(19,4)5/h6-13,15H,14H2,1-5H3/b9-6+,12-11+,16-8+,17-13+

> <INCHI_KEY>
QHNVWXUULMZJKD-OVSJKPMPSA-N

> <FORMULA>
C20H26O

> <MOLECULAR_WEIGHT>
282.4198

> <EXACT_MASS>
282.198365454

> <JCHEM_ACCEPTOR_COUNT>
1

> <JCHEM_AVERAGE_POLARIZABILITY>
35.17278706476937

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
(2E,4E,6E,8E)-3,7-dimethyl-9-(2,6,6-trimethylcyclohexa-1,3-dien-1-yl)nona-2,4,6,8-tetraenal

> <ALOGPS_LOGP>
6.23

> <JCHEM_LOGP>
4.4938298020000005

> <ALOGPS_LOGS>
-4.56

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_BASIC>
-4.061304751803082

> <JCHEM_POLAR_SURFACE_AREA>
17.07

> <JCHEM_REFRACTIVITY>
97.98200000000001

> <JCHEM_ROTATABLE_BOND_COUNT>
5

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
7.84e-03 g/l

> <JCHEM_TRADITIONAL_IUPAC>
α-retinene

> <JCHEM_VEBER_RULE>
1

$$$$

HEADER    PROTEIN                                 06-MAY-13   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   06-MAY-13         0                                  
HETATM    1  C   UNK     0       5.335   6.160   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      10.669   6.160   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       4.001  -0.770   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       0.344   3.490   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       2.324   3.490   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       8.002   4.620   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       6.668   3.850   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       9.336   3.850   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       4.001   3.850   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       4.001   2.310   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      12.003   3.850   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       0.000   1.540   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0      13.337   4.620   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       5.335   4.620   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0      10.669   4.620   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       2.667   0.000   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       2.667   1.540   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       1.334   2.310   0.000  0.00  0.00           C+0
HETATM   21  O   UNK     0      13.337   6.160   0.000  0.00  0.00           O+0
CONECT    1   16                                                            
CONECT    2   17                                                            
CONECT    3   18                                                            
CONECT    4   20                                                            
CONECT    5   20                                                            
CONECT    6    8    9                                                       
CONECT    7   10   14                                                       
CONECT    8    6   16                                                       
CONECT    9    6   17                                                       
CONECT   10    7   18                                                       
CONECT   11   12   16                                                       
CONECT   12   11   19                                                       
CONECT   13   15   17                                                       
CONECT   14    7   20                                                       
CONECT   15   13   21                                                       
CONECT   16    1    8   11                                                  
CONECT   17    2    9   13                                                  
CONECT   18    3   10   19                                                  
CONECT   19   12   18   20                                                  
CONECT   20    4    5   14   19                                             
CONECT   21   15                                                            
MASTER        0    0    0    0    0    0    0    0   21    0   42    0
END

View in JSmol

Synonyms

Value	Source
(all-e)-3,7-Dimethyl-9-(2,6,6-trimethyl-1,3-cyclohexadien-1-yl)-2,4,6,8-nonatetraenal	ChEBI
3,4-Didehydroretinal	ChEBI
3-Dehydroretinal	ChEBI
3-Dehydroretinaldehyde	ChEBI
all-trans-3,4-Dehydroretinal	ChEBI
all-trans-3,4-Didehydroretinal	ChEBI
Dehydroretinal	ChEBI
Dehydroretinaldehyd	ChEBI
Dehydroretinaldehyde	ChEBI
Retinene 2	ChEBI
trans-3-Dehydroretinal	ChEBI
alpha-Retinene	Kegg
all-trans-3-Dehydroretinal	Kegg
a-Retinene	Generator
Α-retinene	Generator
all-trans-Dehydroretinal	HMDB
Didehydroretinal	HMDB
Retinene2	HMDB
Vitamin a2 aldehyde	ChEBI

Chemical Formula

C₂₀H₂₆O

Average Mass

282.4198 Da

Monoisotopic Mass

282.19837 Da

IUPAC Name

(2E,4E,6E,8E)-3,7-dimethyl-9-(2,6,6-trimethylcyclohexa-1,3-dien-1-yl)nona-2,4,6,8-tetraenal

Traditional Name

α-retinene

CAS Registry Number

Not Available

SMILES

C\C(\C=C\C=C(/C)\C=C\C1=C(C)C=CCC1(C)C)=C/C=O

InChI Identifier

InChI=1S/C20H26O/c1-16(8-6-9-17(2)13-15-21)11-12-19-18(3)10-7-14-20(19,4)5/h6-13,15H,14H2,1-5H3/b9-6+,12-11+,16-8+,17-13+

InChI Key

QHNVWXUULMZJKD-OVSJKPMPSA-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
Watasenia scintillans	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as retinoids. These are oxygenated derivatives of 3,7-dimethyl-1-(2,6,6-trimethylcyclohex-1-enyl)nona-1,3,5,7-tetraene and derivatives thereof.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Prenol lipids

Sub Class

Retinoids

Direct Parent

Retinoids

Alternative Parents

Substituents

Retinoid skeleton
Diterpenoid
Enal
Alpha,beta-unsaturated aldehyde
Organic oxygen compound
Organic oxide
Hydrocarbon derivative
Organooxygen compound
Carbonyl group
Aldehyde
Aliphatic homomonocyclic compound

Molecular Framework

Aliphatic homomonocyclic compounds

External Descriptors

retinals (CHEBI:28537 )
Retinoids (C05918 )
Retinoids (LMPR01090006 )

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	6.23	ALOGPS
logP	4.49	ChemAxon
logS	-4.6	ALOGPS
pKa (Strongest Basic)	-4.1	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	1	ChemAxon
Hydrogen Donor Count	0	ChemAxon
Polar Surface Area	17.07 Å²	ChemAxon
Rotatable Bond Count	5	ChemAxon
Refractivity	97.98 m³·mol⁻¹	ChemAxon
Polarizability	35.17 Å³	ChemAxon
Number of Rings	1	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	ChemAxon
Veber's Rule	Yes	ChemAxon
MDDR-like Rule	No	ChemAxon

External Links

HMDB ID

HMDB0035695

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

FDB014413

KNApSAcK ID

Not Available

Chemspider ID

4444397

KEGG Compound ID

C05918

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

5280866

PDB ID

Not Available

ChEBI ID

28537

Good Scents ID

Not Available

References

General References

LOTUS database [Link]

Showing NP-Card for 3-dehydroretinal (NP0269010)

MOL for NP0269010 (3-dehydroretinal)

3D MOL for NP0269010 (3-dehydroretinal)

3D SDF for NP0269010 (3-dehydroretinal)

3D-SDF for NP0269010 (3-dehydroretinal)

PDB for NP0269010 (3-dehydroretinal)

3D PDB for NP0269010 (3-dehydroretinal)

SMILES for NP0269010 (3-dehydroretinal)

INCHI for NP0269010 (3-dehydroretinal)

Structure for NP0269010 (3-dehydroretinal)

3D Structure for NP0269010 (3-dehydroretinal)