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Showing NP-Card for 3,4-Didehydroretinol (NP0333967)

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Record Information
Version2.0
Created at2024-09-09 21:28:34 UTC
Updated at2024-09-09 21:28:34 UTC
NP-MRD IDNP0333967
Secondary Accession NumbersNone
Natural Product Identification
Common Name3,4-Didehydroretinol
DescriptionConstituent of fresh-water fish oils. 3,4-Didehydroretinol is found in fats and oils and fishes.
Structure
Thumb
MOLSDFPDBSMILESInChI

MOL for NP0333967 (3,4-Didehydroretinol)


  Mrv0541 02251208172D          

 21 21  0  0  0  0            999 V2000
    7.6096  -12.3925    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.0844  -10.9634    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.8483  -15.9651    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.7854  -14.4251    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.0715  -14.8381    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.2595  -12.3925    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.7860  -16.6796    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.8477  -13.1070    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.0844  -12.3925    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.6108  -16.6796    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.6103  -13.8216    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.0233  -14.5354    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.3218  -11.6780    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.3735  -15.9651    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.7342  -10.9634    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.0227  -13.1070    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.4969  -11.6780    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.0233  -15.9651    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.6108  -15.2499    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.7854  -15.2505    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.5591  -10.9634    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1 16  1  0  0  0  0
  2 17  1  0  0  0  0
  3 18  1  0  0  0  0
  4 20  1  0  0  0  0
  5 20  1  0  0  0  0
  6  8  1  0  0  0  0
  6  9  2  0  0  0  0
  7 10  2  0  0  0  0
  7 14  1  0  0  0  0
  8 16  2  0  0  0  0
  9 17  1  0  0  0  0
 10 18  1  0  0  0  0
 11 16  1  0  0  0  0
 11 12  2  0  0  0  0
 12 19  1  0  0  0  0
 13 17  2  0  0  0  0
 13 15  1  0  0  0  0
 14 20  1  0  0  0  0
 15 21  1  0  0  0  0
 18 19  2  0  0  0  0
 19 20  1  0  0  0  0
M  END
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3D MOL for NP0333967 (3,4-Didehydroretinol)

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3D SDF for NP0333967 (3,4-Didehydroretinol)

  Mrv0541 02251208172D          

 21 21  0  0  0  0            999 V2000
    7.6096  -12.3925    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.0844  -10.9634    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.8483  -15.9651    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.7854  -14.4251    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.0715  -14.8381    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.2595  -12.3925    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.7860  -16.6796    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.8477  -13.1070    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.0844  -12.3925    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.6108  -16.6796    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.6103  -13.8216    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.0233  -14.5354    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.3218  -11.6780    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.3735  -15.9651    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.7342  -10.9634    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.0227  -13.1070    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.4969  -11.6780    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.0233  -15.9651    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.6108  -15.2499    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.7854  -15.2505    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.5591  -10.9634    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1 16  1  0  0  0  0
  2 17  1  0  0  0  0
  3 18  1  0  0  0  0
  4 20  1  0  0  0  0
  5 20  1  0  0  0  0
  6  8  1  0  0  0  0
  6  9  2  0  0  0  0
  7 10  2  0  0  0  0
  7 14  1  0  0  0  0
  8 16  2  0  0  0  0
  9 17  1  0  0  0  0
 10 18  1  0  0  0  0
 11 16  1  0  0  0  0
 11 12  2  0  0  0  0
 12 19  1  0  0  0  0
 13 17  2  0  0  0  0
 13 15  1  0  0  0  0
 14 20  1  0  0  0  0
 15 21  1  0  0  0  0
 18 19  2  0  0  0  0
 19 20  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0333967

> <DATABASE_NAME>
NP-MRD

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

> <INCHI_IDENTIFIER>
InChI=1S/C20H28O/c1-16(8-6-9-17(2)13-15-21)11-12-19-18(3)10-7-14-20(19,4)5/h6-13,21H,14-15H2,1-5H3/b9-6+,12-11+,16-8+,17-13+

> <INCHI_KEY>
XWCYDHJOKKGVHC-OVSJKPMPSA-N

> <FORMULA>
C20H28O

> <MOLECULAR_WEIGHT>
284.4357

> <EXACT_MASS>
284.214015518

> <JCHEM_ACCEPTOR_COUNT>
1

> <JCHEM_AVERAGE_POLARIZABILITY>
36.02006678531005

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <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-tetraen-1-ol

> <ALOGPS_LOGP>
5.66

> <JCHEM_LOGP>
4.332171516333333

> <ALOGPS_LOGS>
-4.30

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_ACIDIC>
16.435769749539965

> <JCHEM_PKA_STRONGEST_BASIC>
-2.1707943115512176

> <JCHEM_POLAR_SURFACE_AREA>
20.23

> <JCHEM_REFRACTIVITY>
99.04

> <JCHEM_ROTATABLE_BOND_COUNT>
5

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.42e-02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
vitamin A 2

> <JCHEM_VEBER_RULE>
1

$$$$

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3D-SDF for NP0333967 (3,4-Didehydroretinol)
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PDB for NP0333967 (3,4-Didehydroretinol)
HEADER    PROTEIN                                 25-FEB-12   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   25-FEB-12         0                                  
HETATM    1  C   UNK     0      14.205 -23.133   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      18.824 -20.465   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      16.517 -29.802   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      12.666 -26.927   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      11.333 -27.698   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      17.284 -23.133   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      12.667 -31.135   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      16.516 -24.466   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      18.824 -23.133   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      14.207 -31.135   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      14.206 -25.800   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      14.977 -27.133   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      21.134 -21.799   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      11.897 -29.802   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0      21.904 -20.465   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0      14.976 -24.466   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0      19.594 -21.799   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0      14.977 -29.802   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0      14.207 -28.466   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0      12.666 -28.468   0.000  0.00  0.00           C+0
HETATM   21  O   UNK     0      23.444 -20.465   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   16   12                                                       
CONECT   12   11   19                                                       
CONECT   13   17   15                                                       
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

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3D PDB for NP0333967 (3,4-Didehydroretinol)
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SMILES for NP0333967 (3,4-Didehydroretinol)
C\C(=C/CO)\C=C\C=C(/C)\C=C\C1=C(C)C=CCC1(C)C
Download
INCHI for NP0333967 (3,4-Didehydroretinol)
InChI=1S/C20H28O/c1-16(8-6-9-17(2)13-15-21)11-12-19-18(3)10-7-14-20(19,4)5/h6-13,21H,14-15H2,1-5H3/b9-6+,12-11+,16-8+,17-13+
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View in JSmol
Synonyms
ValueSource
3,4-Didehydro-all-trans-retinolChEBI
3,4-Didehydro-retinolChEBI
3-DehydoretinolChEBI
all-trans-3-DehydroretinolChEBI
DehydroretinolChEBI
all-trans-3,4-Didehydro retinolHMDB
3,4-DidehydroretinolHMDB
all-trans-3,4-DidehydroretinolHMDB
VA2HMDB
Vitamin a2, (7-cis)-isomerHMDB
3-DehydroretinolHMDB
Vitamin a2ChEBI
Chemical FormulaC20H28O
Average Mass284.4357 Da
Monoisotopic Mass284.21402 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-tetraen-1-ol
Traditional Namevitamin A 2
CAS Registry NumberNot Available
SMILES
C\C(=C/CO)\C=C\C=C(/C)\C=C\C1=C(C)C=CCC1(C)C
InChI Identifier
InChI=1S/C20H28O/c1-16(8-6-9-17(2)13-15-21)11-12-19-18(3)10-7-14-20(19,4)5/h6-13,21H,14-15H2,1-5H3/b9-6+,12-11+,16-8+,17-13+
InChI KeyXWCYDHJOKKGVHC-OVSJKPMPSA-N
Experimental Spectra
Not Available
Predicted Spectra
Not Available
Chemical Shift Submissions
Not Available
Species
Species of OriginNot Available
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.
KingdomOrganic compounds  
Super ClassLipids and lipid-like molecules  
ClassPrenol lipids  
Sub ClassRetinoids  
Direct ParentRetinoids  
Alternative Parents
Substituents
  • Retinoid skeleton
    • 

  • Diterpenoid
    • 

  • Fatty alcohol
    • 

  • Fatty acyl
    • 

  • Organic oxygen compound
    • 

  • Hydrocarbon derivative
    • 

  • Primary alcohol
    • 

  • Organooxygen compound
    • 

  • Alcohol
    • 

  • Aliphatic homomonocyclic compound
Molecular FrameworkAliphatic homomonocyclic compounds
External Descriptors
Physical Properties
StateNot Available
Experimental Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Predicted Properties
PropertyValueSource
logP5.66ALOGPS
logP4.33ChemAxon
logS-4.3ALOGPS
pKa (Strongest Acidic)16.44ChemAxon
pKa (Strongest Basic)-2.2ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count1ChemAxon
Hydrogen Donor Count1ChemAxon
Polar Surface Area20.23 ŲChemAxon
Rotatable Bond Count5ChemAxon
Refractivity99.04 m³·mol⁻¹ChemAxon
Polarizability36.02 ųChemAxon
Number of Rings1ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleNoChemAxon
HMDB IDHMDB0013117  
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FoodDB IDFDB013830  
KNApSAcK IDNot Available
Chemspider ID4940721  
KEGG Compound IDNot Available
BioCyc IDCPD-10577  
BiGG IDNot Available
Wikipedia LinkDehydroretinal  
METLIN IDNot Available
PubChem Compound6436043  
PDB IDNot Available
ChEBI ID132246  
Good Scents IDNot Available
References
General References
  1. Escaron AL, Green MH, Tanumihardjo SA: Plasma turnover of 3,4-didehydroretinol (vitamin A2) increases in vitamin A-deficient rats fed low versus high dietary fat. J Lipid Res. 2009 Apr;50(4):694-703. doi: 10.1194/jlr.M800479-JLR200. Epub 2008  Nov 30. [PubMed:19043141  ] 
  2. Defo MA, Pierron F, Spear PA, Bernatchez L, Campbell PG, Couture P: Evidence for metabolic imbalance of vitamin A2 in wild fish chronically exposed to metals. Ecotoxicol Environ Saf. 2012 Nov;85:88-95. doi: 10.1016/j.ecoenv.2012.08.017.  Epub 2012 Sep 7. [PubMed:22959581  ] 
  3. Enright JM, Toomey MB, Sato SY, Temple SE, Allen JR, Fujiwara R, Kramlinger VM, Nagy LD, Johnson KM, Xiao Y, How MJ, Johnson SL, Roberts NW, Kefalov VJ, Guengerich FP, Corbo JC: Cyp27c1 Red-Shifts the Spectral Sensitivity of Photoreceptors by Converting Vitamin A1 into A2. Curr Biol. 2015 Dec 7;25(23):3048-57. doi: 10.1016/j.cub.2015.10.018. Epub 2015  Nov 5. [PubMed:26549260  ] 
  4. Kramlinger VM, Nagy LD, Fujiwara R, Johnson KM, Phan TT, Xiao Y, Enright JM, Toomey MB, Corbo JC, Guengerich FP: Human cytochrome P450 27C1 catalyzes 3,4-desaturation of retinoids. FEBS Lett. 2016 May;590(9):1304-12. doi: 10.1002/1873-3468.12167. Epub 2016 Apr  17. [PubMed:27059013  ] 
  5. Kakela R, Hyvarinen H, Kakela A: Vitamins A1 (retinol), A2 (3,4-didehydroretinol) and E (alpha-tocopherol) in the liver and blubber of lacustrine and marine ringed seals (Phoca hispida sp.). Comp Biochem Physiol B Biochem Mol Biol. 1997 Jan;116(1):27-33. doi:  10.1016/s0305-0491(96)00158-7. [PubMed:9080660  ]