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Showing NP-Card for (13Z)-Retinol (NP0334753)

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Record Information
Version2.0
Created at2024-09-10 19:48:52 UTC
Updated at2024-09-10 19:48:52 UTC
NP-MRD IDNP0334753
Secondary Accession NumbersNone
Natural Product Identification
Common Name(13Z)-Retinol
Description9-Cis-Retinol 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, 9-cis-retinol is considered to be an isoprenoid lipid molecule. 9-Cis-Retinol is a very hydrophobic molecule, practically insoluble (in water), and relatively neutral. Within humans, 9-cis-retinol participates in a number of enzymatic reactions. In particular, 9-cis-retinol can be converted into 9-cis-retinal; which is catalyzed by the enzyme retinol dehydrogenase 11. In addition, 9-cis-retinol can be converted into 9-cis-retinal; which is mediated by the enzyme retinol dehydrogenase 11. In humans, 9-cis-retinol is involved in retinol metabolism. Outside of the human body, 9-cis-Retinol is found, on average, in the highest concentration within a few different foods, such as tea leaf willows, walrus, and sourdocks and in a lower concentration in pummelo, green zucchinis, and amaranths. 9-Cis-Retinol has also been detected, but not quantified in, several different foods, such as sea-buckthornberries, vanilla, opium poppies, meringues, and ascidians. This could make 9-cis-retinol a potential biomarker for the consumption of these foods. (13Z)-Retinol was first documented in 1997 (PMID: 9115228). A retinol in which the double bond at position 9 has cis configuration, whilst the remaining acyclic double bonds have trans configuration (PMID: 15572038) (PMID: 11140907).
Structure
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MOLSDFPDBSMILESInChI

MOL for NP0334753 ((13Z)-Retinol)


  Mrv1652303192021392D          

 21 21  0  0  0  0            999 V2000
    2.4749   -1.0808    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4749   -1.9058    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1894   -2.3182    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1894   -0.6683    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9040   -1.9058    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9040   -1.0808    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6500   -1.0808    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0625   -0.3663    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1894    0.1568    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.6184   -0.6683    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9040    0.5692    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9040    1.3942    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1894    1.8067    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.6184    1.8067    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.3329    1.3942    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.0473    1.8067    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.7619    1.3942    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.7619    0.5692    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.4763    1.8067    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.1908    1.3942    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.9052    1.8067    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  1  4  1  0  0  0  0
  1  7  1  0  0  0  0
  1  8  1  0  0  0  0
  2  3  1  0  0  0  0
  3  5  1  0  0  0  0
  4  6  2  0  0  0  0
  4  9  1  0  0  0  0
  5  6  1  0  0  0  0
  6 10  1  0  0  0  0
  9 11  2  0  0  0  0
 11 12  1  0  0  0  0
 12 13  1  0  0  0  0
 12 14  2  0  0  0  0
 14 15  1  0  0  0  0
 15 16  2  0  0  0  0
 16 17  1  0  0  0  0
 17 18  1  0  0  0  0
 17 19  2  0  0  0  0
 19 20  1  0  0  0  0
 20 21  1  0  0  0  0
M  END
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3D MOL for NP0334753 ((13Z)-Retinol)

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3D SDF for NP0334753 ((13Z)-Retinol)

  Mrv1652303192021392D          

 21 21  0  0  0  0            999 V2000
    2.4749   -1.0808    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4749   -1.9058    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1894   -2.3182    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1894   -0.6683    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9040   -1.9058    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9040   -1.0808    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6500   -1.0808    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0625   -0.3663    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1894    0.1568    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.6184   -0.6683    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9040    0.5692    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9040    1.3942    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1894    1.8067    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.6184    1.8067    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.3329    1.3942    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.0473    1.8067    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.7619    1.3942    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.7619    0.5692    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.4763    1.8067    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.1908    1.3942    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.9052    1.8067    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  1  4  1  0  0  0  0
  1  7  1  0  0  0  0
  1  8  1  0  0  0  0
  2  3  1  0  0  0  0
  3  5  1  0  0  0  0
  4  6  2  0  0  0  0
  4  9  1  0  0  0  0
  5  6  1  0  0  0  0
  6 10  1  0  0  0  0
  9 11  2  0  0  0  0
 11 12  1  0  0  0  0
 12 13  1  0  0  0  0
 12 14  2  0  0  0  0
 14 15  1  0  0  0  0
 15 16  2  0  0  0  0
 16 17  1  0  0  0  0
 17 18  1  0  0  0  0
 17 19  2  0  0  0  0
 19 20  1  0  0  0  0
 20 21  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0334753

> <DATABASE_NAME>
NP-MRD

> <SMILES>
C\C(=C/CO)\C=C\C=C(\C)/C=C/C1=C(C)CCCC1(C)C

> <INCHI_IDENTIFIER>
InChI=1S/C20H30O/c1-16(8-6-9-17(2)13-15-21)11-12-19-18(3)10-7-14-20(19,4)5/h6,8-9,11-13,21H,7,10,14-15H2,1-5H3/b9-6+,12-11+,16-8-,17-13+

> <INCHI_KEY>
FPIPGXGPPPQFEQ-MKOSUFFBSA-N

> <FORMULA>
C20H30O

> <MOLECULAR_WEIGHT>
286.4516

> <EXACT_MASS>
286.229665582

> <JCHEM_ACCEPTOR_COUNT>
1

> <JCHEM_ATOM_COUNT>
51

> <JCHEM_AVERAGE_POLARIZABILITY>
35.864701839190474

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
(2E,4E,6Z,8E)-3,7-dimethyl-9-(2,6,6-trimethylcyclohex-1-en-1-yl)nona-2,4,6,8-tetraen-1-ol

> <ALOGPS_LOGP>
6.38

> <JCHEM_LOGP>
4.694093173000001

> <ALOGPS_LOGS>
-4.58

> <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>
97.9234

> <JCHEM_ROTATABLE_BOND_COUNT>
5

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
7.58e-03 g/l

> <JCHEM_TRADITIONAL_IUPAC>
9-cis-retinol

> <JCHEM_VEBER_RULE>
1

$$$$

Download
3D-SDF for NP0334753 ((13Z)-Retinol)
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PDB for NP0334753 ((13Z)-Retinol)
HEADER    PROTEIN                                 19-MAR-20   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   19-MAR-20         0                                  
HETATM    1  C   UNK     0       4.620  -2.017   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       4.620  -3.557   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       5.954  -4.327   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       5.954  -1.247   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       7.287  -3.557   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       7.287  -2.017   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       3.080  -2.017   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       3.850  -0.684   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       5.954   0.293   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       8.621  -1.247   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       7.287   1.063   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       7.287   2.603   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       5.954   3.373   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       8.621   3.373   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       9.955   2.603   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0      11.288   3.373   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0      12.622   2.603   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0      12.622   1.063   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0      13.956   3.373   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0      15.289   2.603   0.000  0.00  0.00           C+0
HETATM   21  O   UNK     0      16.623   3.373   0.000  0.00  0.00           O+0
CONECT    1    2    4    7    8                                             
CONECT    2    1    3                                                       
CONECT    3    2    5                                                       
CONECT    4    1    6    9                                                  
CONECT    5    3    6                                                       
CONECT    6    4    5   10                                                  
CONECT    7    1                                                            
CONECT    8    1                                                            
CONECT    9    4   11                                                       
CONECT   10    6                                                            
CONECT   11    9   12                                                       
CONECT   12   11   13   14                                                  
CONECT   13   12                                                            
CONECT   14   12   15                                                       
CONECT   15   14   16                                                       
CONECT   16   15   17                                                       
CONECT   17   16   18   19                                                  
CONECT   18   17                                                            
CONECT   19   17   20                                                       
CONECT   20   19   21                                                       
CONECT   21   20                                                            
MASTER        0    0    0    0    0    0    0    0   21    0   42    0
END

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3D PDB for NP0334753 ((13Z)-Retinol)
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SMILES for NP0334753 ((13Z)-Retinol)
C\C(=C/CO)\C=C\C=C(\C)/C=C/C1=C(C)CCCC1(C)C
Download
INCHI for NP0334753 ((13Z)-Retinol)
InChI=1S/C20H30O/c1-16(8-6-9-17(2)13-15-21)11-12-19-18(3)10-7-14-20(19,4)5/h6,8-9,11-13,21H,7,10,14-15H2,1-5H3/b9-6+,12-11+,16-8-,17-13+
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Synonyms
ValueSource
(2E,4E,6Z,8E)-3,7-Dimethyl-9-(2,6,6-trimethylcyclohex-1-en-1-yl)nona-2,4,6,8-tetraen-1-olChEBI
(9cis)-RetinolChEBI
9-cis RetinolHMDB
Chemical FormulaC20H30O
Average Mass286.4516 Da
Monoisotopic Mass286.22967 Da
IUPAC Name(2E,4E,6Z,8E)-3,7-dimethyl-9-(2,6,6-trimethylcyclohex-1-en-1-yl)nona-2,4,6,8-tetraen-1-ol
Traditional Name9-cis-retinol
CAS Registry NumberNot Available
SMILES
C\C(=C/CO)\C=C\C=C(\C)/C=C/C1=C(C)CCCC1(C)C
InChI Identifier
InChI=1S/C20H30O/c1-16(8-6-9-17(2)13-15-21)11-12-19-18(3)10-7-14-20(19,4)5/h6,8-9,11-13,21H,7,10,14-15H2,1-5H3/b9-6+,12-11+,16-8-,17-13+
InChI KeyFPIPGXGPPPQFEQ-MKOSUFFBSA-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
logP6.38ALOGPS
logP4.69ChemAxon
logS-4.6ALOGPS
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
Refractivity97.92 m³·mol⁻¹ChemAxon
Polarizability35.86 ųChemAxon
Number of Rings1ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleNoChemAxon
HMDB IDHMDB0006217  
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FoodDB IDFDB013828  
KNApSAcK IDNot Available
Chemspider ID8123435  
KEGG Compound IDC16682  
BioCyc IDNot Available
BiGG ID2265507  
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound9947823  
PDB IDNot Available
ChEBI ID78272  
Good Scents IDNot Available
References
General References
  1. Paik J, Blaner WS, Swisshelm K: Cis-retinol dehydrogenase: 9-cis-retinol metabolism and its effect on proliferation of human MCF7 breast cancer cells. Exp Cell Res. 2005 Feb 1;303(1):183-96. [PubMed:15572038  ] 
  2. Mertz JR, Shang E, Piantedosi R, Wei S, Wolgemuth DJ, Blaner WS: Identification and characterization of a stereospecific human enzyme that catalyzes 9-cis-retinol oxidation. A possible role in 9-cis-retinoic acid formation. J Biol Chem. 1997 May 2;272(18):11744-9. doi: 10.1074/jbc.272.18.11744. [PubMed:9115228  ] 
  3. Wolf G: The oxidation of 9-cis-retinol: a possible synthesis pathway for 9-cis-retinoic acid. Nutr Rev. 2000 Nov;58(11):354-6. doi: 10.1111/j.1753-4887.2000.tb01833.x. [PubMed:11140907  ]