Jump To Section:

Identification Taxonomy Ontology Physical properties Spectra Biological properties Concentrations Links References enzymes (1) Show 1 protein XML

Record Information

Version

5.0

Status

Expected but not Quantified

Creation Date

2006-05-22 14:17:38 UTC

Update Date

2022-03-07 02:49:13 UTC

HMDB ID

HMDB0002152

Secondary Accession Numbers

HMDB02152

Metabolite Identification

Common Name

11-cis-Retinaldehyde

Description

11-cis-retinal is a retinal having 2E,4Z,6E,8E-double bond geometry. It has a role as a chromophore, a human metabolite and a mouse metabolite. It is a diterpene derived from the carotenoid vitamin A which functions as the active component of the visual cycle. It is the prosthetic group of rhodopsin. When stimulated by visible light, rhodopsin transforms this cis-isomer of retinal to the trans-isomer (11-trans-retinal). This transformation straightens-out the bend of the retinal molecule and causes a change in the shape of rhodopsin triggering the visual process. A series of energy-requiring enzyme-catalyzed reactions convert the 11-trans-retinal back to the cis-isomer. 11-cis-retinal functions in the retina in the transduction of light into the neural signals necessary for vision. 11-cis-retinal, while attached to opsin in rhodopsin is isomerized to all-trans-retinal by light. This is the event that triggers the nerve impulse to the brain which allows for the perception of light. All-trans-retinal is then released from opsin and reduced to all-trans-retinol. All-trans-retinol is isomerized to 11-cis-retinol in the dark, and then oxidized to 11-cis-retinal. 11-cis-retinal recombines with opsin to re-form rhodopsin. Night blindness or defective vision at low illumination results from a failure to resynthesize 11-cis retinal rapidly.

Structure

MOL 3D MOL SDF 3D SDF PDB 3D PDB SMILES InChI

HMDB0002152
     RDKit          3D
11-cis-Retinaldehyde
 49 49  0  0  0  0  0  0  0  0999 V2000
   -3.1860   -0.2385    3.0415 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4132   -0.5983    1.6209 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4098   -0.5145    0.7352 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1300   -0.0640    1.2381 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0183    0.0974    0.5760 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2266    0.5712    1.2397 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1837    0.8420    2.6726 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3366    0.7290    0.5403 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5737    1.1809    1.1015 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.6595    1.3173    0.4237 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.9088    1.0678   -0.9552 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0036    0.4788   -1.9209 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.1387    1.3344   -1.4297 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.5390    1.1361   -2.8083 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.7690    1.4482   -3.0441 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5557   -0.8558   -0.6910 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5650   -1.9461   -1.0178 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2570    0.3749   -1.5203 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9265   -1.4079   -1.0273 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0366   -0.8065   -0.2388 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7846   -1.0454    1.2348 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3676   -0.8374    3.4983 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9487    0.8596    3.1193 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1285   -0.3789    3.5970 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0473    0.1882    2.3137 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0145   -0.1197   -0.4748 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7475   -0.1075    3.1403 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3996    1.6055    2.9416 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.1204    1.0224    3.1913 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.1673    0.5027   -0.4969 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.6266    1.4350    2.1606 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.5267    1.6929    1.0520 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.6004   -0.4944   -1.5051 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.5628    0.0569   -2.8312 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.1826    1.0914   -2.2638 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.8581    1.7265   -0.6953 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.9899    0.7840   -3.6325 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9397   -2.2554   -0.1502 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9809   -1.7090   -1.9263 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1411   -2.8892   -1.2669 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2119    0.6962   -2.0109 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8941    1.2246   -0.9240 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4998    0.1299   -2.2869 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9222   -2.5117   -0.9460 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1075   -1.1844   -2.1122 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.1829    0.2513   -0.4687 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.9654   -1.3413   -0.4938 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9614   -2.0994    1.4794 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.5248   -0.4396    1.7983 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  2  0
  3  4  1  0
  4  5  2  0
  5  6  1  0
  6  7  1  0
  6  8  2  0
  8  9  1  0
  9 10  2  0
 10 11  1  0
 11 12  1  0
 11 13  2  0
 13 14  1  0
 14 15  2  0
  3 16  1  0
 16 17  1  0
 16 18  1  0
 16 19  1  0
 19 20  1  0
 20 21  1  0
 21  2  1  0
  1 22  1  0
  1 23  1  0
  1 24  1  0
  4 25  1  0
  5 26  1  0
  7 27  1  0
  7 28  1  0
  7 29  1  0
  8 30  1  0
  9 31  1  0
 10 32  1  0
 12 33  1  0
 12 34  1  0
 12 35  1  0
 13 36  1  0
 14 37  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
 19 44  1  0
 19 45  1  0
 20 46  1  0
 20 47  1  0
 21 48  1  0
 21 49  1  0
M  END


  Mrv1652303192021402D          

 21 21  0  0  0  0            999 V2000
   -0.7145    0.4125    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
    0.7145    0.4125    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
    0.0000   -0.8250    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
    0.4125    1.5395    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
    3.5724    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2868    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0013    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.7158   -0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.7158   -1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0013   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2868   -0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4125    1.5395    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579    1.6500    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
    1.4289   -0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.4302   -2.0625    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  3  8  1  0  0  0  0
  4  3  2  0  0  0  0
 20  4  1  0  0  0  0
  2  5  1  0  0  0  0
  5  4  1  0  0  0  0
  6  1  1  0  0  0  0
  6  3  1  0  0  0  0
 16  6  1  0  0  0  0
  7  6  1  0  0  0  0
  8 19  2  0  0  0  0
 17  9  2  0  0  0  0
  9 10  1  0  0  0  0
 10 11  2  0  0  0  0
 11 14  1  0  0  0  0
 14 12  2  0  0  0  0
 12 13  1  0  0  0  0
 13 21  2  0  0  0  0
 14 15  1  0  0  0  0
 19 17  1  0  0  0  0
 17 18  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0002152

> <DATABASE_NAME>
hmdb

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

> <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/h6,8-9,11-13,15H,7,10,14H2,1-5H3/b9-6-,12-11+,16-8+,17-13+

> <INCHI_KEY>
NCYCYZXNIZJOKI-IOUUIBBYSA-N

> <FORMULA>
C20H28O

> <MOLECULAR_WEIGHT>
284.4357

> <EXACT_MASS>
284.214015518

> <JCHEM_ACCEPTOR_COUNT>
1

> <JCHEM_ATOM_COUNT>
49

> <JCHEM_AVERAGE_POLARIZABILITY>
34.820546205282355

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

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

> <ALOGPS_LOGP>
6.62

> <JCHEM_LOGP>
4.855751458666667

> <ALOGPS_LOGS>
-4.83

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_BASIC>
-4.061304726121949

> <JCHEM_POLAR_SURFACE_AREA>
17.07

> <JCHEM_REFRACTIVITY>
96.86540000000001

> <JCHEM_ROTATABLE_BOND_COUNT>
5

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
4.20e-03 g/l

> <JCHEM_TRADITIONAL_IUPAC>
11-cis-retinal

> <JCHEM_VEBER_RULE>
1

$$$$

HMDB0002152
     RDKit          3D
11-cis-Retinaldehyde
 49 49  0  0  0  0  0  0  0  0999 V2000
   -3.1860   -0.2385    3.0415 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4132   -0.5983    1.6209 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4098   -0.5145    0.7352 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1300   -0.0640    1.2381 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0183    0.0974    0.5760 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2266    0.5712    1.2397 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1837    0.8420    2.6726 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3366    0.7290    0.5403 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5737    1.1809    1.1015 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.6595    1.3173    0.4237 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.9088    1.0678   -0.9552 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0036    0.4788   -1.9209 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.1387    1.3344   -1.4297 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.5390    1.1361   -2.8083 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.7690    1.4482   -3.0441 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5557   -0.8558   -0.6910 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5650   -1.9461   -1.0178 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2570    0.3749   -1.5203 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9265   -1.4079   -1.0273 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0366   -0.8065   -0.2388 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7846   -1.0454    1.2348 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3676   -0.8374    3.4983 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9487    0.8596    3.1193 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1285   -0.3789    3.5970 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0473    0.1882    2.3137 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0145   -0.1197   -0.4748 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7475   -0.1075    3.1403 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3996    1.6055    2.9416 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.1204    1.0224    3.1913 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.1673    0.5027   -0.4969 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.6266    1.4350    2.1606 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.5267    1.6929    1.0520 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.6004   -0.4944   -1.5051 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.5628    0.0569   -2.8312 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.1826    1.0914   -2.2638 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.8581    1.7265   -0.6953 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.9899    0.7840   -3.6325 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9397   -2.2554   -0.1502 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9809   -1.7090   -1.9263 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1411   -2.8892   -1.2669 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2119    0.6962   -2.0109 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8941    1.2246   -0.9240 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4998    0.1299   -2.2869 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9222   -2.5117   -0.9460 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1075   -1.1844   -2.1122 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.1829    0.2513   -0.4687 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.9654   -1.3413   -0.4938 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9614   -2.0994    1.4794 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.5248   -0.4396    1.7983 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  2  0
  3  4  1  0
  4  5  2  0
  5  6  1  0
  6  7  1  0
  6  8  2  0
  8  9  1  0
  9 10  2  0
 10 11  1  0
 11 12  1  0
 11 13  2  0
 13 14  1  0
 14 15  2  0
  3 16  1  0
 16 17  1  0
 16 18  1  0
 16 19  1  0
 19 20  1  0
 20 21  1  0
 21  2  1  0
  1 22  1  0
  1 23  1  0
  1 24  1  0
  4 25  1  0
  5 26  1  0
  7 27  1  0
  7 28  1  0
  7 29  1  0
  8 30  1  0
  9 31  1  0
 10 32  1  0
 12 33  1  0
 12 34  1  0
 12 35  1  0
 13 36  1  0
 14 37  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
 19 44  1  0
 19 45  1  0
 20 46  1  0
 20 47  1  0
 21 48  1  0
 21 49  1  0
M  END

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      -1.334   0.770   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -1.334  -0.770   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       1.334   0.770   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       0.000  -1.540   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       0.000   1.540   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       0.770   2.874   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       2.667   1.540   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       6.668   0.770   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       8.002   1.540   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       9.336   0.770   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      10.669  -1.540   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      10.669  -3.080   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       9.336  -0.770   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       8.002  -1.540   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0      -0.770   2.874   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       5.335   1.540   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       5.335   3.080   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       4.001   0.770   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       2.667  -1.540   0.000  0.00  0.00           C+0
HETATM   21  O   UNK     0      12.003  -3.850   0.000  0.00  0.00           O+0
CONECT    1    2    6                                                       
CONECT    2    1    5                                                       
CONECT    3    8    4    6                                                  
CONECT    4    3   20    5                                                  
CONECT    5    2    4                                                       
CONECT    6    1    3   16    7                                             
CONECT    7    6                                                            
CONECT    8    3   19                                                       
CONECT    9   17   10                                                       
CONECT   10    9   11                                                       
CONECT   11   10   14                                                       
CONECT   12   14   13                                                       
CONECT   13   12   21                                                       
CONECT   14   11   12   15                                                  
CONECT   15   14                                                            
CONECT   16    6                                                            
CONECT   17    9   19   18                                                  
CONECT   18   17                                                            
CONECT   19    8   17                                                       
CONECT   20    4                                                            
CONECT   21   13                                                            
MASTER        0    0    0    0    0    0    0    0   21    0   42    0
END

COMPND    HMDB0002152
HETATM    1  C1  UNL     1      -3.186  -0.239   3.041  1.00  0.00           C  
HETATM    2  C2  UNL     1      -3.413  -0.598   1.621  1.00  0.00           C  
HETATM    3  C3  UNL     1      -2.410  -0.514   0.735  1.00  0.00           C  
HETATM    4  C4  UNL     1      -1.130  -0.064   1.238  1.00  0.00           C  
HETATM    5  C5  UNL     1      -0.018   0.097   0.576  1.00  0.00           C  
HETATM    6  C6  UNL     1       1.227   0.571   1.240  1.00  0.00           C  
HETATM    7  C7  UNL     1       1.184   0.842   2.673  1.00  0.00           C  
HETATM    8  C8  UNL     1       2.337   0.729   0.540  1.00  0.00           C  
HETATM    9  C9  UNL     1       3.574   1.181   1.102  1.00  0.00           C  
HETATM   10  C10 UNL     1       4.660   1.317   0.424  1.00  0.00           C  
HETATM   11  C11 UNL     1       4.909   1.068  -0.955  1.00  0.00           C  
HETATM   12  C12 UNL     1       4.004   0.479  -1.921  1.00  0.00           C  
HETATM   13  C13 UNL     1       6.139   1.334  -1.430  1.00  0.00           C  
HETATM   14  C14 UNL     1       6.539   1.136  -2.808  1.00  0.00           C  
HETATM   15  O1  UNL     1       7.769   1.448  -3.044  1.00  0.00           O  
HETATM   16  C15 UNL     1      -2.556  -0.856  -0.691  1.00  0.00           C  
HETATM   17  C16 UNL     1      -1.565  -1.946  -1.018  1.00  0.00           C  
HETATM   18  C17 UNL     1      -2.257   0.375  -1.520  1.00  0.00           C  
HETATM   19  C18 UNL     1      -3.926  -1.408  -1.027  1.00  0.00           C  
HETATM   20  C19 UNL     1      -5.037  -0.807  -0.239  1.00  0.00           C  
HETATM   21  C20 UNL     1      -4.785  -1.045   1.235  1.00  0.00           C  
HETATM   22  H1  UNL     1      -2.368  -0.837   3.498  1.00  0.00           H  
HETATM   23  H2  UNL     1      -2.949   0.860   3.119  1.00  0.00           H  
HETATM   24  H3  UNL     1      -4.129  -0.379   3.597  1.00  0.00           H  
HETATM   25  H4  UNL     1      -1.047   0.188   2.314  1.00  0.00           H  
HETATM   26  H5  UNL     1      -0.014  -0.120  -0.475  1.00  0.00           H  
HETATM   27  H6  UNL     1       0.748  -0.107   3.140  1.00  0.00           H  
HETATM   28  H7  UNL     1       0.400   1.605   2.942  1.00  0.00           H  
HETATM   29  H8  UNL     1       2.120   1.022   3.191  1.00  0.00           H  
HETATM   30  H9  UNL     1       2.167   0.503  -0.497  1.00  0.00           H  
HETATM   31  H10 UNL     1       3.627   1.435   2.161  1.00  0.00           H  
HETATM   32  H11 UNL     1       5.527   1.693   1.052  1.00  0.00           H  
HETATM   33  H12 UNL     1       3.600  -0.494  -1.505  1.00  0.00           H  
HETATM   34  H13 UNL     1       4.563   0.057  -2.831  1.00  0.00           H  
HETATM   35  H14 UNL     1       3.183   1.091  -2.264  1.00  0.00           H  
HETATM   36  H15 UNL     1       6.858   1.727  -0.695  1.00  0.00           H  
HETATM   37  H16 UNL     1       5.990   0.784  -3.632  1.00  0.00           H  
HETATM   38  H17 UNL     1      -0.940  -2.255  -0.150  1.00  0.00           H  
HETATM   39  H18 UNL     1      -0.981  -1.709  -1.926  1.00  0.00           H  
HETATM   40  H19 UNL     1      -2.141  -2.889  -1.267  1.00  0.00           H  
HETATM   41  H20 UNL     1      -3.212   0.696  -2.011  1.00  0.00           H  
HETATM   42  H21 UNL     1      -1.894   1.225  -0.924  1.00  0.00           H  
HETATM   43  H22 UNL     1      -1.500   0.130  -2.287  1.00  0.00           H  
HETATM   44  H23 UNL     1      -3.922  -2.512  -0.946  1.00  0.00           H  
HETATM   45  H24 UNL     1      -4.107  -1.184  -2.112  1.00  0.00           H  
HETATM   46  H25 UNL     1      -5.183   0.251  -0.469  1.00  0.00           H  
HETATM   47  H26 UNL     1      -5.965  -1.341  -0.494  1.00  0.00           H  
HETATM   48  H27 UNL     1      -4.961  -2.099   1.479  1.00  0.00           H  
HETATM   49  H28 UNL     1      -5.525  -0.440   1.798  1.00  0.00           H  
CONECT    1    2   22   23   24
CONECT    2    3    3   21
CONECT    3    4   16
CONECT    4    5    5   25
CONECT    5    6   26
CONECT    6    7    8    8
CONECT    7   27   28   29
CONECT    8    9   30
CONECT    9   10   10   31
CONECT   10   11   32
CONECT   11   12   13   13
CONECT   12   33   34   35
CONECT   13   14   36
CONECT   14   15   15   37
CONECT   16   17   18   19
CONECT   17   38   39   40
CONECT   18   41   42   43
CONECT   19   20   44   45
CONECT   20   21   46   47
CONECT   21   48   49
END

HMDB0002152
     RDKit          3D
11-cis-Retinaldehyde
 49 49  0  0  0  0  0  0  0  0999 V2000
   -3.1860   -0.2385    3.0415 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4132   -0.5983    1.6209 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4098   -0.5145    0.7352 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1300   -0.0640    1.2381 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0183    0.0974    0.5760 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2266    0.5712    1.2397 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1837    0.8420    2.6726 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3366    0.7290    0.5403 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5737    1.1809    1.1015 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.6595    1.3173    0.4237 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.9088    1.0678   -0.9552 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0036    0.4788   -1.9209 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.1387    1.3344   -1.4297 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.5390    1.1361   -2.8083 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.7690    1.4482   -3.0441 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5557   -0.8558   -0.6910 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5650   -1.9461   -1.0178 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2570    0.3749   -1.5203 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9265   -1.4079   -1.0273 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0366   -0.8065   -0.2388 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7846   -1.0454    1.2348 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3676   -0.8374    3.4983 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9487    0.8596    3.1193 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1285   -0.3789    3.5970 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0473    0.1882    2.3137 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0145   -0.1197   -0.4748 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7475   -0.1075    3.1403 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3996    1.6055    2.9416 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.1204    1.0224    3.1913 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.1673    0.5027   -0.4969 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.6266    1.4350    2.1606 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.5267    1.6929    1.0520 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.6004   -0.4944   -1.5051 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.5628    0.0569   -2.8312 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.1826    1.0914   -2.2638 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.8581    1.7265   -0.6953 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.9899    0.7840   -3.6325 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9397   -2.2554   -0.1502 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9809   -1.7090   -1.9263 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1411   -2.8892   -1.2669 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2119    0.6962   -2.0109 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8941    1.2246   -0.9240 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4998    0.1299   -2.2869 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9222   -2.5117   -0.9460 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1075   -1.1844   -2.1122 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.1829    0.2513   -0.4687 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.9654   -1.3413   -0.4938 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9614   -2.0994    1.4794 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.5248   -0.4396    1.7983 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  2  0
  3  4  1  0
  4  5  2  0
  5  6  1  0
  6  7  1  0
  6  8  2  0
  8  9  1  0
  9 10  2  0
 10 11  1  0
 11 12  1  0
 11 13  2  0
 13 14  1  0
 14 15  2  0
  3 16  1  0
 16 17  1  0
 16 18  1  0
 16 19  1  0
 19 20  1  0
 20 21  1  0
 21  2  1  0
  1 22  1  0
  1 23  1  0
  1 24  1  0
  4 25  1  0
  5 26  1  0
  7 27  1  0
  7 28  1  0
  7 29  1  0
  8 30  1  0
  9 31  1  0
 10 32  1  0
 12 33  1  0
 12 34  1  0
 12 35  1  0
 13 36  1  0
 14 37  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
 19 44  1  0
 19 45  1  0
 20 46  1  0
 20 47  1  0
 21 48  1  0
 21 49  1  0
M  END

View in JSmol View Stereo Labels

Synonyms

Value	Source
(2E,4Z,6E,8E)-3,7-Dimethyl-9-(2,6,6-trimethylcyclohex-1-en-1-yl)nona-2,4,6,8-tetraenal	ChEBI
11-cis-Retinene	ChEBI
11-cis-Vitamin a aldehyde	ChEBI
11-cis-Retinal	HMDB
cis-11-Retinal	HMDB
11 cis Retinal	MeSH, HMDB
Retinaldehyde	MeSH, HMDB
Retinene	MeSH, HMDB
Retinal	MeSH, HMDB
Aldehyde, vitamin a	MeSH, HMDB
Vitamin a aldehyde	MeSH, HMDB
Axerophthal	MeSH, HMDB

Chemical Formula

C₂₀H₂₈O

Average Molecular Weight

284.4357

Monoisotopic Molecular Weight

284.214015518

IUPAC Name

(2E,4Z,6E,8E)-3,7-dimethyl-9-(2,6,6-trimethylcyclohex-1-en-1-yl)nona-2,4,6,8-tetraenal

Traditional Name

11-cis-retinal

CAS Registry Number

564-87-4

SMILES

C/C(/C=C\C=C(/C)\C=C\C1=C(C)CCCC1(C)C)=C\C=O

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/h6,8-9,11-13,15H,7,10,14H2,1-5H3/b9-6-,12-11+,16-8+,17-13+

InChI Key

NCYCYZXNIZJOKI-IOUUIBBYSA-N

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

retinal (CHEBI:16066 )
Retinoids (C02110 )
Retinoids (LMPR01090003 )

Ontology

Not Available

Testicle (HMDB: HMDB0002152)

Cellular substructure

Source

Exogenous

Exogenous (HMDB: HMDB0002152)

Food

Animal origin

Poultry

Pheasant (FooDB: FOOD00430)
Squab (FooDB: FOOD00481)
Turkey (FooDB: FOOD00494)
Quail (FooDB: FOOD00541)
Anatidae (FooDB: FOOD00576)
Rock ptarmigan (FooDB: FOOD00597)
Columbidae (Dove, Pigeon) (FooDB: FOOD00610)
Chicken (FooDB: FOOD00329)
Mallard duck (FooDB: FOOD00353)
Emu (FooDB: FOOD00360)
Greylag goose (FooDB: FOOD00368)
Guinea hen (FooDB: FOOD00373)
Ostrich (FooDB: FOOD00422)
Velvet duck (FooDB: FOOD00427)

Lagomorph

Ovis

Sheep (Mutton, Lamb) (FooDB: FOOD00473)

Bovine

Venison

Deer (FooDB: FOOD00524)
Mule deer (FooDB: FOOD00348)
Elk (FooDB: FOOD00359)

Caprae

Domestic goat (FooDB: FOOD00529)

Swine

Domestic pig (FooDB: FOOD00536)
Wild boar (FooDB: FOOD00307)

Equine

Horse (FooDB: FOOD00378)

Endogenous

Endogenous (HMDB: HMDB0002152)

Process

Naturally occurring process

Biological process

Biochemical pathway

Metabolic pathway

Retinol Metabolism (PathBank: SMP0087353)

Disease pathway

Vitamin A Deficiency (PathBank: SMP0120500)

Role

Not Available

Physical Properties

State

Solid

Experimental Molecular Properties

Property	Value	Reference
Melting Point	63.5 - 64.4 °C	Not Available
Boiling Point	Not Available	Not Available
Water Solubility	Not Available	Not Available
LogP	Not Available	Not Available

Experimental Chromatographic Properties

Not Available

Predicted Molecular Properties

Property	Value	Source
Water Solubility	0.0042 g/L	ALOGPS
logP	6.62	ALOGPS
logP	4.86	ChemAxon
logS	-4.8	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	96.87 m³·mol⁻¹	ChemAxon
Polarizability	34.82 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

Predicted Chromatographic Properties

Predicted Collision Cross Sections

Predictor	Adduct Type	CCS Value (Å²)	Reference
DarkChem	[M+H]+	173.524	31661259
DarkChem	[M-H]-	173.48	31661259
DeepCCS	[M+H]+	180.133	30932474
DeepCCS	[M-H]-	177.775	30932474
DeepCCS	[M-2H]-	211.437	30932474
DeepCCS	[M+Na]+	186.663	30932474
AllCCS	[M+H]+	174.0	32859911
AllCCS	[M+H-H2O]+	170.7	32859911
AllCCS	[M+NH4]+	177.1	32859911
AllCCS	[M+Na]+	177.9	32859911
AllCCS	[M-H]-	178.3	32859911
AllCCS	[M+Na-2H]-	178.9	32859911
AllCCS	[M+HCOO]-	179.7	32859911

Predicted Retention Times

Underivatized

Chromatographic Method	Retention Time	Reference
Measured using a Waters Acquity ultraperformance liquid chromatography (UPLC) ethylene-bridged hybrid (BEH) C18 column (100 mm × 2.1 mm; 1.7 μmparticle diameter). Predicted by Afia on May 17, 2022. Predicted by Afia on May 17, 2022.	8.21 minutes	32390414
Predicted by Siyang on May 30, 2022	27.1501 minutes	33406817
Predicted by Siyang using ReTip algorithm on June 8, 2022	1.5 minutes	32390414
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid	3428.0 seconds	40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid	881.0 seconds	40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid	341.3 seconds	40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid	576.7 seconds	40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	337.9 seconds	40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid	1067.2 seconds	40023050
BfG_NTS_RP1 =Agilent Zorbax Eclipse Plus C18 (2.1 mm x 150 mm, 3.5 um) with Water:ACN and 0.1% Formic Acid	1039.8 seconds	40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)	101.8 seconds	40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid	2311.8 seconds	40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid	761.2 seconds	40023050
UFZ_Phenomenex = Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex with Water:MeOH and 0.1% Formic Acid	1747.1 seconds	40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	924.4 seconds	40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	605.9 seconds	40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate	594.5 seconds	40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA	867.4 seconds	40023050
Meister zic-pHILIC pH9.3 = Merck SeQuant ZIC-pHILIC column with ACN:Water 5mM NH4Ac pH9.3 and 5mM ammonium acetate in water	8.5 seconds	40023050

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
11-cis-Retinaldehyde	C/C(/C=C\C=C(/C)\C=C\C1=C(C)CCCC1(C)C)=C\C=O	3063.2	Standard polar	33892256
11-cis-Retinaldehyde	C/C(/C=C\C=C(/C)\C=C\C1=C(C)CCCC1(C)C)=C\C=O	2469.4	Standard non polar	33892256
11-cis-Retinaldehyde	C/C(/C=C\C=C(/C)\C=C\C1=C(C)CCCC1(C)C)=C\C=O	2398.5	Semi standard non polar	33892256

Spectra

Biological Properties

Cellular Locations

Cytoplasm
Extracellular
Membrane

Biospecimen Locations

Not Available

Tissue Locations

Testis

Pathways

Name	SMPDB/PathBank	KEGG
Retinol Metabolism
Vitamin A Deficiency		Not Available

Normal Concentrations

Not Available

Abnormal Concentrations

Not Available

Associated Disorders and Diseases

Disease References

None

Associated OMIM IDs

None

External Links

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

FDB022871

KNApSAcK ID

Not Available

Chemspider ID

KEGG Compound ID

BioCyc ID

BiGG ID

Wikipedia Link

Not Available

METLIN ID

6513

PubChem Compound

5280490

PDB ID

Not Available

ChEBI ID

16066

Food Biomarker Ontology

Not Available

VMH ID

RETINAL_11_CIS

MarkerDB ID

Not Available

Good Scents ID

Not Available

References

Synthesis Reference

Ito, Masayoshi; Wada, Akimori. Preparation of 11-cis-Retinal and their intermediates. Jpn. Kokai Tokkyo Koho (1998), 12 pp.

Material Safety Data Sheet (MSDS)

Download (PDF)

General References

Bankson DD, Russell RM, Sadowski JA: Determination of retinyl esters and retinol in serum or plasma by normal-phase liquid chromatography: method and applications. Clin Chem. 1986 Jan;32(1 Pt 1):35-40. [PubMed:3940733 ]
Futterman S, Saari JC: Occurrence of 11-cis-retinal-binding protein restricted to the retina. Invest Ophthalmol Vis Sci. 1977 Aug;16(8):768-71. [PubMed:560359 ]
Brunk E, Sahoo S, Zielinski DC, Altunkaya A, Drager A, Mih N, Gatto F, Nilsson A, Preciat Gonzalez GA, Aurich MK, Prlic A, Sastry A, Danielsdottir AD, Heinken A, Noronha A, Rose PW, Burley SK, Fleming RMT, Nielsen J, Thiele I, Palsson BO: Recon3D enables a three-dimensional view of gene variation in human metabolism. Nat Biotechnol. 2018 Mar;36(3):272-281. doi: 10.1038/nbt.4072. Epub 2018 Feb 19. [PubMed:29457794 ]

Enzymes

Enzyme Details

1. 11-cis retinol dehydrogenase

General function:: Involved in oxidoreductase activity
Specific function:: Stereospecific 11-cis retinol dehydrogenase, which catalyzes the final step in the biosynthesis of 11-cis retinaldehyde, the universal chromophore of visual pigments. Also able to oxidize 9-cis-retinol and 13-cis-retinol, but not all-trans-retinol. Active in the presence of NAD as cofactor but not in the presence of NADP.
Gene Name:: RDH5
Uniprot ID:: Q92781
Molecular weight:: 34978.425

Showing metabocard for 11-cis-Retinaldehyde (HMDB0002152)

MOL for HMDB0002152 (11-cis-Retinaldehyde)

3D MOL for HMDB0002152 (11-cis-Retinaldehyde)

3D SDF for HMDB0002152 (11-cis-Retinaldehyde)

3D-SDF for HMDB0002152 (11-cis-Retinaldehyde)

PDB for HMDB0002152 (11-cis-Retinaldehyde)

3D PDB for HMDB0002152 (11-cis-Retinaldehyde)

SMILES for HMDB0002152 (11-cis-Retinaldehyde)

INCHI for HMDB0002152 (11-cis-Retinaldehyde)

Structure for HMDB0002152 (11-cis-Retinaldehyde)

3D Structure for HMDB0002152 (11-cis-Retinaldehyde)

Predicted Collision Cross Sections

Predicted Retention Times

Underivatized

Predicted Kovats Retention Indices

Underivatized

Enzymes