NP-MRD: Showing NP-Card for Retinal (NP0001019)

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Record Information

Version

1.0

Created at

2005-11-16 15:48:42 UTC

Updated at

2024-04-19 10:04:05 UTC

NP-MRD ID

NP0001019

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Retinal

Description

Retinal is a carotenoid constituent of visual pigments. It is the oxidized form of retinol which functions as the active component of the visual cycle. It is bound to the protein opsin forming the complex rhodopsin. When stimulated by visible light, the retinal component of the rhodopsin complex undergoes isomerization at the 11-position of the double bond to the cis-form; this is reversed in "dark" reactions to return to the native trans-configuration.

Structure

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

HMDB0001358
     RDKit          3D
Retinal
 49 49  0  0  0  0  0  0  0  0999 V2000
   -3.2811    0.9418    1.9748 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3824    1.5605    0.6611 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3738    1.3741   -0.2312 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2561    0.5703    0.2218 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3767   -0.0616    0.5771 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6904   -0.8292    1.0102 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8677   -1.4556    2.3283 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7157   -1.0675    0.1431 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8341   -1.8707    0.6070 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.8588   -2.1432   -0.1827 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.9938   -2.9292    0.2413 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.1667   -3.5394    1.5954 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.0105   -3.1728   -0.5914 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.1495   -3.9702   -0.1442 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.0784   -4.1604   -0.9537 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5840    2.0468   -1.5020 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6808    1.3161   -2.2656 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3543    2.1264   -2.3871 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9767    3.5008   -1.2601 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1973    3.6614   -0.4149 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5595    2.4024    0.3307 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2207    1.1771    2.5783 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4138    1.3807    2.5095 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1810   -0.1540    1.9177 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6749    0.5907   -1.0956 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0120   -0.2014    1.8420 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8023   -1.1405    2.8231 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0587   -1.1943    3.0426 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7808   -2.5679    2.2045 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6398   -0.6525   -0.8370 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8403   -2.2648    1.6015 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.7981   -1.7494   -1.1798 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.2564   -4.6654    1.5371 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.0446   -3.1012    2.1159 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.2834   -3.3704    2.2453 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.9245   -2.7592   -1.5732 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.2209   -4.3929    0.8370 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8459    0.3557   -1.7717 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2687    1.0858   -3.2893 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5914    1.9385   -2.3808 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1960    1.1755   -2.9264 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5000    2.9165   -3.1775 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4466    2.3921   -1.8189 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0743    3.9701   -0.7754 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1393    3.9657   -2.2361 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0956    3.9757   -1.0176 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0075    4.4913    0.2991 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.3154    1.7771   -0.1680 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0095    2.7204    1.2927 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
 9999.479210002.2128    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10000.193910001.8005    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10000.908410002.2128    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10001.622910001.8005    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10002.337210002.2128    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10003.052710001.8005    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10003.765910002.2128    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10004.481310001.8005    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10005.198710002.2128    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10005.912010001.8005    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
10003.765910003.0375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10000.908410003.0375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9999.047310000.2001    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9999.577510001.1195    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9998.052110003.0375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9998.050710002.2132    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9997.336110001.8007    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9997.336110000.9754    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9998.050710000.5630    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9998.765410000.9754    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9998.765410001.8007    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0  0  0  0
  2  3  1  0  0  0  0
  3  4  2  0  0  0  0
  3 12  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  2  0  0  0  0
  6  7  1  0  0  0  0
  7  8  2  0  0  0  0
  7 11  1  0  0  0  0
  8  9  1  0  0  0  0
  9 10  2  0  0  0  0
 16 17  1  0  0  0  0
 16 21  2  0  0  0  0
 17 18  1  0  0  0  0
 18 19  1  0  0  0  0
 19 20  1  0  0  0  0
 20 21  1  0  0  0  0
  1 21  1  0  0  0  0
 20 13  1  0  0  0  0
 20 14  1  0  0  0  0
 16 15  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0001019

> <DATABASE_NAME>
NP-MRD

> <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-OVSJKPMPSA-N

> <FORMULA>
C20H28O

> <MOLECULAR_WEIGHT>
284.4357

> <EXACT_MASS>
284.214015518

> <JCHEM_ACCEPTOR_COUNT>
1

> <JCHEM_ATOM_COUNT>
49

> <JCHEM_AVERAGE_POLARIZABILITY>
35.69258909408052

> <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-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>
96.8654

> <JCHEM_ROTATABLE_BOND_COUNT>
5

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
4.20e-03 g/l

> <JCHEM_TRADITIONAL_IUPAC>
retinaldehyde

> <JCHEM_VEBER_RULE>
1

$$$$

HMDB0001358
     RDKit          3D
Retinal
 49 49  0  0  0  0  0  0  0  0999 V2000
   -3.2811    0.9418    1.9748 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3824    1.5605    0.6611 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3738    1.3741   -0.2312 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2561    0.5703    0.2218 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3767   -0.0616    0.5771 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6904   -0.8292    1.0102 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8677   -1.4556    2.3283 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7157   -1.0675    0.1431 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8341   -1.8707    0.6070 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.8588   -2.1432   -0.1827 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.9938   -2.9292    0.2413 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.1667   -3.5394    1.5954 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.0105   -3.1728   -0.5914 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.1495   -3.9702   -0.1442 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.0784   -4.1604   -0.9537 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5840    2.0468   -1.5020 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6808    1.3161   -2.2656 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3543    2.1264   -2.3871 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9767    3.5008   -1.2601 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1973    3.6614   -0.4149 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5595    2.4024    0.3307 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2207    1.1771    2.5783 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4138    1.3807    2.5095 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1810   -0.1540    1.9177 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6749    0.5907   -1.0956 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0120   -0.2014    1.8420 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8023   -1.1405    2.8231 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0587   -1.1943    3.0426 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7808   -2.5679    2.2045 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6398   -0.6525   -0.8370 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8403   -2.2648    1.6015 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.7981   -1.7494   -1.1798 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.2564   -4.6654    1.5371 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.0446   -3.1012    2.1159 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.2834   -3.3704    2.2453 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.9245   -2.7592   -1.5732 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.2209   -4.3929    0.8370 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8459    0.3557   -1.7717 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2687    1.0858   -3.2893 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5914    1.9385   -2.3808 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1960    1.1755   -2.9264 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5000    2.9165   -3.1775 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4466    2.3921   -1.8189 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0743    3.9701   -0.7754 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1393    3.9657   -2.2361 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0956    3.9757   -1.0176 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0075    4.4913    0.2991 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.3154    1.7771   -0.1680 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0095    2.7204    1.2927 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    8665.6958670.797   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0    8667.0298670.028   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0    8668.3628670.797   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0    8669.6968670.028   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0    8671.0298670.797   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0    8672.3658670.028   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0    8673.6968670.797   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0    8675.0328670.028   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0    8676.3718670.797   0.000  0.00  0.00           C+0
HETATM   10  O   UNK     0    8677.7028670.028   0.000  0.00  0.00           O+0
HETATM   11  C   UNK     0    8673.6968672.337   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0    8668.3628672.337   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0    8664.8888667.040   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0    8665.8788668.756   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0    8663.0318672.337   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0    8663.0288670.798   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0    8661.6948670.028   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0    8661.6948668.487   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0    8663.0288667.718   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0    8664.3628668.487   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0    8664.3628670.028   0.000  0.00  0.00           C+0
CONECT    1    2   21                                                       
CONECT    2    1    3                                                       
CONECT    3    2    4   12                                                  
CONECT    4    3    5                                                       
CONECT    5    4    6                                                       
CONECT    6    5    7                                                       
CONECT    7    6    8   11                                                  
CONECT    8    7    9                                                       
CONECT    9    8   10                                                       
CONECT   10    9                                                            
CONECT   11    7                                                            
CONECT   12    3                                                            
CONECT   13   20                                                            
CONECT   14   20                                                            
CONECT   15   16                                                            
CONECT   16   17   21   15                                                  
CONECT   17   16   18                                                       
CONECT   18   17   19                                                       
CONECT   19   18   20                                                       
CONECT   20   19   21   13   14                                             
CONECT   21   16   20    1                                                  
MASTER        0    0    0    0    0    0    0    0   21    0   42    0
END

COMPND    HMDB0001358
HETATM    1  C1  UNL     1      -3.281   0.942   1.975  1.00  0.00           C  
HETATM    2  C2  UNL     1      -3.382   1.561   0.661  1.00  0.00           C  
HETATM    3  C3  UNL     1      -2.374   1.374  -0.231  1.00  0.00           C  
HETATM    4  C4  UNL     1      -1.256   0.570   0.222  1.00  0.00           C  
HETATM    5  C5  UNL     1      -0.377  -0.062   0.577  1.00  0.00           C  
HETATM    6  C6  UNL     1       0.690  -0.829   1.010  1.00  0.00           C  
HETATM    7  C7  UNL     1       0.868  -1.456   2.328  1.00  0.00           C  
HETATM    8  C8  UNL     1       1.716  -1.068   0.143  1.00  0.00           C  
HETATM    9  C9  UNL     1       2.834  -1.871   0.607  1.00  0.00           C  
HETATM   10  C10 UNL     1       3.859  -2.143  -0.183  1.00  0.00           C  
HETATM   11  C11 UNL     1       4.994  -2.929   0.241  1.00  0.00           C  
HETATM   12  C12 UNL     1       5.167  -3.539   1.595  1.00  0.00           C  
HETATM   13  C13 UNL     1       6.010  -3.173  -0.591  1.00  0.00           C  
HETATM   14  C14 UNL     1       7.149  -3.970  -0.144  1.00  0.00           C  
HETATM   15  O1  UNL     1       8.078  -4.160  -0.954  1.00  0.00           O  
HETATM   16  C15 UNL     1      -2.584   2.047  -1.502  1.00  0.00           C  
HETATM   17  C16 UNL     1      -3.681   1.316  -2.266  1.00  0.00           C  
HETATM   18  C17 UNL     1      -1.354   2.126  -2.387  1.00  0.00           C  
HETATM   19  C18 UNL     1      -2.977   3.501  -1.260  1.00  0.00           C  
HETATM   20  C19 UNL     1      -4.197   3.661  -0.415  1.00  0.00           C  
HETATM   21  C20 UNL     1      -4.559   2.402   0.331  1.00  0.00           C  
HETATM   22  H1  UNL     1      -4.221   1.177   2.578  1.00  0.00           H  
HETATM   23  H2  UNL     1      -2.414   1.381   2.509  1.00  0.00           H  
HETATM   24  H3  UNL     1      -3.181  -0.154   1.918  1.00  0.00           H  
HETATM   25  H4  UNL     1      -0.675   0.591  -1.096  1.00  0.00           H  
HETATM   26  H5  UNL     1      -1.012  -0.201   1.842  1.00  0.00           H  
HETATM   27  H6  UNL     1       1.802  -1.140   2.823  1.00  0.00           H  
HETATM   28  H7  UNL     1       0.059  -1.194   3.043  1.00  0.00           H  
HETATM   29  H8  UNL     1       0.781  -2.568   2.205  1.00  0.00           H  
HETATM   30  H9  UNL     1       1.640  -0.653  -0.837  1.00  0.00           H  
HETATM   31  H10 UNL     1       2.840  -2.265   1.601  1.00  0.00           H  
HETATM   32  H11 UNL     1       3.798  -1.749  -1.180  1.00  0.00           H  
HETATM   33  H12 UNL     1       5.256  -4.665   1.537  1.00  0.00           H  
HETATM   34  H13 UNL     1       6.045  -3.101   2.116  1.00  0.00           H  
HETATM   35  H14 UNL     1       4.283  -3.370   2.245  1.00  0.00           H  
HETATM   36  H15 UNL     1       5.924  -2.759  -1.573  1.00  0.00           H  
HETATM   37  H16 UNL     1       7.221  -4.393   0.837  1.00  0.00           H  
HETATM   38  H17 UNL     1      -3.846   0.356  -1.772  1.00  0.00           H  
HETATM   39  H18 UNL     1      -3.269   1.086  -3.289  1.00  0.00           H  
HETATM   40  H19 UNL     1      -4.591   1.939  -2.381  1.00  0.00           H  
HETATM   41  H20 UNL     1      -1.196   1.176  -2.926  1.00  0.00           H  
HETATM   42  H21 UNL     1      -1.500   2.916  -3.178  1.00  0.00           H  
HETATM   43  H22 UNL     1      -0.447   2.392  -1.819  1.00  0.00           H  
HETATM   44  H23 UNL     1      -2.074   3.970  -0.775  1.00  0.00           H  
HETATM   45  H24 UNL     1      -3.139   3.966  -2.236  1.00  0.00           H  
HETATM   46  H25 UNL     1      -5.096   3.976  -1.018  1.00  0.00           H  
HETATM   47  H26 UNL     1      -4.007   4.491   0.299  1.00  0.00           H  
HETATM   48  H27 UNL     1      -5.315   1.777  -0.168  1.00  0.00           H  
HETATM   49  H28 UNL     1      -5.009   2.720   1.293  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

HMDB0001358
     RDKit          3D
Retinal
 49 49  0  0  0  0  0  0  0  0999 V2000
   -3.2811    0.9418    1.9748 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3824    1.5605    0.6611 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3738    1.3741   -0.2312 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2561    0.5703    0.2218 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3767   -0.0616    0.5771 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6904   -0.8292    1.0102 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8677   -1.4556    2.3283 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7157   -1.0675    0.1431 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8341   -1.8707    0.6070 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.8588   -2.1432   -0.1827 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.9938   -2.9292    0.2413 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.1667   -3.5394    1.5954 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.0105   -3.1728   -0.5914 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.1495   -3.9702   -0.1442 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.0784   -4.1604   -0.9537 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5840    2.0468   -1.5020 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6808    1.3161   -2.2656 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3543    2.1264   -2.3871 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9767    3.5008   -1.2601 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1973    3.6614   -0.4149 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5595    2.4024    0.3307 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2207    1.1771    2.5783 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4138    1.3807    2.5095 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1810   -0.1540    1.9177 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6749    0.5907   -1.0956 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0120   -0.2014    1.8420 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8023   -1.1405    2.8231 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0587   -1.1943    3.0426 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7808   -2.5679    2.2045 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6398   -0.6525   -0.8370 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8403   -2.2648    1.6015 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.7981   -1.7494   -1.1798 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.2564   -4.6654    1.5371 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.0446   -3.1012    2.1159 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.2834   -3.3704    2.2453 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.9245   -2.7592   -1.5732 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.2209   -4.3929    0.8370 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8459    0.3557   -1.7717 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2687    1.0858   -3.2893 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5914    1.9385   -2.3808 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1960    1.1755   -2.9264 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5000    2.9165   -3.1775 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4466    2.3921   -1.8189 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0743    3.9701   -0.7754 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1393    3.9657   -2.2361 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0956    3.9757   -1.0176 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0075    4.4913    0.2991 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.3154    1.7771   -0.1680 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0095    2.7204    1.2927 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

Synonyms

Value	Source
all-e-Retinal	ChEBI
all-trans-Retinaldehyde	ChEBI
all-trans-Retinene	ChEBI
all-trans-Vitamin a aldehyde	ChEBI
Axerophthal	ChEBI
e-Retinal	ChEBI
Retinaldehyde	ChEBI
Retinene	ChEBI
Retinene 1	ChEBI
Retinyl aldehyde	ChEBI
trans-Retinal	ChEBI
trans-Vitamin a aldehyde	ChEBI
Vitamin a aldehyde	ChEBI
Vitamin a1 aldehyde	ChEBI
all-trans-Retinal	Kegg
Aldehyde, vitamin a	HMDB
11 cis Retinal	HMDB
11-cis-Retinal	HMDB
3,7-Dimethyl-9-(2,6,6-trimethyl-1-cyclohexen-1-yl)-2,4,6,8-nonatetraenal	HMDB
all-epsilon-Retinal	HMDB
alpha-Retinene	HMDB
epsilon-Retinal	HMDB

Chemical Formula

C₂₀H₂₈O

Average Mass

284.4357 Da

Monoisotopic Mass

284.21402 Da

IUPAC Name

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

Traditional Name

retinaldehyde

CAS Registry Number

116-31-4

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-OVSJKPMPSA-N

Experimental Spectra

Spectrum Type	Description	Depositor Email	Depositor Organization	Depositor	Deposition Date	View
HSQC NMR	[¹H, ¹³C] NMR Spectrum (2D, 600 MHz, CD3OD, experimental)	bgnzk@missouri.edu	MU Metabolomics Center, University of Missouri, Columbia. MO, USA	Dr. Bharat Goel	2024-01-10	View Spectrum
HMBC NMR	[¹H, ¹³C] NMR Spectrum (2D, 600 MHz, CD3OD, experimental)	bgnzk@missouri.edu	MU Metabolomics Center, University of Missouri, Columbia. MO, USA	Dr. Bharat Goel	2024-01-10	View Spectrum
COSY NMR	[¹H, ¹H] NMR Spectrum (2D, 600 MHz, CD3OD, experimental)	bgnzk@missouri.edu	MU Metabolomics Center, University of Missouri, Columbia. MO, USA	Dr. Bharat Goel	2024-01-10	View Spectrum
1D NMR	[¹H, ] NMR Spectrum (2D, 600 MHz, CD3OD, experimental)	bgnzk@missouri.edu	MU Metabolomics Center, University of Missouri, Columbia. MO, USA	Dr. Bharat Goel	2024-01-10	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, CDCl₃, experimental)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600.133705802 MHz, CD₃OD, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
2D NMR	[¹H, ¹³C]-HSQC NMR Spectrum (2D, 600 MHz, CDCl₃, experimental)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum

Predicted Spectra

Not Available

Chemical Shift Submissions

Not Available

Species

Species of Origin

Species Name	Source	Reference
Anas platyrhynchos	FooDB	FooDB
Anatidae	FooDB	FooDB
Anser anser	FooDB	FooDB
Bison bison	FooDB	FooDB
Bos taurus	FooDB	FooDB
Bos taurus X Bison bison	FooDB	FooDB
Bubalus bubalis	FooDB	FooDB
Capra aegagrus hircus	FooDB	FooDB
Capsicum annuum	KNApSAcK Database	22123792
Cervidae	FooDB	FooDB
Cervus canadensis	FooDB	FooDB
Columba	FooDB	FooDB
Columbidae	FooDB	FooDB
Dromaius novaehollandiae	FooDB	FooDB
Equus caballus	FooDB	FooDB
Galleria mellonella	LOTUS Database	35616633
Gallus gallus	FooDB	FooDB
Homo sapiens	LOTUS Database	35616633
Lagopus muta	FooDB	FooDB
Leporidae	FooDB	FooDB
Lepus timidus	FooDB	FooDB
Melanitta fusca	FooDB	FooDB
Meleagris gallopavo	FooDB	FooDB
Mus musculus	LOTUS Database	35616633
Numida meleagris	FooDB	FooDB
Odocoileus	FooDB	FooDB
Oryctolagus	FooDB	FooDB
Ovis aries	FooDB	FooDB
Panax ginseng	LOTUS Database	35616633
Phasianidae	FooDB	FooDB
Phasianus colchicus	FooDB	FooDB
Rana temporaria	LOTUS Database	35616633
Struthio camelus	FooDB	FooDB
Suberites domuncula	LOTUS Database	35616633
Sus scrofa	FooDB	FooDB
Sus scrofa domestica	FooDB	FooDB

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:17898 )
Retinoids (C00376 )
Retinoids (LMPR01090002 )

Physical Properties

State

Solid

Experimental Properties

Property	Value	Reference
Melting Point	63 °C	Not Available
Boiling Point	Not Available	Not Available
Water Solubility	0.0049 mg/L @ 25 °C (est)	The Good Scents Company Information System
LogP	Not Available	Not Available

Predicted 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	35.69 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

HMDB0001358

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

KNApSAcK ID

Chemspider ID

KEGG Compound ID

BioCyc ID

BiGG ID

Not Available

Wikipedia Link

Retinal

METLIN ID

Not Available

PubChem Compound

638015

PDB ID

Not Available

ChEBI ID

17898

Good Scents ID

rw1784341

References

General References

Chang M, Herbert WN: Retinal arteriolar occlusions following amniotic fluid embolism. Ophthalmology. 1984 Dec;91(12):1634-7. [PubMed:6521996 ]
Nguyen QD, Van Do D, Feke GT, Demirjian ZN, Lashkari K: Heparin-induced antiheparin-platelet antibody associated with retinal venous thrombosis. Ophthalmology. 2003 Mar;110(3):600-3. [PubMed:12623829 ]
Aarli JA, Mork SJ, Myrseth E, Larsen JL: Glioblastoma associated with multiple sclerosis: coincidence or induction? Eur Neurol. 1989;29(6):312-6. [PubMed:2691257 ]
Wu WC, Lai CC, Liu JH, Singh T, Li LM, Peumans WJ, Van Damme EJ, Wu AM: Differential Binding to Glycotopes Among the Layers of Three Mammalian Retinal Neurons by Man-Containing N-linked Glycan, T(alpha) (Galbeta1-3GalNAcalpha1-), Tn (GalNAcalpha1-Ser/Thr) and I (beta)/II (beta) (Galbeta1-3/4GlcNAcbeta-) Reactive Lectins. Neurochem Res. 2006 May 23;. [PubMed:16718528 ]
Jankowska R, Witkowska D, Porebska I, Kuropatwa M, Kurowska E, Gorczyca WA: Serum antibodies to retinal antigens in lung cancer and sarcoidosis. Pathobiology. 2004;71(6):323-8. [PubMed:15627843 ]
Weiland JD, Liu W, Humayun MS: Retinal prosthesis. Annu Rev Biomed Eng. 2005;7:361-401. [PubMed:16004575 ]
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Showing NP-Card for Retinal (NP0001019)

MOL for NP0001019 (Retinal)

3D MOL for NP0001019 (Retinal)

3D SDF for NP0001019 (Retinal)

3D-SDF for NP0001019 (Retinal)

PDB for NP0001019 (Retinal)

3D PDB for NP0001019 (Retinal)

SMILES for NP0001019 (Retinal)

INCHI for NP0001019 (Retinal)

Structure for NP0001019 (Retinal)

3D Structure for NP0001019 (Retinal)