NP-MRD: Showing NP-Card for 13-cis-Retinal (NP0001435)

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Record Information

Version

1.0

Created at

2007-05-22 17:57:51 UTC

Updated at

2021-06-30 02:06:15 UTC

NP-MRD ID

NP0001435

Secondary Accession Numbers

None

Natural Product Identification

Common Name

13-cis-Retinal

Description

13-Cis-Retinal is a naturally occurring retinoid. Retinoids are vitamin A analogs that have profound biological activities. Several retinoids have been reported to have antiinflammatory activity in certain animal models of arthritis, such as adjuvant-induced and streptococcal cell wall-induced arthritis in rats. Some retinoids also have been shown to possess antiinftammatory activity in man by their ability to modulate inflammatory diseases of the skin. It has been reported, for example, that retinoid treatment can inhibit neutrophil accumulation in cutaneous disorders such as psoriasis. (PMID:2123476 ).

Structure

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

HMDB0006220
     RDKit          3D
13-cis-Retinal
 49 49  0  0  0  0  0  0  0  0999 V2000
   -3.2054    1.7080   -1.6548 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5958    0.5315   -0.8302 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6014   -0.1460   -0.2110 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2719    0.3430   -0.4124 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1346   -0.0945    0.0672 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1705    0.5339   -0.2466 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1531    1.6922   -1.1346 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2609    0.0499    0.2622 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5660    0.6177   -0.0054 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.6746    0.0995    0.5316 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.9641    0.6980    0.2387 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.0094    1.8975   -0.6711 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.0918    0.2193    0.7478 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.1018   -0.9238    1.6221 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.2345   -1.3069    2.0591 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0556   -1.3002    0.5738 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7776   -0.8245    1.8219 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0556   -2.3274    0.9787 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1121   -2.0302   -0.2910 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.3516   -1.1460   -0.2413 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0212    0.2261   -0.7444 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1110    2.1668   -2.0793 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7284    2.5020   -1.0206 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5566    1.4378   -2.5159 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1334    1.2278   -1.0693 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1274   -0.9291    0.7260 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.1061    2.1514   -1.3888 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6322    1.3808   -2.0772 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5512    2.4835   -0.6213 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2241   -0.8164    0.9195 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.7171    1.4729   -0.6392 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.5312   -0.7547    1.1656 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.4681    2.7515   -0.2240 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.5057    1.5736   -1.6131 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.0580    2.1539   -0.8530 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.0064    0.7537    0.4559 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.2150   -1.4368    1.9006 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4158   -1.6282    2.2062 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9983   -0.5734    2.5914 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3354    0.1034    1.6357 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7009   -3.2592    1.2211 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4044   -2.7096    0.1913 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5965   -2.1196    1.9562 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7473   -2.0432   -1.3189 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3463   -3.0138    0.1024 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.7881   -1.1457    0.7786 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.0983   -1.6194   -0.9096 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.4420    0.3303   -1.7935 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.5293    1.0426   -0.1870 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


  Mrv1652307301919572D          

 21 21  0  0  0  0            999 V2000
    2.8579    3.3000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.7158    3.3000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1842    1.8695    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2448    1.8695    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2868    2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724    2.0625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0013    2.0625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434    2.0625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.4302    2.0625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.3532    1.2202    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579    2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.7158    2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.0868    0.7324    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  8  6  1  0  0  0  0
  9  6  2  0  0  0  0
 10  7  1  0  0  0  0
 12 11  2  0  0  0  0
 14  7  1  0  0  0  0
 15 13  1  0  0  0  0
 16  1  1  0  0  0  0
 16  8  2  0  0  0  0
 16 11  1  0  0  0  0
 17  2  1  0  0  0  0
 17  9  1  0  0  0  0
 17 13  2  0  0  0  0
 18  3  1  0  0  0  0
 18 10  1  0  0  0  0
 19 12  1  0  0  0  0
 19 18  2  0  0  0  0
 20  4  1  0  0  0  0
 20  5  1  0  0  0  0
 20 14  1  0  0  0  0
 20 19  1  0  0  0  0
 21 15  2  0  0  0  0
M  END
> <DATABASE_ID>
NP0001435

> <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-HWCYFHEPSA-N

> <FORMULA>
C20H28O

> <MOLECULAR_WEIGHT>
284.4357

> <EXACT_MASS>
284.214015518

> <JCHEM_ACCEPTOR_COUNT>
1

> <JCHEM_ATOM_COUNT>
49

> <JCHEM_AVERAGE_POLARIZABILITY>
35.469533558432445

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

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

> <JCHEM_LOGP>
4.855751458666667

> <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

> <JCHEM_TRADITIONAL_IUPAC>
13-cis retinal

> <JCHEM_VEBER_RULE>
1

$$$$

HMDB0006220
     RDKit          3D
13-cis-Retinal
 49 49  0  0  0  0  0  0  0  0999 V2000
   -3.2054    1.7080   -1.6548 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5958    0.5315   -0.8302 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6014   -0.1460   -0.2110 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2719    0.3430   -0.4124 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1346   -0.0945    0.0672 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1705    0.5339   -0.2466 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1531    1.6922   -1.1346 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2609    0.0499    0.2622 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5660    0.6177   -0.0054 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.6746    0.0995    0.5316 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.9641    0.6980    0.2387 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.0094    1.8975   -0.6711 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.0918    0.2193    0.7478 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.1018   -0.9238    1.6221 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.2345   -1.3069    2.0591 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0556   -1.3002    0.5738 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7776   -0.8245    1.8219 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0556   -2.3274    0.9787 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1121   -2.0302   -0.2910 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.3516   -1.1460   -0.2413 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0212    0.2261   -0.7444 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1110    2.1668   -2.0793 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7284    2.5020   -1.0206 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5566    1.4378   -2.5159 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1334    1.2278   -1.0693 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1274   -0.9291    0.7260 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.1061    2.1514   -1.3888 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6322    1.3808   -2.0772 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5512    2.4835   -0.6213 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2241   -0.8164    0.9195 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.7171    1.4729   -0.6392 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.5312   -0.7547    1.1656 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.4681    2.7515   -0.2240 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.5057    1.5736   -1.6131 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.0580    2.1539   -0.8530 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.0064    0.7537    0.4559 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.2150   -1.4368    1.9006 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4158   -1.6282    2.2062 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9983   -0.5734    2.5914 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3354    0.1034    1.6357 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7009   -3.2592    1.2211 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4044   -2.7096    0.1913 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5965   -2.1196    1.9562 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7473   -2.0432   -1.3189 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3463   -3.0138    0.1024 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.7881   -1.1457    0.7786 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.0983   -1.6194   -0.9096 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.4420    0.3303   -1.7935 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.5293    1.0426   -0.1870 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                                 30-JUL-19   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   30-JUL-19         0                                  
HETATM    1  C   UNK     0       5.335   6.160   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      10.669   6.160   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       4.001  -0.770   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       0.344   3.490   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       2.324   3.490   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       8.002   4.620   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       6.668   3.850   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       9.336   3.850   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       4.001   3.850   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       4.001   2.310   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      12.003   3.850   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       0.000   1.540   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0      11.859   2.278   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       5.335   4.620   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0      10.669   4.620   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       2.667   0.000   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       2.667   1.540   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       1.334   2.310   0.000  0.00  0.00           C+0
HETATM   21  O   UNK     0      13.229   1.367   0.000  0.00  0.00           O+0
CONECT    1   16                                                            
CONECT    2   17                                                            
CONECT    3   18                                                            
CONECT    4   20                                                            
CONECT    5   20                                                            
CONECT    6    8    9                                                       
CONECT    7   10   14                                                       
CONECT    8    6   16                                                       
CONECT    9    6   17                                                       
CONECT   10    7   18                                                       
CONECT   11   12   16                                                       
CONECT   12   11   19                                                       
CONECT   13   15   17                                                       
CONECT   14    7   20                                                       
CONECT   15   13   21                                                       
CONECT   16    1    8   11                                                  
CONECT   17    2    9   13                                                  
CONECT   18    3   10   19                                                  
CONECT   19   12   18   20                                                  
CONECT   20    4    5   14   19                                             
CONECT   21   15                                                            
MASTER        0    0    0    0    0    0    0    0   21    0   42    0
END

COMPND    HMDB0006220
HETATM    1  C1  UNL     1      -3.205   1.708  -1.655  1.00  0.00           C  
HETATM    2  C2  UNL     1      -3.596   0.531  -0.830  1.00  0.00           C  
HETATM    3  C3  UNL     1      -2.601  -0.146  -0.211  1.00  0.00           C  
HETATM    4  C4  UNL     1      -1.272   0.343  -0.412  1.00  0.00           C  
HETATM    5  C5  UNL     1      -0.135  -0.095   0.067  1.00  0.00           C  
HETATM    6  C6  UNL     1       1.171   0.534  -0.247  1.00  0.00           C  
HETATM    7  C7  UNL     1       1.153   1.692  -1.135  1.00  0.00           C  
HETATM    8  C8  UNL     1       2.261   0.050   0.262  1.00  0.00           C  
HETATM    9  C9  UNL     1       3.566   0.618  -0.005  1.00  0.00           C  
HETATM   10  C10 UNL     1       4.675   0.100   0.532  1.00  0.00           C  
HETATM   11  C11 UNL     1       5.964   0.698   0.239  1.00  0.00           C  
HETATM   12  C12 UNL     1       6.009   1.898  -0.671  1.00  0.00           C  
HETATM   13  C13 UNL     1       7.092   0.219   0.748  1.00  0.00           C  
HETATM   14  C14 UNL     1       7.102  -0.924   1.622  1.00  0.00           C  
HETATM   15  O1  UNL     1       8.234  -1.307   2.059  1.00  0.00           O  
HETATM   16  C15 UNL     1      -3.056  -1.300   0.574  1.00  0.00           C  
HETATM   17  C16 UNL     1      -3.778  -0.825   1.822  1.00  0.00           C  
HETATM   18  C17 UNL     1      -2.056  -2.327   0.979  1.00  0.00           C  
HETATM   19  C18 UNL     1      -4.112  -2.030  -0.291  1.00  0.00           C  
HETATM   20  C19 UNL     1      -5.352  -1.146  -0.241  1.00  0.00           C  
HETATM   21  C20 UNL     1      -5.021   0.226  -0.744  1.00  0.00           C  
HETATM   22  H1  UNL     1      -4.111   2.167  -2.079  1.00  0.00           H  
HETATM   23  H2  UNL     1      -2.728   2.502  -1.021  1.00  0.00           H  
HETATM   24  H3  UNL     1      -2.557   1.438  -2.516  1.00  0.00           H  
HETATM   25  H4  UNL     1      -1.133   1.228  -1.069  1.00  0.00           H  
HETATM   26  H5  UNL     1      -0.127  -0.929   0.726  1.00  0.00           H  
HETATM   27  H6  UNL     1       2.106   2.151  -1.389  1.00  0.00           H  
HETATM   28  H7  UNL     1       0.632   1.381  -2.077  1.00  0.00           H  
HETATM   29  H8  UNL     1       0.551   2.483  -0.621  1.00  0.00           H  
HETATM   30  H9  UNL     1       2.224  -0.816   0.920  1.00  0.00           H  
HETATM   31  H10 UNL     1       3.717   1.473  -0.639  1.00  0.00           H  
HETATM   32  H11 UNL     1       4.531  -0.755   1.166  1.00  0.00           H  
HETATM   33  H12 UNL     1       5.468   2.751  -0.224  1.00  0.00           H  
HETATM   34  H13 UNL     1       5.506   1.574  -1.613  1.00  0.00           H  
HETATM   35  H14 UNL     1       7.058   2.154  -0.853  1.00  0.00           H  
HETATM   36  H15 UNL     1       8.006   0.754   0.456  1.00  0.00           H  
HETATM   37  H16 UNL     1       6.215  -1.437   1.901  1.00  0.00           H  
HETATM   38  H17 UNL     1      -4.416  -1.628   2.206  1.00  0.00           H  
HETATM   39  H18 UNL     1      -2.998  -0.573   2.591  1.00  0.00           H  
HETATM   40  H19 UNL     1      -4.335   0.103   1.636  1.00  0.00           H  
HETATM   41  H20 UNL     1      -2.701  -3.259   1.221  1.00  0.00           H  
HETATM   42  H21 UNL     1      -1.404  -2.710   0.191  1.00  0.00           H  
HETATM   43  H22 UNL     1      -1.596  -2.120   1.956  1.00  0.00           H  
HETATM   44  H23 UNL     1      -3.747  -2.043  -1.319  1.00  0.00           H  
HETATM   45  H24 UNL     1      -4.346  -3.014   0.102  1.00  0.00           H  
HETATM   46  H25 UNL     1      -5.788  -1.146   0.779  1.00  0.00           H  
HETATM   47  H26 UNL     1      -6.098  -1.619  -0.910  1.00  0.00           H  
HETATM   48  H27 UNL     1      -5.442   0.330  -1.793  1.00  0.00           H  
HETATM   49  H28 UNL     1      -5.529   1.043  -0.187  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

HMDB0006220
     RDKit          3D
13-cis-Retinal
 49 49  0  0  0  0  0  0  0  0999 V2000
   -3.2054    1.7080   -1.6548 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5958    0.5315   -0.8302 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6014   -0.1460   -0.2110 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2719    0.3430   -0.4124 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1346   -0.0945    0.0672 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1705    0.5339   -0.2466 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1531    1.6922   -1.1346 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2609    0.0499    0.2622 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5660    0.6177   -0.0054 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.6746    0.0995    0.5316 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.9641    0.6980    0.2387 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.0094    1.8975   -0.6711 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.0918    0.2193    0.7478 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.1018   -0.9238    1.6221 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.2345   -1.3069    2.0591 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0556   -1.3002    0.5738 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7776   -0.8245    1.8219 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0556   -2.3274    0.9787 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1121   -2.0302   -0.2910 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.3516   -1.1460   -0.2413 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0212    0.2261   -0.7444 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1110    2.1668   -2.0793 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7284    2.5020   -1.0206 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5566    1.4378   -2.5159 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1334    1.2278   -1.0693 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1274   -0.9291    0.7260 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.1061    2.1514   -1.3888 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6322    1.3808   -2.0772 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5512    2.4835   -0.6213 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2241   -0.8164    0.9195 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.7171    1.4729   -0.6392 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.5312   -0.7547    1.1656 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.4681    2.7515   -0.2240 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.5057    1.5736   -1.6131 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.0580    2.1539   -0.8530 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.0064    0.7537    0.4559 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.2150   -1.4368    1.9006 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4158   -1.6282    2.2062 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9983   -0.5734    2.5914 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3354    0.1034    1.6357 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7009   -3.2592    1.2211 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4044   -2.7096    0.1913 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5965   -2.1196    1.9562 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7473   -2.0432   -1.3189 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3463   -3.0138    0.1024 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.7881   -1.1457    0.7786 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.0983   -1.6194   -0.9096 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.4420    0.3303   -1.7935 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.5293    1.0426   -0.1870 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 NMR Assignments

Synonyms

Value	Source
(13cis)-Retinal	ChEBI
(2Z,4E,6E,8E)-3,7-Dimethyl-9-(2,6,6-trimethylcyclohex-1-en-1-yl)nona-2,4,6,8-tetraenal	ChEBI
13-cis-Retinaldehyde	ChEBI
RETINAL	ChEBI
13Z-Retinal	HMDB
cis-13-Retinal	HMDB
Neoretinene a	HMDB
Neovitamin a aldehyde	HMDB
13-cis-Retinal	MeSH, HMDB

Chemical Formula

C₂₀H₂₈O

Average Mass

284.4357 Da

Monoisotopic Mass

284.21402 Da

IUPAC Name

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

Traditional Name

13-cis retinal

CAS Registry Number

472-86-6

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-HWCYFHEPSA-N

Experimental Spectra

Spectrum Type	Description	Depositor Email	Depositor Organization	Depositor	Deposition Date	View
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

Spectrum Type	Description	Depositor ID	Depositor Organization	Depositor	Deposition Date	View
1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 25 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 252 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 50 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 75 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 101 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 126 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 151 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 176 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 201 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 226 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum

Chemical Shift Submissions

Not Available

Species

Species of Origin

Species Name	Source	Reference
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
Cervidae	FooDB	FooDB
Cervus canadensis	FooDB	FooDB
Columba	FooDB	FooDB
Columbidae	FooDB	FooDB
Dromaius novaehollandiae	FooDB	FooDB
Equus caballus	FooDB	FooDB
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
Numida meleagris	FooDB	FooDB
Odocoileus	FooDB	FooDB
Oryctolagus	FooDB	FooDB
Ovis aries	FooDB	FooDB
Phasianidae	FooDB	FooDB
Phasianus colchicus	FooDB	FooDB
Struthio camelus	FooDB	FooDB
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:45487 )
Retinoids (LMPR01090018 )

Physical Properties

State

Solid

Experimental Properties

Property	Value	Reference
Melting Point	Not Available	Not Available
Boiling Point	Not Available	Not Available
Water Solubility	Not Available	Not Available
LogP	Not Available	Not Available

Predicted Properties

Property	Value	Source
Water Solubility	0.0042 g/L	ALOGPS
logP	4.86	ChemAxon
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	35.47 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

HMDB0006220

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

FDB023844

KNApSAcK ID

Not Available

Chemspider ID

4940755

KEGG Compound ID

Not Available

BioCyc ID

CPD-13525

BiGG ID

2455100

Wikipedia Link

Retinal

METLIN ID

Not Available

PubChem Compound

6436079

PDB ID

Not Available

ChEBI ID

45487

Good Scents ID

Not Available

References

General References

Hope WC, Patel BJ, Fiedler-Nagy C, Wittreich BH: Retinoids inhibit phospholipase A2 in human synovial fluid and arachidonic acid release from rat peritoneal macrophages. Inflammation. 1990 Oct;14(5):543-59. [PubMed:2123476 ]
Jakdetchai O, Eberhardt P, Asido M, Kaur J, Kriebel CN, Mao J, Leeder AJ, Brown LJ, Brown RCD, Becker-Baldus J, Bamann C, Wachtveitl J, Glaubitz C: Probing the photointermediates of light-driven sodium ion pump KR2 by DNP-enhanced solid-state NMR. Sci Adv. 2021 Mar 12;7(11). pii: 7/11/eabf4213. doi: 10.1126/sciadv.abf4213. Print 2021 Mar. [PubMed:33712469 ]
VanGordon MR, Prignano LA, Dempski RE, Rick SW, Rempe SB: Channelrhodopsin C1C2: Photocycle kinetics and interactions near the central gate. Biophys J. 2021 May 4;120(9):1835-1845. doi: 10.1016/j.bpj.2021.03.002. Epub 2021 Mar 9. [PubMed:33705762 ]
Nakamizo Y, Fujisawa T, Kikukawa T, Okamura A, Baba H, Unno M: Low-temperature Raman spectroscopy of sodium-pump rhodopsin from Indibacter alkaliphilus: insight of Na(+) binding for active Na(+) transport. Phys Chem Chem Phys. 2021 Jan 28;23(3):2072-2079. doi: 10.1039/d0cp05652a. [PubMed:33433533 ]
Kandori H: Biophysics of rhodopsins and optogenetics. Biophys Rev. 2020 Apr;12(2):355-361. doi: 10.1007/s12551-020-00645-0. Epub 2020 Feb 17. [PubMed:32065378 ]
Han S, Kim SH, Cho JC, Song J, Bleckner G, Jung KH: Photochemical characterization of flavobacterial rhodopsin: The importance of the helix E region for heat stability. Biochim Biophys Acta Bioenerg. 2020 Jan 1;1861(1):148092. doi: 10.1016/j.bbabio.2019.148092. Epub 2019 Nov 6. [PubMed:31669491 ]
Yang T, Zhang W, Cheng J, Nie Y, Xin Q, Yuan S, Dou Y: Formation Mechanism of Ion Channel in Channelrhodopsin-2: Molecular Dynamics Simulation and Steering Molecular Dynamics Simulations. Int J Mol Sci. 2019 Aug 2;20(15). pii: ijms20153780. doi: 10.3390/ijms20153780. [PubMed:31382458 ]
Miyahara T, Nakatsuji H: Light-Driven Proton, Sodium Ion, and Chloride Ion Transfer Mechanisms in Rhodopsins: SAC-CI Study. J Phys Chem A. 2019 Mar 7;123(9):1766-1784. doi: 10.1021/acs.jpca.8b10203. Epub 2019 Feb 27. [PubMed:30762358 ]
Ghanbarpour A, Nairat M, Nosrati M, Santos EM, Vasileiou C, Dantus M, Borhan B, Geiger JH: Mimicking Microbial Rhodopsin Isomerization in a Single Crystal. J Am Chem Soc. 2019 Jan 30;141(4):1735-1741. doi: 10.1021/jacs.8b12493. Epub 2019 Jan 14. [PubMed:30580520 ]
Roy PP, Kato Y, Abe-Yoshizumi R, Pieri E, Ferre N, Kandori H, Buckup T: Mapping the ultrafast vibrational dynamics of all-trans and 13-cis retinal isomerization in Anabaena Sensory Rhodopsin. Phys Chem Chem Phys. 2018 Dec 12;20(48):30159-30173. doi: 10.1039/c8cp05469j. [PubMed:30484447 ]
Inoue S, Yoshizawa S, Nakajima Y, Kojima K, Tsukamoto T, Kikukawa T, Sudo Y: Spectroscopic characteristics of Rubricoccus marinus xenorhodopsin (RmXeR) and a putative model for its inward H(+) transport mechanism. Phys Chem Chem Phys. 2018 Jan 31;20(5):3172-3183. doi: 10.1039/c7cp05033j. [PubMed:29034950 ]
Kajimoto K, Kikukawa T, Nakashima H, Yamaryo H, Saito Y, Fujisawa T, Demura M, Unno M: Transient Resonance Raman Spectroscopy of a Light-Driven Sodium-Ion-Pump Rhodopsin from Indibacter alkaliphilus. J Phys Chem B. 2017 May 4;121(17):4431-4437. doi: 10.1021/acs.jpcb.7b02421. Epub 2017 Apr 21. [PubMed:28421760 ]
Schnedermann C, Muders V, Ehrenberg D, Schlesinger R, Kukura P, Heberle J: Vibronic Dynamics of the Ultrafast all-trans to 13-cis Photoisomerization of Retinal in Channelrhodopsin-1. J Am Chem Soc. 2016 Apr 13;138(14):4757-62. doi: 10.1021/jacs.5b12251. Epub 2016 Mar 30. [PubMed:26999496 ]

Showing NP-Card for 13-cis-Retinal (NP0001435)

MOL for NP0001435 (13-cis-Retinal)

3D MOL for NP0001435 (13-cis-Retinal)

3D SDF for NP0001435 (13-cis-Retinal)

3D-SDF for NP0001435 (13-cis-Retinal)

PDB for NP0001435 (13-cis-Retinal)

3D PDB for NP0001435 (13-cis-Retinal)

SMILES for NP0001435 (13-cis-Retinal)

INCHI for NP0001435 (13-cis-Retinal)

Structure for NP0001435 (13-cis-Retinal)

3D Structure for NP0001435 (13-cis-Retinal)