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Record Information

Version

5.0

Status

Detected but not Quantified

Creation Date

2012-09-11 20:51:13 UTC

Update Date

2022-09-22 18:35:10 UTC

HMDB ID

HMDB0035830

Secondary Accession Numbers

HMDB35830

Metabolite Identification

Common Name

Genipin

Description

Genipin is found in beverages. Genipin is a constituent of Genipa americana (genipap) Genipin is an aglycone derived from an iridoid glycoside called geniposide present in fruit of Gardenia jasminoides. Genipin is an excellent natural cross-linker for proteins, collagen, gelatin, and chitosan cross-linking. It has a low acute toxicity, with LD50 i.v. 382 mg/kg in mice, therefore, much less toxic than glutaraldehyde and many other commonly used synthetic cross-linking regents. It is also used for pharmaceutical purposes, such as choleretic action for liver diseases control

Structure

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

HMDB0035830
     RDKit          3D
Genipin
 30 31  0  0  0  0  0  0  0  0999 V2000
    4.9320    0.6972   -0.3275 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7376    0.3686    0.3498 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.5208    0.2182   -0.3313 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5679    0.3948   -1.5762 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.2883   -0.1169    0.3387 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2793   -0.2945    1.6468 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0986   -0.6225    2.3409 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1277   -0.8584    1.6194 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1995   -0.5648    2.4629 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1231    0.0947    0.4978 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1973    0.0707   -0.4737 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6281   -0.3231   -0.3103 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7612   -1.6435    0.1079 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7009    0.4820   -1.6364 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2246    0.8007   -1.4606 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0684   -0.2587   -0.4116 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.7653    0.1362    0.1540 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.9123    0.4417   -1.4001 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.0869    1.7973   -0.1591 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2000   -0.1861    2.2023 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1269   -1.9209    1.3664 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3290    0.4276    2.4578 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8805    1.1025    0.8974 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1118    0.3480    0.4327 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2086   -0.2153   -1.2456 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7733   -2.1963   -0.7101 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1940    0.5968   -2.5841 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1075    1.7881   -0.9746 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3318    0.6691   -2.3841 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0948   -1.2331   -0.8894 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  2  0
  3  5  1  0
  5  6  2  0
  6  7  1  0
  7  8  1  0
  8  9  1  0
  8 10  1  0
 10 11  1  0
 11 12  1  0
 12 13  1  0
 11 14  2  0
 14 15  1  0
 15 16  1  0
 16  5  1  0
 16 10  1  0
  1 17  1  0
  1 18  1  0
  1 19  1  0
  6 20  1  0
  8 21  1  0
  9 22  1  0
 10 23  1  0
 12 24  1  0
 12 25  1  0
 13 26  1  0
 14 27  1  0
 15 28  1  0
 15 29  1  0
 16 30  1  0
M  END


  Mrv0541 05061308442D          

 16 17  0  0  0  0            999 V2000
    3.9934    3.3000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2949    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7798    1.0799    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5249   -1.0396    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9934    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7798   -0.2549    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5645    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2789    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5645    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2789    2.0625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2789   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0769   -1.6527    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.5645    2.4750    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.2789   -1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.9934    2.4750    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.9934    0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  3  2  1  0  0  0  0
  6  2  2  0  0  0  0
  6  4  1  0  0  0  0
  7  3  1  0  0  0  0
  8  5  2  0  0  0  0
  8  7  1  0  0  0  0
  9  6  1  0  0  0  0
  9  7  1  0  0  0  0
 10  8  1  0  0  0  0
 11  9  1  0  0  0  0
 12  4  1  0  0  0  0
 13 10  2  0  0  0  0
 14 11  1  0  0  0  0
 15  1  1  0  0  0  0
 15 10  1  0  0  0  0
 16  5  1  0  0  0  0
 16 11  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0035830

> <DATABASE_NAME>
hmdb

> <SMILES>
COC(=O)C1=COC(O)C2C1CC=C2CO

> <INCHI_IDENTIFIER>
InChI=1S/C11H14O5/c1-15-10(13)8-5-16-11(14)9-6(4-12)2-3-7(8)9/h2,5,7,9,11-12,14H,3-4H2,1H3

> <INCHI_KEY>
AZKVWQKMDGGDSV-UHFFFAOYSA-N

> <FORMULA>
C11H14O5

> <MOLECULAR_WEIGHT>
226.2259

> <EXACT_MASS>
226.084123558

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_AVERAGE_POLARIZABILITY>
22.433060913491364

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
methyl 1-hydroxy-7-(hydroxymethyl)-1H,4aH,5H,7aH-cyclopenta[c]pyran-4-carboxylate

> <ALOGPS_LOGP>
0.07

> <JCHEM_LOGP>
-0.44389565966666605

> <ALOGPS_LOGS>
-1.50

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
15.150537367169974

> <JCHEM_PKA_STRONGEST_ACIDIC>
12.036945977145045

> <JCHEM_PKA_STRONGEST_BASIC>
-2.7354177854672015

> <JCHEM_POLAR_SURFACE_AREA>
75.99000000000001

> <JCHEM_REFRACTIVITY>
56.093300000000006

> <JCHEM_ROTATABLE_BOND_COUNT>
3

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
7.18e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
methyl 1-hydroxy-7-(hydroxymethyl)-1H,4aH,5H,7aH-cyclopenta[c]pyran-4-carboxylate

> <JCHEM_VEBER_RULE>
0

$$$$

HMDB0035830
     RDKit          3D
Genipin
 30 31  0  0  0  0  0  0  0  0999 V2000
    4.9320    0.6972   -0.3275 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7376    0.3686    0.3498 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.5208    0.2182   -0.3313 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5679    0.3948   -1.5762 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.2883   -0.1169    0.3387 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2793   -0.2945    1.6468 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0986   -0.6225    2.3409 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1277   -0.8584    1.6194 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1995   -0.5648    2.4629 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1231    0.0947    0.4978 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1973    0.0707   -0.4737 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6281   -0.3231   -0.3103 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7612   -1.6435    0.1079 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7009    0.4820   -1.6364 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2246    0.8007   -1.4606 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0684   -0.2587   -0.4116 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.7653    0.1362    0.1540 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.9123    0.4417   -1.4001 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.0869    1.7973   -0.1591 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2000   -0.1861    2.2023 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1269   -1.9209    1.3664 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3290    0.4276    2.4578 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8805    1.1025    0.8974 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1118    0.3480    0.4327 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2086   -0.2153   -1.2456 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7733   -2.1963   -0.7101 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1940    0.5968   -2.5841 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1075    1.7881   -0.9746 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3318    0.6691   -2.3841 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0948   -1.2331   -0.8894 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  2  0
  3  5  1  0
  5  6  2  0
  6  7  1  0
  7  8  1  0
  8  9  1  0
  8 10  1  0
 10 11  1  0
 11 12  1  0
 12 13  1  0
 11 14  2  0
 14 15  1  0
 15 16  1  0
 16  5  1  0
 16 10  1  0
  1 17  1  0
  1 18  1  0
  1 19  1  0
  6 20  1  0
  8 21  1  0
  9 22  1  0
 10 23  1  0
 12 24  1  0
 12 25  1  0
 13 26  1  0
 14 27  1  0
 15 28  1  0
 15 29  1  0
 16 30  1  0
M  END

HEADER    PROTEIN                                 06-MAY-13   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   06-MAY-13         0                                  
HETATM    1  C   UNK     0       7.454   6.160   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       2.417   0.770   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       3.322   2.016   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       2.846  -1.941   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       7.454   1.540   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       3.322  -0.476   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       4.787   1.540   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       6.121   2.310   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       4.787   0.000   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       6.121   3.850   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       6.121  -0.770   0.000  0.00  0.00           C+0
HETATM   12  O   UNK     0       3.877  -3.085   0.000  0.00  0.00           O+0
HETATM   13  O   UNK     0       4.787   4.620   0.000  0.00  0.00           O+0
HETATM   14  O   UNK     0       6.121  -2.310   0.000  0.00  0.00           O+0
HETATM   15  O   UNK     0       7.454   4.620   0.000  0.00  0.00           O+0
HETATM   16  O   UNK     0       7.454   0.000   0.000  0.00  0.00           O+0
CONECT    1   15                                                            
CONECT    2    3    6                                                       
CONECT    3    2    7                                                       
CONECT    4    6   12                                                       
CONECT    5    8   16                                                       
CONECT    6    2    4    9                                                  
CONECT    7    3    8    9                                                  
CONECT    8    5    7   10                                                  
CONECT    9    6    7   11                                                  
CONECT   10    8   13   15                                                  
CONECT   11    9   14   16                                                  
CONECT   12    4                                                            
CONECT   13   10                                                            
CONECT   14   11                                                            
CONECT   15    1   10                                                       
CONECT   16    5   11                                                       
MASTER        0    0    0    0    0    0    0    0   16    0   34    0
END

COMPND    HMDB0035830
HETATM    1  C1  UNL     1       4.932   0.697  -0.328  1.00  0.00           C  
HETATM    2  O1  UNL     1       3.738   0.369   0.350  1.00  0.00           O  
HETATM    3  C2  UNL     1       2.521   0.218  -0.331  1.00  0.00           C  
HETATM    4  O2  UNL     1       2.568   0.395  -1.576  1.00  0.00           O  
HETATM    5  C3  UNL     1       1.288  -0.117   0.339  1.00  0.00           C  
HETATM    6  C4  UNL     1       1.279  -0.294   1.647  1.00  0.00           C  
HETATM    7  O3  UNL     1       0.099  -0.623   2.341  1.00  0.00           O  
HETATM    8  C5  UNL     1      -1.128  -0.858   1.619  1.00  0.00           C  
HETATM    9  O4  UNL     1      -2.200  -0.565   2.463  1.00  0.00           O  
HETATM   10  C6  UNL     1      -1.123   0.095   0.498  1.00  0.00           C  
HETATM   11  C7  UNL     1      -2.197   0.071  -0.474  1.00  0.00           C  
HETATM   12  C8  UNL     1      -3.628  -0.323  -0.310  1.00  0.00           C  
HETATM   13  O5  UNL     1      -3.761  -1.644   0.108  1.00  0.00           O  
HETATM   14  C9  UNL     1      -1.701   0.482  -1.636  1.00  0.00           C  
HETATM   15  C10 UNL     1      -0.225   0.801  -1.461  1.00  0.00           C  
HETATM   16  C11 UNL     1       0.068  -0.259  -0.412  1.00  0.00           C  
HETATM   17  H1  UNL     1       5.765   0.136   0.154  1.00  0.00           H  
HETATM   18  H2  UNL     1       4.912   0.442  -1.400  1.00  0.00           H  
HETATM   19  H3  UNL     1       5.087   1.797  -0.159  1.00  0.00           H  
HETATM   20  H4  UNL     1       2.200  -0.186   2.202  1.00  0.00           H  
HETATM   21  H5  UNL     1      -1.127  -1.921   1.366  1.00  0.00           H  
HETATM   22  H6  UNL     1      -2.329   0.428   2.458  1.00  0.00           H  
HETATM   23  H7  UNL     1      -0.881   1.103   0.897  1.00  0.00           H  
HETATM   24  H8  UNL     1      -4.112   0.348   0.433  1.00  0.00           H  
HETATM   25  H9  UNL     1      -4.209  -0.215  -1.246  1.00  0.00           H  
HETATM   26  H10 UNL     1      -3.773  -2.196  -0.710  1.00  0.00           H  
HETATM   27  H11 UNL     1      -2.194   0.597  -2.584  1.00  0.00           H  
HETATM   28  H12 UNL     1      -0.108   1.788  -0.975  1.00  0.00           H  
HETATM   29  H13 UNL     1       0.332   0.669  -2.384  1.00  0.00           H  
HETATM   30  H14 UNL     1      -0.095  -1.233  -0.889  1.00  0.00           H  
CONECT    1    2   17   18   19
CONECT    2    3
CONECT    3    4    4    5
CONECT    5    6    6   16
CONECT    6    7   20
CONECT    7    8
CONECT    8    9   10   21
CONECT    9   22
CONECT   10   11   16   23
CONECT   11   12   14   14
CONECT   12   13   24   25
CONECT   13   26
CONECT   14   15   27
CONECT   15   16   28   29
CONECT   16   30
END

HMDB0035830
     RDKit          3D
Genipin
 30 31  0  0  0  0  0  0  0  0999 V2000
    4.9320    0.6972   -0.3275 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7376    0.3686    0.3498 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.5208    0.2182   -0.3313 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5679    0.3948   -1.5762 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.2883   -0.1169    0.3387 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2793   -0.2945    1.6468 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0986   -0.6225    2.3409 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1277   -0.8584    1.6194 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1995   -0.5648    2.4629 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1231    0.0947    0.4978 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1973    0.0707   -0.4737 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6281   -0.3231   -0.3103 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7612   -1.6435    0.1079 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7009    0.4820   -1.6364 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2246    0.8007   -1.4606 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0684   -0.2587   -0.4116 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.7653    0.1362    0.1540 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.9123    0.4417   -1.4001 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.0869    1.7973   -0.1591 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2000   -0.1861    2.2023 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1269   -1.9209    1.3664 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3290    0.4276    2.4578 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8805    1.1025    0.8974 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1118    0.3480    0.4327 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2086   -0.2153   -1.2456 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7733   -2.1963   -0.7101 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1940    0.5968   -2.5841 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1075    1.7881   -0.9746 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3318    0.6691   -2.3841 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0948   -1.2331   -0.8894 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  2  0
  3  5  1  0
  5  6  2  0
  6  7  1  0
  7  8  1  0
  8  9  1  0
  8 10  1  0
 10 11  1  0
 11 12  1  0
 12 13  1  0
 11 14  2  0
 14 15  1  0
 15 16  1  0
 16  5  1  0
 16 10  1  0
  1 17  1  0
  1 18  1  0
  1 19  1  0
  6 20  1  0
  8 21  1  0
  9 22  1  0
 10 23  1  0
 12 24  1  0
 12 25  1  0
 13 26  1  0
 14 27  1  0
 15 28  1  0
 15 29  1  0
 16 30  1  0
M  END

View in JSmol View NMR Assignments View Stereo Labels

Synonyms

Value	Source
Methyl 1-hydroxy-7-(hydroxymethyl)-1H,4ah,5H,7ah-cyclopenta[c]pyran-4-carboxylic acid	HMDB

Chemical Formula

C₁₁H₁₄O₅

Average Molecular Weight

226.2259

Monoisotopic Molecular Weight

226.084123558

IUPAC Name

methyl 1-hydroxy-7-(hydroxymethyl)-1H,4aH,5H,7aH-cyclopenta[c]pyran-4-carboxylate

Traditional Name

methyl 1-hydroxy-7-(hydroxymethyl)-1H,4aH,5H,7aH-cyclopenta[c]pyran-4-carboxylate

CAS Registry Number

6902-77-8

SMILES

COC(=O)C1=COC(O)C2C1CC=C2CO

InChI Identifier

InChI=1S/C11H14O5/c1-15-10(13)8-5-16-11(14)9-6(4-12)2-3-7(8)9/h2,5,7,9,11-12,14H,3-4H2,1H3

InChI Key

AZKVWQKMDGGDSV-UHFFFAOYSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as iridoids and derivatives. These are monoterpenes containing a skeleton structurally characterized by the presence of a cylopentane fused to a pyran ( forming a 4,7-dimethylcyclopenta[c]pyran), or a derivative where the pentane moiety is open.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Prenol lipids

Sub Class

Monoterpenoids

Direct Parent

Iridoids and derivatives

Alternative Parents

Substituents

Iridoid-skeleton
Bicyclic monoterpenoid
Methyl ester
Vinylogous ester
Alpha,beta-unsaturated carboxylic ester
Enoate ester
Carboxylic acid ester
Hemiacetal
Carboxylic acid derivative
Oxacycle
Monocarboxylic acid or derivatives
Organoheterocyclic compound
Hydrocarbon derivative
Organic oxide
Alcohol
Organic oxygen compound
Organooxygen compound
Primary alcohol
Carbonyl group
Aliphatic heteropolycyclic compound

Molecular Framework

Aliphatic heteropolycyclic compounds

External Descriptors

Not Available

Ontology

Not Available

Physical Properties

State

Solid

Experimental Molecular Properties

Property	Value	Reference
Melting Point	120 - 121 °C	Not Available
Boiling Point	Not Available	Not Available
Water Solubility	100300 mg/L @ 25 °C (est)	The Good Scents Company Information System
LogP	Not Available	Not Available

Experimental Chromatographic Properties

Not Available

Predicted Molecular Properties

Property	Value	Source
Water Solubility	7.18 g/L	ALOGPS
logP	0.07	ALOGPS
logP	-0.44	ChemAxon
logS	-1.5	ALOGPS
pKa (Strongest Acidic)	12.04	ChemAxon
pKa (Strongest Basic)	-2.7	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	4	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	75.99 Å²	ChemAxon
Rotatable Bond Count	3	ChemAxon
Refractivity	56.09 m³·mol⁻¹	ChemAxon
Polarizability	22.43 Å³	ChemAxon
Number of Rings	2	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

Predicted Chromatographic Properties

Predicted Collision Cross Sections

Predictor	Adduct Type	CCS Value (Å²)	Reference
DarkChem	[M+H]+	153.452	31661259
DarkChem	[M-H]-	149.137	31661259
DeepCCS	[M+H]+	148.187	30932474
DeepCCS	[M-H]-	145.829	30932474
DeepCCS	[M-2H]-	179.987	30932474
DeepCCS	[M+Na]+	154.754	30932474
AllCCS	[M+H]+	150.2	32859911
AllCCS	[M+H-H2O]+	146.3	32859911
AllCCS	[M+NH4]+	153.8	32859911
AllCCS	[M+Na]+	154.8	32859911
AllCCS	[M-H]-	151.1	32859911
AllCCS	[M+Na-2H]-	151.2	32859911
AllCCS	[M+HCOO]-	151.5	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.	3.78 minutes	32390414
Predicted by Siyang on May 30, 2022	9.7175 minutes	33406817
Predicted by Siyang using ReTip algorithm on June 8, 2022	2.01 minutes	32390414
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid	1477.5 seconds	40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid	247.8 seconds	40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid	111.3 seconds	40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid	171.9 seconds	40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	54.5 seconds	40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid	244.4 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	344.9 seconds	40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)	215.6 seconds	40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid	726.5 seconds	40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid	297.0 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	935.9 seconds	40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	211.4 seconds	40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	283.4 seconds	40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate	417.1 seconds	40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA	205.6 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	147.0 seconds	40023050

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
Genipin	COC(=O)C1=COC(O)C2C1CC=C2CO	2994.8	Standard polar	33892256
Genipin	COC(=O)C1=COC(O)C2C1CC=C2CO	1851.0	Standard non polar	33892256
Genipin	COC(=O)C1=COC(O)C2C1CC=C2CO	1916.9	Semi standard non polar	33892256

Derivatized

Derivative Name / Structure	SMILES	Kovats RI Value	Column Type	Reference
Genipin,1TMS,isomer #1	COC(=O)C1=COC(O[Si](C)(C)C)C2C(CO)=CCC12	1975.4	Semi standard non polar	33892256
Genipin,1TMS,isomer #2	COC(=O)C1=COC(O)C2C(CO[Si](C)(C)C)=CCC12	1962.8	Semi standard non polar	33892256
Genipin,2TMS,isomer #1	COC(=O)C1=COC(O[Si](C)(C)C)C2C(CO[Si](C)(C)C)=CCC12	2030.3	Semi standard non polar	33892256
Genipin,1TBDMS,isomer #1	COC(=O)C1=COC(O[Si](C)(C)C(C)(C)C)C2C(CO)=CCC12	2183.5	Semi standard non polar	33892256
Genipin,1TBDMS,isomer #2	COC(=O)C1=COC(O)C2C(CO[Si](C)(C)C(C)(C)C)=CCC12	2176.3	Semi standard non polar	33892256
Genipin,2TBDMS,isomer #1	COC(=O)C1=COC(O[Si](C)(C)C(C)(C)C)C2C(CO[Si](C)(C)C(C)(C)C)=CCC12	2447.7	Semi standard non polar	33892256

Spectra

GC-MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Predicted GC-MS	Predicted GC-MS Spectrum - Genipin GC-MS (Non-derivatized) - 70eV, Positive	splash10-0002-9500000000-2409d17d401e88924426	2017-09-01	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Genipin GC-MS (2 TMS) - 70eV, Positive	splash10-014i-4980000000-ca18f1a900ae4cd73f93	2017-10-06	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Genipin GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	Wishart Lab	View Spectrum

MS/MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Experimental LC-MS/MS	LC-MS/MS Spectrum - Genipin LC-ESI-QTOF , negative-QTOF	splash10-0udi-0910000000-35002af93563dfe76481	2017-09-14	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - Genipin LC-ESI-QTOF , negative-QTOF	splash10-0udi-0900000000-04804adc03388840c90d	2017-09-14	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - Genipin 10V, Negative-QTOF	splash10-0udi-0910000000-7819ff2252201bad96c6	2021-09-20	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - Genipin 20V, Negative-QTOF	splash10-0udi-0900000000-04804adc03388840c90d	2021-09-20	HMDB team, MONA	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Genipin 10V, Positive-QTOF	splash10-056r-0690000000-e314a3c7623690c4254a	2015-04-24	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Genipin 20V, Positive-QTOF	splash10-0a6s-2940000000-b60c31612ff6af2aa444	2015-04-24	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Genipin 40V, Positive-QTOF	splash10-002b-9800000000-848a0a7c4c880f96b1af	2015-04-24	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Genipin 10V, Negative-QTOF	splash10-004i-1690000000-de3544e658f08c1f7e6f	2015-04-25	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Genipin 20V, Negative-QTOF	splash10-00mk-1930000000-65e8bc938f4a26c99d83	2015-04-25	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Genipin 40V, Negative-QTOF	splash10-00ks-9600000000-389443ccaf5a29642052	2015-04-25	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Genipin 10V, Negative-QTOF	splash10-004i-0190000000-ac8ca4fb9caa5d769716	2021-09-23	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Genipin 20V, Negative-QTOF	splash10-004j-1960000000-614695d528ab6adc9650	2021-09-23	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Genipin 40V, Negative-QTOF	splash10-002n-6900000000-207ebabcf3252c46e3ea	2021-09-23	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Genipin 10V, Positive-QTOF	splash10-004j-0970000000-cdc0e1823e4904e582a0	2021-09-25	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Genipin 20V, Positive-QTOF	splash10-056r-0940000000-5e507006469235e7b796	2021-09-25	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Genipin 40V, Positive-QTOF	splash10-004i-4900000000-7d0220e35ff86f862d87	2021-09-25	Wishart Lab	View Spectrum

NMR Spectra

Spectrum Type	Description	Deposition Date	Source	View
Predicted 1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 100 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 200 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 300 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 400 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 500 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 600 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 700 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 800 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 900 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum

Biological Properties

Cellular Locations

Cytoplasm
Extracellular
Membrane

Biospecimen Locations

Blood
Urine

Tissue Locations

Not Available

Pathways

Not Available

Name	SMPDB/PathBank	KEGG

Normal Concentrations

Not Available

Abnormal Concentrations

Biospecimen	Status	Value	Age	Sex	Condition	Reference	Details
Blood	Expected but not Quantified	Not Quantified	Adult (>18 years old)	Both	Asthma	33739820	details
Urine	Detected but not Quantified	Not Quantified	Adult (>18 years old)	Both	Asthma	33739820	details

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

KNApSAcK ID

Chemspider ID

KEGG Compound ID

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Genipin

METLIN ID

Not Available

PubChem Compound

23340

PDB ID

Not Available

ChEBI ID

94318

Food Biomarker Ontology

Not Available

VMH ID

Not Available

MarkerDB ID

Not Available

Good Scents ID

rw1851921

References

Synthesis Reference

Not Available

Material Safety Data Sheet (MSDS)

Not Available

General References

Cao H, Feng Q, Xu W, Li X, Kang Z, Ren Y, Du L: Genipin induced apoptosis associated with activation of the c-Jun NH2-terminal kinase and p53 protein in HeLa cells. Biol Pharm Bull. 2010;33(8):1343-8. [PubMed:20686229 ]
Tian JS, Cui YL, Hu LM, Gao S, Chi W, Dong TJ, Liu LP: Antidepressant-like effect of genipin in mice. Neurosci Lett. 2010 Aug 2;479(3):236-9. doi: 10.1016/j.neulet.2010.05.069. Epub 2010 Jun 1. [PubMed:20561935 ]
Kim BC, Kim HG, Lee SA, Lim S, Park EH, Kim SJ, Lim CJ: Genipin-induced apoptosis in hepatoma cells is mediated by reactive oxygen species/c-Jun NH2-terminal kinase-dependent activation of mitochondrial pathway. Biochem Pharmacol. 2005 Nov 1;70(9):1398-407. [PubMed:16143311 ]
Koo HJ, Lim KH, Jung HJ, Park EH: Anti-inflammatory evaluation of gardenia extract, geniposide and genipin. J Ethnopharmacol. 2006 Feb 20;103(3):496-500. Epub 2005 Sep 19. [PubMed:16169698 ]
Simons K, Toomre D: Lipid rafts and signal transduction. Nat Rev Mol Cell Biol. 2000 Oct;1(1):31-9. [PubMed:11413487 ]
Watson AD: Thematic review series: systems biology approaches to metabolic and cardiovascular disorders. Lipidomics: a global approach to lipid analysis in biological systems. J Lipid Res. 2006 Oct;47(10):2101-11. Epub 2006 Aug 10. [PubMed:16902246 ]
Sethi JK, Vidal-Puig AJ: Thematic review series: adipocyte biology. Adipose tissue function and plasticity orchestrate nutritional adaptation. J Lipid Res. 2007 Jun;48(6):1253-62. Epub 2007 Mar 20. [PubMed:17374880 ]
Lingwood D, Simons K: Lipid rafts as a membrane-organizing principle. Science. 2010 Jan 1;327(5961):46-50. doi: 10.1126/science.1174621. [PubMed:20044567 ]
(). Yannai, Shmuel. (2004) Dictionary of food compounds with CD-ROM: Additives, flavors, and ingredients. Boca Raton: Chapman & Hall/CRC.. .
Gunstone, Frank D., John L. Harwood, and Albert J. Dijkstra (2007). The lipid handbook with CD-ROM. CRC Press.

Showing metabocard for Genipin (HMDB0035830)

MOL for HMDB0035830 (Genipin)

3D MOL for HMDB0035830 (Genipin)

3D SDF for HMDB0035830 (Genipin)

3D-SDF for HMDB0035830 (Genipin)

PDB for HMDB0035830 (Genipin)

3D PDB for HMDB0035830 (Genipin)

SMILES for HMDB0035830 (Genipin)

INCHI for HMDB0035830 (Genipin)

Structure for HMDB0035830 (Genipin)

3D Structure for HMDB0035830 (Genipin)

Predicted Collision Cross Sections

Predicted Retention Times

Underivatized

Predicted Kovats Retention Indices

Underivatized

Derivatized

GC-MS Spectra

MS/MS Spectra

NMR Spectra