MiMeDB: Showing metabocard for Berkelic acid (MMDBc0004608)

Record Information

Version

2.0

Status

Detected and Quantified

Creation Date

2021-05-14 22:32:16 UTC

Update Date

2025-10-07 16:04:54 UTC

Metabolite ID

MMDBc0004608

Metabolite Identification

Common Name

Berkelic acid

Description

Berkelic acid is a tetracyclic metabolite belonging to the class of natural products. Its total synthesis has been a focus of recent research, with notable advancements in regioselective spiroacetal/pyran formation enabling concise synthetic routes (PMID:38439742 ). A scalable synthesis of the triol segment and the tetracyclic skeleton was achieved through a tandem process, culminating in an efficient total synthesis completed in eight linear steps (PMID:33252181 ). This methodology has been pivotal in constructing the core structure of berkelic acid (PMID:30924665 ). Furthermore, a biosynthetically inspired approach has been utilized to synthesize berkelic acid and its analogs, alongside biological evaluations that highlight its potential (PMID:29867257 ). Studies indicate that the originally assigned structure of berkelic acid is unstable, leading to the formation of a mixture of four diastereomers, which were characterized using X-ray crystallography (PMID:29867257 ). Additionally, analogs such as C22-epi-berkelic acid and C26-oxoberkelic acid have been synthesized and evaluated against human cancer cell lines, reflecting the compound's relevance in medicinal chemistry (PMID:29867257 ).

Structure

MOL SDF PDB SMILES InChI


  Mrv1652305152100322D          

 42 45  0  0  1  0            999 V2000
   -3.1957    2.3537    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.3792    3.4292    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7494    1.7003    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.5160    1.5658    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.7428    3.2275    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6175    1.7651    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.2429    2.6156    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8188    1.9716    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2406    1.3831    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4419    1.5895    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0843    0.2061    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2733   -1.1774    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.5409    1.5905    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3120    0.8254    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2225    0.1552    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1926    1.0044    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.4939   -0.3825    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0161    0.9540    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.1363    1.0010    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.8515   -1.7659    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5132    0.6189    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.3546    1.4542    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2926   -0.1760    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6502   -1.5595    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8708   -0.7645    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2284   -2.1480    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.4043    2.7272    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.8794    2.0907    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8901    0.2369    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.6309   -2.5609    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.6434    0.6814    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.0271   -1.9416    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.0078   -2.9430    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.1155    3.5000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.2180    2.5909    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.5267   -0.2880    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.9351    1.2075    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.6696   -0.5581    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.6114    1.7152    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.8215    0.7753    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3569    1.7960    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0914    0.0304    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  6  1  1  0  0  0  0
  7  2  1  0  0  0  0
  8  6  1  0  0  0  0
  9  8  1  0  0  0  0
 10  9  1  0  0  0  0
 16  3  1  6  0  0  0
 17 11  1  0  0  0  0
 17 12  2  0  0  0  0
 18 13  1  1  0  0  0
 18 15  1  0  0  0  0
 18 16  1  0  0  0  0
 19 10  1  1  0  0  0
 19 11  1  0  0  0  0
 20 12  1  0  0  0  0
 21 14  1  0  0  0  0
 22 13  1  0  0  0  0
 23 17  1  0  0  0  0
 23 21  1  0  0  0  0
 24 20  2  0  0  0  0
 25 23  2  0  0  0  0
 25 24  1  0  0  0  0
 26 24  1  0  0  0  0
 28  4  1  0  0  0  0
 28  7  1  0  0  0  0
 28 22  1  0  0  0  0
 28 27  1  0  0  0  0
 29 14  1  0  0  0  0
 29 16  1  0  0  0  0
 30 20  1  0  0  0  0
 31 22  2  0  0  0  0
 32 26  2  0  0  0  0
 33 26  1  0  0  0  0
 34 27  2  0  0  0  0
 35  5  1  0  0  0  0
 35 27  1  0  0  0  0
 36 15  1  0  0  0  0
 29 36  1  6  0  0  0
 37 19  1  0  0  0  0
 37 21  1  0  0  0  0
 38 25  1  0  0  0  0
 38 29  1  0  0  0  0
 16 39  1  1  0  0  0
 18 40  1  6  0  0  0
 19 41  1  6  0  0  0
 42 21  1  0  0  0  0
M  END


  Mrv1652305152100322D          

 42 45  0  0  1  0            999 V2000
   -3.1957    2.3537    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.3792    3.4292    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7494    1.7003    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.5160    1.5658    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.7428    3.2275    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6175    1.7651    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.2429    2.6156    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8188    1.9716    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2406    1.3831    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4419    1.5895    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0843    0.2061    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2733   -1.1774    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.5409    1.5905    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3120    0.8254    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2225    0.1552    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1926    1.0044    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.4939   -0.3825    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0161    0.9540    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.1363    1.0010    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.8515   -1.7659    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5132    0.6189    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.3546    1.4542    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2926   -0.1760    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6502   -1.5595    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8708   -0.7645    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2284   -2.1480    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.4043    2.7272    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.8794    2.0907    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8901    0.2369    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.6309   -2.5609    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.6434    0.6814    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.0271   -1.9416    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.0078   -2.9430    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.1155    3.5000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.2180    2.5909    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.5267   -0.2880    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.9351    1.2075    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.6696   -0.5581    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.6114    1.7152    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.8215    0.7753    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3569    1.7960    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0914    0.0304    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  6  1  1  0  0  0  0
  7  2  1  0  0  0  0
  8  6  1  0  0  0  0
  9  8  1  0  0  0  0
 10  9  1  0  0  0  0
 16  3  1  6  0  0  0
 17 11  1  0  0  0  0
 17 12  2  0  0  0  0
 18 13  1  1  0  0  0
 18 15  1  0  0  0  0
 18 16  1  0  0  0  0
 19 10  1  1  0  0  0
 19 11  1  0  0  0  0
 20 12  1  0  0  0  0
 21 14  1  0  0  0  0
 22 13  1  0  0  0  0
 23 17  1  0  0  0  0
 23 21  1  0  0  0  0
 24 20  2  0  0  0  0
 25 23  2  0  0  0  0
 25 24  1  0  0  0  0
 26 24  1  0  0  0  0
 28  4  1  0  0  0  0
 28  7  1  0  0  0  0
 28 22  1  0  0  0  0
 28 27  1  0  0  0  0
 29 14  1  0  0  0  0
 29 16  1  0  0  0  0
 30 20  1  0  0  0  0
 31 22  2  0  0  0  0
 32 26  2  0  0  0  0
 33 26  1  0  0  0  0
 34 27  2  0  0  0  0
 35  5  1  0  0  0  0
 35 27  1  0  0  0  0
 36 15  1  0  0  0  0
 29 36  1  6  0  0  0
 37 19  1  0  0  0  0
 37 21  1  0  0  0  0
 38 25  1  0  0  0  0
 38 29  1  0  0  0  0
 16 39  1  1  0  0  0
 18 40  1  6  0  0  0
 19 41  1  6  0  0  0
 42 21  1  0  0  0  0
M  END
> <DATABASE_ID>
MMDBc0004608

> <DATABASE_NAME>
MIME

> <SMILES>
[H][C@]1(CC(=O)C(C)(CC)C(=O)OC)CO[C@]2(CC3([H])O[C@]([H])(CCCCC)CC4=CC(O)=C(C(O)=O)C(O2)=C34)[C@]1([H])C

> <INCHI_IDENTIFIER>
InChI=1S/C29H40O9/c1-6-8-9-10-19-11-17-12-20(30)24(26(32)33)25-23(17)21(37-19)14-29(38-25)16(3)18(15-36-29)13-22(31)28(4,7-2)27(34)35-5/h12,16,18-19,21,30H,6-11,13-15H2,1-5H3,(H,32,33)/t16-,18+,19-,21?,28?,29+/m1/s1

> <INCHI_KEY>
KUPCHRRTAPZASB-YKVDFVGGSA-N

> <FORMULA>
C29H40O9

> <MOLECULAR_WEIGHT>
532.63

> <EXACT_MASS>
532.267232868

> <JCHEM_ACCEPTOR_COUNT>
8

> <JCHEM_ATOM_COUNT>
78

> <JCHEM_AVERAGE_POLARIZABILITY>
56.76496550857762

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2S,3R,4R,7'R)-4-(3-ethyl-4-methoxy-3-methyl-2,4-dioxobutyl)-11'-hydroxy-3-methyl-7'-pentyl-2',6'-dioxaspiro[oxolane-2,3'-tricyclo[7.3.1.0^{5,13}]tridecane]-1'(13'),9',11'-triene-12'-carboxylic acid

> <ALOGPS_LOGP>
4.22

> <JCHEM_LOGP>
6.73685213

> <ALOGPS_LOGS>
-5.36

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
4

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
13.335689063420851

> <JCHEM_PKA_STRONGEST_ACIDIC>
2.447646512503785

> <JCHEM_PKA_STRONGEST_BASIC>
-3.934644707336052

> <JCHEM_POLAR_SURFACE_AREA>
128.59

> <JCHEM_REFRACTIVITY>
138.56910000000005

> <JCHEM_ROTATABLE_BOND_COUNT>
11

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
2.31e-03 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(2S,3R,4R,7'R)-4-(3-ethyl-4-methoxy-3-methyl-2,4-dioxobutyl)-11'-hydroxy-3-methyl-7'-pentyl-2',6'-dioxaspiro[oxolane-2,3'-tricyclo[7.3.1.0^{5,13}]tridecane]-1'(13'),9',11'-triene-12'-carboxylic acid

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 15-MAY-21   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   15-MAY-21         0                                  
HETATM    1  C   UNK     0      -5.965   4.393   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      10.041   6.401   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       5.132   3.174   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      12.163   2.923   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      14.453   6.025   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      -4.886   3.295   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       9.787   4.882   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      -3.395   3.680   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      -2.316   2.582   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      -0.825   2.967   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      -0.157   0.385   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       0.510  -2.198   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       8.476   2.969   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       4.316   1.541   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       7.882   0.290   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       5.960   1.875   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       0.922  -0.714   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       7.497   1.781   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       0.254   1.869   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       1.589  -3.296   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0       2.825   1.155   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0       9.995   2.714   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0       2.413  -0.329   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0       3.080  -2.911   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0       3.492  -1.427   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0       4.160  -4.010   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0      11.955   5.091   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0      10.975   3.903   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0       5.395   0.442   0.000  0.00  0.00           C+0
HETATM   30  O   UNK     0       1.178  -4.780   0.000  0.00  0.00           O+0
HETATM   31  O   UNK     0      10.534   1.272   0.000  0.00  0.00           O+0
HETATM   32  O   UNK     0       5.651  -3.624   0.000  0.00  0.00           O+0
HETATM   33  O   UNK     0       3.748  -5.494   0.000  0.00  0.00           O+0
HETATM   34  O   UNK     0      11.416   6.533   0.000  0.00  0.00           O+0
HETATM   35  O   UNK     0      13.474   4.836   0.000  0.00  0.00           O+0
HETATM   36  O   UNK     0       6.583  -0.538   0.000  0.00  0.00           O+0
HETATM   37  O   UNK     0       1.745   2.254   0.000  0.00  0.00           O+0
HETATM   38  O   UNK     0       4.983  -1.042   0.000  0.00  0.00           O+0
HETATM   39  H   UNK     0       6.741   3.202   0.000  0.00  0.00           H+0
HETATM   40  H   UNK     0       9.000   1.447   0.000  0.00  0.00           H+0
HETATM   41  H   UNK     0       0.666   3.352   0.000  0.00  0.00           H+0
HETATM   42  H   UNK     0       3.904   0.057   0.000  0.00  0.00           H+0
CONECT    1    6                                                            
CONECT    2    7                                                            
CONECT    3   16                                                            
CONECT    4   28                                                            
CONECT    5   35                                                            
CONECT    6    1    8                                                       
CONECT    7    2   28                                                       
CONECT    8    6    9                                                       
CONECT    9    8   10                                                       
CONECT   10    9   19                                                       
CONECT   11   17   19                                                       
CONECT   12   17   20                                                       
CONECT   13   18   22                                                       
CONECT   14   21   29                                                       
CONECT   15   18   36                                                       
CONECT   16    3   18   29   39                                             
CONECT   17   11   12   23                                                  
CONECT   18   13   15   16   40                                             
CONECT   19   10   11   37   41                                             
CONECT   20   12   24   30                                                  
CONECT   21   14   23   37   42                                             
CONECT   22   13   28   31                                                  
CONECT   23   17   21   25                                                  
CONECT   24   20   25   26                                                  
CONECT   25   23   24   38                                                  
CONECT   26   24   32   33                                                  
CONECT   27   28   34   35                                                  
CONECT   28    4    7   22   27                                             
CONECT   29   14   16   36   38                                             
CONECT   30   20                                                            
CONECT   31   22                                                            
CONECT   32   26                                                            
CONECT   33   26                                                            
CONECT   34   27                                                            
CONECT   35    5   27                                                       
CONECT   36   15   29                                                       
CONECT   37   19   21                                                       
CONECT   38   25   29                                                       
CONECT   39   16                                                            
CONECT   40   18                                                            
CONECT   41   19                                                            
CONECT   42   21                                                            
MASTER        0    0    0    0    0    0    0    0   42    0   90    0
END

Synonyms

Value	Source
Berkelate	Generator

Molecular Formula

C₂₉H₄₀O₉

Average Mass

532.63

Monoisotopic Mass

532.267232868

IUPAC Name

(2S,3R,4R,7'R)-4-(3-ethyl-4-methoxy-3-methyl-2,4-dioxobutyl)-11'-hydroxy-3-methyl-7'-pentyl-2',6'-dioxaspiro[oxolane-2,3'-tricyclo[7.3.1.0^{5,13}]tridecane]-1'(13'),9',11'-triene-12'-carboxylic acid

Traditional Name

(2S,3R,4R,7'R)-4-(3-ethyl-4-methoxy-3-methyl-2,4-dioxobutyl)-11'-hydroxy-3-methyl-7'-pentyl-2',6'-dioxaspiro[oxolane-2,3'-tricyclo[7.3.1.0^{5,13}]tridecane]-1'(13'),9',11'-triene-12'-carboxylic acid

CAS Registry Number

Not Available

SMILES

[H][C@]1(CC(=O)C(C)(CC)C(=O)OC)CO[C@]2(CC3([H])O[C@]([H])(CCCCC)CC4=CC(O)=C(C(O)=O)C(O2)=C34)[C@]1([H])C

InChI Identifier

InChI=1S/C29H40O9/c1-6-8-9-10-19-11-17-12-20(30)24(26(32)33)25-23(17)21(37-19)14-29(38-25)16(3)18(15-36-29)13-22(31)28(4,7-2)27(34)35-5/h12,16,18-19,21,30H,6-11,13-15H2,1-5H3,(H,32,33)/t16-,18+,19-,21?,28?,29+/m1/s1

InChI Key

KUPCHRRTAPZASB-YKVDFVGGSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as salicylic acid and derivatives. Salicylic acid and derivatives are compounds containing a 2-hydroxybenzoic acid moiety or a derivative thereof.

Kingdom

Organic compounds

Super Class

Benzenoids

Class

Benzene and substituted derivatives

Sub Class

Benzoic acids and derivatives

Direct Parent

Salicylic acid and derivatives

Alternative Parents

Substituents

2-benzopyran
1-benzopyran
Salicylic acid or derivatives
Isochromane
Benzopyran
Chromane
1-hydroxy-2-unsubstituted benzenoid
Ketal
Fatty acid ester
Beta-keto acid
Fatty acyl
Keto acid
Dicarboxylic acid or derivatives
Vinylogous acid
Methyl ester
Tetrahydrofuran
Ketone
Carboxylic acid ester
Oxacycle
Organoheterocyclic compound
Ether
Dialkyl ether
Carboxylic acid
Carboxylic acid derivative
Acetal
Organic oxygen compound
Organic oxide
Hydrocarbon derivative
Organooxygen compound
Carbonyl group
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic heteropolycyclic compounds

External Descriptors

Not Available

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
Water Solubility	0.0023 g/L	ALOGPS
logP	4.22	ALOGPS
logP	6.74	ChemAxon
logS	-5.4	ALOGPS
pKa (Strongest Acidic)	2.45	ChemAxon
pKa (Strongest Basic)	-3.9	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	8	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	128.59 Å²	ChemAxon
Rotatable Bond Count	11	ChemAxon
Refractivity	138.57 m³·mol⁻¹	ChemAxon
Polarizability	56.76 Å³	ChemAxon
Number of Rings	4	ChemAxon
Bioavailability	No	ChemAxon
Rule of Five	No	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	Yes	ChemAxon

Spectra

Not Available

Chromatographic Retention Times and Retention Indices

Retention Times

Chromatography Type	Technique	Column	Deposition Date	Retention Time (s)
Liquid Chromatography	HILIC	Waters Acquity UPLC-BEH Amide column (eluted)	2025-10-23	145.6
Liquid Chromatography	HILIC	Accucore 150 Amide HILIC (eluted)	2025-10-23	38.1
Liquid Chromatography	Reversed-phase	Hypersil Gold 1.9 µm C18 (eluted)	2025-10-23	748.2
Liquid Chromatography	Reversed-phase	Agilent Zorbax Eclipse Plus C18 (2.1 mm x 150 mm, 3.5 um) (eluted)	2025-10-23	1070.8
Liquid Chromatography	Reversed-phase	XBridge C18 3.5u 2.1x50 mm (eluted)	2025-10-23	1062.4
Liquid Chromatography	Reversed-phase	Ascentis Express C18 (void)	2025-10-23	414.2
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC HSS T3 C18 (eluted)	2025-10-23	3725.6
Liquid Chromatography	HILIC	Merck SeQuant ZIC-HILIC (void)	2025-10-23	92.8
Liquid Chromatography	HILIC	Merck SeQuant ZIC-pHILIC (eluted)	2025-10-23	376.2
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC HSS T3 C18 (eluted)	2025-10-23	812.0
Liquid Chromatography	HILIC	Merck SeQuant ZIC-HILIC (void)	2025-10-23	364.5
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC HSS T3 C18 (eluted)	2025-10-23	186.6
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC BEH C18 (eluted)	2025-10-23	267.1
Liquid Chromatography	HILIC	Merck SeQuant ZIC-pHILIC column (void)	2025-10-23	8.7
Liquid Chromatography	HILIC	Merck SeQuant ZIC-pHILIC column (eluted)	2025-10-23	238.1
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC BEH C18 (eluted)	2025-10-23	300.8
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC BEH C18 (eluted)	2025-10-23	563.1
Liquid Chromatography	Reversed-phase	Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex (eluted)	2025-10-23	2121.0
Liquid Chromatography	Reversed-phase	Waters Atlantis T3 (2.1 x 150 mm, 5 um) (eluted)	2025-10-23	1825.3

Retention Indices

Chromatography Type	Peak Label	SMILES	Stationary Phase	Deposition Date	Retention Index
Gas Chromatography	Berkelic acid_TMS_1	CCCCC[C@@H]1CC2=CC(O[Si](C)(C)C)=C(C(=O)O)C3=C2C(C[C@]2(OC[C@H](CC(=O)C(C)(CC)C(=O)OC)[C@H]2C)O3)O1	standard non polar	2025-10-23	2446.34
Gas Chromatography	Berkelic acid_TMS_2	CCCCC[C@@H]1CC2=CC(O)=C(C(=O)O[Si](C)(C)C)C3=C2C(C[C@]2(OC[C@H](CC(=O)C(C)(CC)C(=O)OC)[C@H]2C)O3)O1	standard non polar	2025-10-23	1376.25
Gas Chromatography	Berkelic acid_TMS_3	CCCCC[C@@H]1CC2=CC(O)=C(C(=O)O)C3=C2C(C[C@]2(OC[C@H](C=C(O[Si](C)(C)C)C(C)(CC)C(=O)OC)[C@H]2C)O3)O1	standard non polar	2025-10-23	2852.94
Gas Chromatography	Berkelic acid_TMS_4	CCCCC[C@@H]1CC2=CC(O[Si](C)(C)C)=C(C(=O)O[Si](C)(C)C)C3=C2C(C[C@]2(OC[C@H](CC(=O)C(C)(CC)C(=O)OC)[C@H]2C)O3)O1	standard non polar	2025-10-23	1682.32
Gas Chromatography	Berkelic acid_TMS_5	CCCCC[C@@H]1CC2=CC(O[Si](C)(C)C)=C(C(=O)O)C3=C2C(C[C@]2(OC[C@H](C=C(O[Si](C)(C)C)C(C)(CC)C(=O)OC)[C@H]2C)O3)O1	standard non polar	2025-10-23	1461.55
Gas Chromatography	Berkelic acid_TMS_6	CCCCC[C@@H]1CC2=CC(O)=C(C(=O)O[Si](C)(C)C)C3=C2C(C[C@]2(OC[C@H](C=C(O[Si](C)(C)C)C(C)(CC)C(=O)OC)[C@H]2C)O3)O1	standard non polar	2025-10-23	2436.97
Gas Chromatography	Berkelic acid_TMS_7	CCCCC[C@@H]1CC2=CC(O[Si](C)(C)C)=C(C(=O)O[Si](C)(C)C)C3=C2C(C[C@]2(OC[C@H](C=C(O[Si](C)(C)C)C(C)(CC)C(=O)OC)[C@H]2C)O3)O1	standard non polar	2025-10-23	1628.86
Gas Chromatography	Berkelic acid_TMS_1	CCCCC[C@@H]1CC2=CC(O[Si](C)(C)C)=C(C(=O)O)C3=C2C(C[C@]2(OC[C@H](CC(=O)C(C)(CC)C(=O)OC)[C@H]2C)O3)O1	standard polar	2025-10-23	2747.75
Gas Chromatography	Berkelic acid_TMS_2	CCCCC[C@@H]1CC2=CC(O)=C(C(=O)O[Si](C)(C)C)C3=C2C(C[C@]2(OC[C@H](CC(=O)C(C)(CC)C(=O)OC)[C@H]2C)O3)O1	standard polar	2025-10-23	2242.4
Gas Chromatography	Berkelic acid_TMS_3	CCCCC[C@@H]1CC2=CC(O)=C(C(=O)O)C3=C2C(C[C@]2(OC[C@H](C=C(O[Si](C)(C)C)C(C)(CC)C(=O)OC)[C@H]2C)O3)O1	standard polar	2025-10-23	2092.66
Gas Chromatography	Berkelic acid_TMS_4	CCCCC[C@@H]1CC2=CC(O[Si](C)(C)C)=C(C(=O)O[Si](C)(C)C)C3=C2C(C[C@]2(OC[C@H](CC(=O)C(C)(CC)C(=O)OC)[C@H]2C)O3)O1	standard polar	2025-10-23	1998.1
Gas Chromatography	Berkelic acid_TMS_5	CCCCC[C@@H]1CC2=CC(O[Si](C)(C)C)=C(C(=O)O)C3=C2C(C[C@]2(OC[C@H](C=C(O[Si](C)(C)C)C(C)(CC)C(=O)OC)[C@H]2C)O3)O1	standard polar	2025-10-23	1905.89
Gas Chromatography	Berkelic acid_TMS_6	CCCCC[C@@H]1CC2=CC(O)=C(C(=O)O[Si](C)(C)C)C3=C2C(C[C@]2(OC[C@H](C=C(O[Si](C)(C)C)C(C)(CC)C(=O)OC)[C@H]2C)O3)O1	standard polar	2025-10-23	1862.24
Gas Chromatography	Berkelic acid_TMS_7	CCCCC[C@@H]1CC2=CC(O[Si](C)(C)C)=C(C(=O)O[Si](C)(C)C)C3=C2C(C[C@]2(OC[C@H](C=C(O[Si](C)(C)C)C(C)(CC)C(=O)OC)[C@H]2C)O3)O1	standard polar	2025-10-23	2749.65

Biological Properties

Cellular Locations

Not Available

Biospecimen Locations

Not Available

Tissue Locations

Not Available

Associated OMIM IDs

114500 (Colorectal cancer)
610247 (Eosinophilic esophagitis)

Human Proteins and Enzymes

Protein ID	Protein Name	Protein Type	Uniprot ID	Species

Human Pathways

Pathways

Name	SMPDB/PathBank

Microbial Pathways

Pathways

Not Available

Metabolic Reactions

Reactions

This table shows at most 20 reactions. For the full list of associated reactions:

See All Associated Reactions

Reaction ID	Precursor	Product	Enzyme	Reaction Type	Data Source	Reference

Health Effects and Bioactivity

Health Outcome/Bioactivity	Metabolite Response/Effect	Evidence Type	Host and Biospecimen	Data Source	Reference

Microbial Sources

Superkingdom/Kingdom	Phylum	Total species	Hosts and Body Sites	Microbial Links
Eukaryota/Fungi	Ascomycota	1	Human feces	Metabolic reconstruction

Exposure Sources

Other Exposures

Source Type	Data Source	Reference

Host Biospecimen and Location

Host and Biospecimen	Status	Mean	Std	Min	Max	Units	Age	Sex	Health Condition	Data Source	Reference

External Links

HMDB ID

Not Available

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

Not Available

KNApSAcK ID

Not Available

Chemspider ID

78436691

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Berkelic acid

METLIN ID

Not Available

PubChem Compound

139584175

PDB ID

Not Available

ChEBI ID

Not Available

Food Biomarker Ontology

Not Available

CMMC Knowledgebase

Not Available

General References

van Santen JA, Poynton EF, Iskakova D, McMann E, Alsup TA, Clark TN, Fergusson CH, Fewer DP, Hughes AH, McCadden CA, Parra J, Soldatou S, Rudolf JD, Janssen EM, Duncan KR, Linington RG: The Natural Products Atlas 2.0: a database of microbially-derived natural products. Nucleic Acids Res. 2022 Jan 7;50(D1):D1317-D1323. doi: 10.1093/nar/gkab941. [PubMed:34718710 ]

Showing metabocard for Berkelic acid (MMDBc0004608)

MOL for #<Metabolite:0x00007f9aa2c6f590>

3D MOL for #<Metabolite:0x00007f9aa2c6f590>

3D SDF for #<Metabolite:0x00007f9aa2c6f590>

3D-SDF for #<Metabolite:0x00007f9aa2c6f590>

PDB for #<Metabolite:0x00007f9aa2c6f590>

3D PDB for #<Metabolite:0x00007f9aa2c6f590>

SMILES for #<Metabolite:0x00007f9aa2c6f590>

INCHI for #<Metabolite:0x00007f9aa2c6f590>

Structure for #<Metabolite:0x00007f9aa2c6f590>

3D Structure for #<Metabolite:0x00007f9aa2c6f590>