NP-MRD: Showing NP-Card for Crocin 4 (NP0049308)

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Record Information

Version

2.0

Created at

2022-03-17 21:10:24 UTC

Updated at

2022-03-17 21:10:25 UTC

NP-MRD ID

NP0049308

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Crocin 4

Description

Crocin 4, also known as macrocin, belongs to the class of organic compounds known as diterpenoids. These are terpene compounds formed by four isoprene units. Crocin 4 is an extremely weak basic (essentially neutral) compound (based on its pKa). Outside of the human body, Crocin 4 has been detected, but not quantified in, herbs and spices and saffrons. Crocin 4 is found in Streptomyces fradiae. This could make crocin 4 a potential biomarker for the consumption of these foods.

Structure

MOL SDF PDB SMILES InChI


  Mrv0541 05061310522D          

 36 36  0  0  0  0            999 V2000
   -3.5724   -3.7125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145   -5.3625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.1447   -2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -2.8875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.1447   -4.9500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5724   -5.3625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8579   -4.9500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0013   -2.8875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145   -3.7125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2868   -4.9500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1434   -5.3625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0013   -3.7125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4289   -4.1250    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
   -0.7145   -2.8875    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
   -4.2868   -4.1250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4289   -4.9500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.4302   -2.8875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000   -2.4750    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
    0.0000    0.8250    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
   -6.4302   -3.7125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000   -1.6500    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 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    2.0625    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145    1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145   -0.4125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.7158   -4.1250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145   -1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -7.1447   -4.1250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  7  6  2  0  0  0  0
 10  6  1  0  0  0  0
 11  7  1  0  0  0  0
 12  8  2  0  0  0  0
 13  9  2  0  0  0  0
 14  8  1  0  0  0  0
 15  9  1  0  0  0  0
 17  1  1  0  0  0  0
 17 10  2  0  0  0  0
 17 12  1  0  0  0  0
 18  2  1  0  0  0  0
 18 11  2  0  0  0  0
 18 13  1  0  0  0  0
 19  3  1  0  0  0  0
 19 14  2  0  0  0  0
 20  4  1  0  0  0  0
 20 15  2  0  0  0  0
 21 16  1  0  0  0  0
 22 21  1  0  0  0  0
 23 22  1  0  0  0  0
 24 23  1  0  0  0  0
 25 19  1  0  0  0  0
 26 20  1  0  0  0  0
 27 24  1  0  0  0  0
 28 16  1  0  0  0  0
 29 22  1  0  0  0  0
 30 23  1  0  0  0  0
 31 24  1  0  0  0  0
 32 25  2  0  0  0  0
 33 26  2  0  0  0  0
 34  5  1  0  0  0  0
 34 25  1  0  0  0  0
 35 21  1  0  0  0  0
 35 27  1  0  0  0  0
 36 26  1  0  0  0  0
 36 27  1  0  0  0  0
M  END


  Mrv0541 05061310522D          

 36 36  0  0  0  0            999 V2000
   -3.5724   -3.7125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145   -5.3625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.1447   -2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -2.8875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.1447   -4.9500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5724   -5.3625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8579   -4.9500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0013   -2.8875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145   -3.7125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2868   -4.9500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1434   -5.3625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0013   -3.7125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4289   -4.1250    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
   -0.7145   -2.8875    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
   -4.2868   -4.1250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4289   -4.9500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.4302   -2.8875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000   -2.4750    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
    0.0000    0.8250    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
   -6.4302   -3.7125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000   -1.6500    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 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    2.0625    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145    1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145   -0.4125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.7158   -4.1250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145   -1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -7.1447   -4.1250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  7  6  2  0  0  0  0
 10  6  1  0  0  0  0
 11  7  1  0  0  0  0
 12  8  2  0  0  0  0
 13  9  2  0  0  0  0
 14  8  1  0  0  0  0
 15  9  1  0  0  0  0
 17  1  1  0  0  0  0
 17 10  2  0  0  0  0
 17 12  1  0  0  0  0
 18  2  1  0  0  0  0
 18 11  2  0  0  0  0
 18 13  1  0  0  0  0
 19  3  1  0  0  0  0
 19 14  2  0  0  0  0
 20  4  1  0  0  0  0
 20 15  2  0  0  0  0
 21 16  1  0  0  0  0
 22 21  1  0  0  0  0
 23 22  1  0  0  0  0
 24 23  1  0  0  0  0
 25 19  1  0  0  0  0
 26 20  1  0  0  0  0
 27 24  1  0  0  0  0
 28 16  1  0  0  0  0
 29 22  1  0  0  0  0
 30 23  1  0  0  0  0
 31 24  1  0  0  0  0
 32 25  2  0  0  0  0
 33 26  2  0  0  0  0
 34  5  1  0  0  0  0
 34 25  1  0  0  0  0
 35 21  1  0  0  0  0
 35 27  1  0  0  0  0
 36 26  1  0  0  0  0
 36 27  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0049308

> <DATABASE_NAME>
NP-MRD

> <SMILES>
COC(=O)C(\C)=C/C=C/C(/C)=C/C=C/C=C(/C)\C=C\C=C(/C)C(=O)OC1OC(CO)C(O)C(O)C1O

> <INCHI_IDENTIFIER>
InChI=1S/C27H36O9/c1-17(12-8-14-19(3)25(32)34-5)10-6-7-11-18(2)13-9-15-20(4)26(33)36-27-24(31)23(30)22(29)21(16-28)35-27/h6-15,21-24,27-31H,16H2,1-5H3/b7-6+,12-8+,13-9+,17-10+,18-11-,19-14-,20-15+

> <INCHI_KEY>
ATQIQIBBBWQWOT-QNFREAFUSA-N

> <FORMULA>
C27H36O9

> <MOLECULAR_WEIGHT>
504.5693

> <EXACT_MASS>
504.23593275

> <JCHEM_ACCEPTOR_COUNT>
7

> <JCHEM_AVERAGE_POLARIZABILITY>
56.202251173113396

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
1-methyl 3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl (2Z,4E,6E,8E,10Z,12E,14E)-2,6,11,15-tetramethylhexadeca-2,4,6,8,10,12,14-heptaenedioate

> <ALOGPS_LOGP>
3.19

> <JCHEM_LOGP>
2.744695860000001

> <ALOGPS_LOGS>
-4.36

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
13.194438899493232

> <JCHEM_PKA_STRONGEST_ACIDIC>
12.195723003642504

> <JCHEM_PKA_STRONGEST_BASIC>
-2.9810938228983064

> <JCHEM_POLAR_SURFACE_AREA>
142.75

> <JCHEM_REFRACTIVITY>
140.99710000000005

> <JCHEM_ROTATABLE_BOND_COUNT>
12

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
2.21e-02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
1-methyl 3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl (2Z,4E,6E,8E,10Z,12E,14E)-2,6,11,15-tetramethylhexadeca-2,4,6,8,10,12,14-heptaenedioate

> <JCHEM_VEBER_RULE>
0

$$$$

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      -6.668  -6.930   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -1.334 -10.010   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0     -13.337  -4.620   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       1.334  -5.390   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0     -13.337  -9.240   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      -6.668 -10.010   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      -5.335  -9.240   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      -9.336  -5.390   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      -1.334  -6.930   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      -8.002  -9.240   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      -4.001 -10.010   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      -9.336  -6.930   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      -2.667  -7.700   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0     -10.669  -4.620   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0      -1.334  -5.390   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       4.001   2.310   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0      -8.002  -7.700   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0      -2.667  -9.240   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0     -12.003  -5.390   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       0.000  -4.620   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0       2.667   1.540   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0       1.334   2.310   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0       0.000   1.540   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0     -12.003  -6.930   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0       0.000  -3.080   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM   28  O   UNK     0       4.001   3.850   0.000  0.00  0.00           O+0
HETATM   29  O   UNK     0       1.334   3.850   0.000  0.00  0.00           O+0
HETATM   30  O   UNK     0      -1.334   2.310   0.000  0.00  0.00           O+0
HETATM   31  O   UNK     0      -1.334  -0.770   0.000  0.00  0.00           O+0
HETATM   32  O   UNK     0     -10.669  -7.700   0.000  0.00  0.00           O+0
HETATM   33  O   UNK     0      -1.334  -2.310   0.000  0.00  0.00           O+0
HETATM   34  O   UNK     0     -13.337  -7.700   0.000  0.00  0.00           O+0
HETATM   35  O   UNK     0       2.667   0.000   0.000  0.00  0.00           O+0
HETATM   36  O   UNK     0       1.334  -2.310   0.000  0.00  0.00           O+0
CONECT    1   17                                                            
CONECT    2   18                                                            
CONECT    3   19                                                            
CONECT    4   20                                                            
CONECT    5   34                                                            
CONECT    6    7   10                                                       
CONECT    7    6   11                                                       
CONECT    8   12   14                                                       
CONECT    9   13   15                                                       
CONECT   10    6   17                                                       
CONECT   11    7   18                                                       
CONECT   12    8   17                                                       
CONECT   13    9   18                                                       
CONECT   14    8   19                                                       
CONECT   15    9   20                                                       
CONECT   16   21   28                                                       
CONECT   17    1   10   12                                                  
CONECT   18    2   11   13                                                  
CONECT   19    3   14   25                                                  
CONECT   20    4   15   26                                                  
CONECT   21   16   22   35                                                  
CONECT   22   21   23   29                                                  
CONECT   23   22   24   30                                                  
CONECT   24   23   27   31                                                  
CONECT   25   19   32   34                                                  
CONECT   26   20   33   36                                                  
CONECT   27   24   35   36                                                  
CONECT   28   16                                                            
CONECT   29   22                                                            
CONECT   30   23                                                            
CONECT   31   24                                                            
CONECT   32   25                                                            
CONECT   33   26                                                            
CONECT   34    5   25                                                       
CONECT   35   21   27                                                       
CONECT   36   26   27                                                       
MASTER        0    0    0    0    0    0    0    0   36    0   72    0
END

View in JSmol

Synonyms

Value	Source
Macrocin	HMDB
1-Methyl 3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl (2Z,6E,8E,10Z,12E,14E)-2,6,11,15-tetramethylhexadeca-2,4,6,8,10,12,14-heptaenedioic acid	Generator

Chemical Formula

C₂₇H₃₆O₉

Average Mass

504.5693 Da

Monoisotopic Mass

504.23593 Da

IUPAC Name

1-methyl 3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl (2Z,4E,6E,8E,10Z,12E,14E)-2,6,11,15-tetramethylhexadeca-2,4,6,8,10,12,14-heptaenedioate

Traditional Name

1-methyl 3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl (2Z,4E,6E,8E,10Z,12E,14E)-2,6,11,15-tetramethylhexadeca-2,4,6,8,10,12,14-heptaenedioate

CAS Registry Number

55750-86-2

SMILES

COC(=O)C(\C)=C/C=C/C(/C)=C/C=C/C=C(/C)\C=C\C=C(/C)C(=O)OC1OC(CO)C(O)C(O)C1O

InChI Identifier

InChI=1S/C27H36O9/c1-17(12-8-14-19(3)25(32)34-5)10-6-7-11-18(2)13-9-15-20(4)26(33)36-27-24(31)23(30)22(29)21(16-28)35-27/h6-15,21-24,27-31H,16H2,1-5H3/b7-6+,12-8+,13-9+,17-10+,18-11-,19-14-,20-15+

InChI Key

ATQIQIBBBWQWOT-QNFREAFUSA-N

Experimental Spectra

Not Available

Predicted Spectra

Not Available

Chemical Shift Submissions

Not Available

Species

Species of Origin

Species Name	Source	Reference
Crocus sativus	FooDB	Dr. Duke's Phytochemical and Ethnobotanical Databases
Streptomyces fradiae	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as diterpenoids. These are terpene compounds formed by four isoprene units.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Prenol lipids

Sub Class

Diterpenoids

Direct Parent

Diterpenoids

Alternative Parents

Substituents

Diterpenoid
Hexose monosaccharide
Fatty acid ester
Dicarboxylic acid or derivatives
Monosaccharide
Oxane
Fatty acyl
Enoate ester
Methyl ester
Alpha,beta-unsaturated carboxylic ester
Secondary alcohol
Carboxylic acid ester
Oxacycle
Organoheterocyclic compound
Carboxylic acid derivative
Polyol
Acetal
Organic oxygen compound
Carbonyl group
Primary alcohol
Organic oxide
Hydrocarbon derivative
Alcohol
Organooxygen compound
Aliphatic heteromonocyclic compound

Molecular Framework

Aliphatic heteromonocyclic compounds

External Descriptors

Not Available

Physical Properties

State

Not Available

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
logP	3.19	ALOGPS
logP	2.74	ChemAxon
logS	-4.4	ALOGPS
pKa (Strongest Acidic)	12.2	ChemAxon
pKa (Strongest Basic)	-3	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	7	ChemAxon
Hydrogen Donor Count	4	ChemAxon
Polar Surface Area	142.75 Å²	ChemAxon
Rotatable Bond Count	12	ChemAxon
Refractivity	141 m³·mol⁻¹	ChemAxon
Polarizability	56.2 Å³	ChemAxon
Number of Rings	1	ChemAxon
Bioavailability	No	ChemAxon
Rule of Five	No	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

External Links

HMDB ID

HMDB0039122

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

FDB018632

KNApSAcK ID

Not Available

Chemspider ID

Not Available

KEGG Compound ID

C00744

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

131752554

PDB ID

Not Available

ChEBI ID

17371

Good Scents ID

Not Available

References

General References

Showing NP-Card for Crocin 4 (NP0049308)

MOL for NP0049308 (Crocin 4)

3D MOL for NP0049308 (Crocin 4)

3D SDF for NP0049308 (Crocin 4)

3D-SDF for NP0049308 (Crocin 4)

PDB for NP0049308 (Crocin 4)

3D PDB for NP0049308 (Crocin 4)

SMILES for NP0049308 (Crocin 4)

INCHI for NP0049308 (Crocin 4)

Structure for NP0049308 (Crocin 4)

3D Structure for NP0049308 (Crocin 4)