Np mrd loader

Showing NP-Card for alpha-Crocin (NP0333972)

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Record Information
Version2.0
Created at2024-09-09 21:29:57 UTC
Updated at2024-09-09 21:29:58 UTC
NP-MRD IDNP0333972
Secondary Accession NumbersNone
Natural Product Identification
Common Namealpha-Crocin
DescriptionThe colouring principle of saffron Crocin is a natural carotenoid chemical compound that is found in the flowers crocus and gardenia. It is the diester formed from the disaccharide gentiobiose and the dicarboxylic acid crocetin.
Structure
Thumb
MOLSDFPDBSMILESInChI

MOL for NP0333972 (alpha-Crocin)


  Mrv2104 05252300022D          

 78 81  0  0  0  0            999 V2000
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M  END
Download

3D MOL for NP0333972 (alpha-Crocin)

Download
3D SDF for NP0333972 (alpha-Crocin)

  Mrv2104 05252300022D          

 78 81  0  0  0  0            999 V2000
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  8 72  1  0  0  0  0
  8 12  2  0  0  0  0
  8 14  1  0  0  0  0
  9 73  1  0  0  0  0
  9 19  2  0  0  0  0
 10 74  1  0  0  0  0
 10 20  2  0  0  0  0
 11 75  1  0  0  0  0
 11 19  1  0  0  0  0
 12 76  1  0  0  0  0
 12 20  1  0  0  0  0
 13 77  1  0  0  0  0
 13 21  2  0  0  0  0
 14 78  1  0  0  0  0
 14 22  2  0  0  0  0
 15 23  1  0  0  0  0
 15 45  1  0  0  0  0
 16 24  1  0  0  0  0
 16 46  1  0  0  0  0
 17 25  1  0  0  0  0
 17 61  1  0  0  0  0
 18 26  1  0  0  0  0
 18 62  1  0  0  0  0
 21 39  1  0  0  0  0
 22 40  1  0  0  0  0
 23 27  1  0  0  0  0
 23 63  1  0  0  0  0
 24 28  1  0  0  0  0
 24 64  1  0  0  0  0
 25 29  1  0  0  0  0
 25 65  1  0  0  0  0
 26 30  1  0  0  0  0
 26 66  1  0  0  0  0
 27 31  1  0  0  0  0
 27 47  1  0  0  0  0
 28 32  1  0  0  0  0
 28 48  1  0  0  0  0
 29 33  1  0  0  0  0
 29 49  1  0  0  0  0
 30 34  1  0  0  0  0
 30 50  1  0  0  0  0
 31 35  1  0  0  0  0
 31 51  1  0  0  0  0
 32 36  1  0  0  0  0
 32 52  1  0  0  0  0
 33 37  1  0  0  0  0
 33 53  1  0  0  0  0
 34 38  1  0  0  0  0
 34 54  1  0  0  0  0
 35 41  1  0  0  0  0
 35 55  1  0  0  0  0
 36 42  1  0  0  0  0
 36 56  1  0  0  0  0
 37 43  1  0  0  0  0
 37 57  1  0  0  0  0
 38 44  1  0  0  0  0
 38 58  1  0  0  0  0
 39 59  2  0  0  0  0
 39 67  1  0  0  0  0
 40 60  2  0  0  0  0
 40 68  1  0  0  0  0
 41 61  1  0  0  0  0
 41 63  1  0  0  0  0
 42 62  1  0  0  0  0
 42 64  1  0  0  0  0
 43 65  1  0  0  0  0
 43 67  1  0  0  0  0
 44 66  1  0  0  0  0
 44 68  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0333972

> <DATABASE_NAME>
NP-MRD

> <SMILES>
[H]\C(=C(\[H])/C(/[H])=C(/C)\C(\[H])=C(/[H])\C(\[H])=C(/C)C(=O)OC1OC(COC2OC(CO)C(O)C(O)C2O)C(O)C(O)C1O)\C(\[H])=C(/C)C([H])=C([H])C(\[H])=C(\C)C(=O)OC1OC(COC2OC(CO)C(O)C(O)C2O)C(O)C(O)C1O

> <INCHI_IDENTIFIER>
InChI=1/C44H64O24/c1-19(11-7-13-21(3)39(59)67-43-37(57)33(53)29(49)25(65-43)17-61-41-35(55)31(51)27(47)23(15-45)63-41)9-5-6-10-20(2)12-8-14-22(4)40(60)68-44-38(58)34(54)30(50)26(66-44)18-62-42-36(56)32(52)28(48)24(16-46)64-42/h5-14,23-38,41-58H,15-18H2,1-4H3/b6-5+,11-7+,12-8+,19-9-,20-10+,21-13+,22-14-

> <INCHI_KEY>
SEBIKDIMAPSUBY-WOPHWFRHNA-N

> <FORMULA>
C44H64O24

> <MOLECULAR_WEIGHT>
976.972

> <EXACT_MASS>
976.378752941

> <JCHEM_ACCEPTOR_COUNT>
22

> <JCHEM_ATOM_COUNT>
132

> <JCHEM_AVERAGE_POLARIZABILITY>
100.9849548258299

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
14

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
bis[3,4,5-trihydroxy-6-({[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}methyl)oxan-2-yl] (2Z,6E,8E,10Z,12E,14E)-2,6,11,15-tetramethylhexadeca-2,4,6,8,10,12,14-heptaenedioate

> <JCHEM_LOGP>
-3.210937580666667

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
4

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
12.088030392139236

> <JCHEM_PKA_STRONGEST_ACIDIC>
11.668685014311508

> <JCHEM_PKA_STRONGEST_BASIC>
-3.6786130721304944

> <JCHEM_POLAR_SURFACE_AREA>
391.2000000000001

> <JCHEM_REFRACTIVITY>
233.48580000000015

> <JCHEM_ROTATABLE_BOND_COUNT>
20

> <JCHEM_RULE_OF_FIVE>
0

> <JCHEM_TRADITIONAL_IUPAC>
bis[3,4,5-trihydroxy-6-({[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}methyl)oxan-2-yl] (2Z,6E,8E,10Z,12E,14E)-2,6,11,15-tetramethylhexadeca-2,4,6,8,10,12,14-heptaenedioate

> <JCHEM_VEBER_RULE>
0

$$$$

Download
3D-SDF for NP0333972 (alpha-Crocin)
Download
PDB for NP0333972 (alpha-Crocin)
HEADER    PROTEIN                                 25-MAY-23   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   25-MAY-23         0                                  
HETATM    1  C   UNK     0       6.668 -23.870   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      12.003 -30.030   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       8.002 -16.940   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      17.338 -30.030   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       9.336 -25.410   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      10.669 -26.180   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       9.336 -20.790   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      14.670 -28.490   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       9.336 -23.870   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      10.669 -27.720   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       8.002 -21.560   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      13.337 -27.720   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       9.336 -19.250   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      16.004 -27.720   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0      12.003 -10.010   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0      21.339 -18.480   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       8.002 -13.860   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0      22.673 -23.870   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       8.002 -23.100   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0      12.003 -28.490   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0       8.002 -18.480   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0      17.338 -28.490   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0      12.003 -11.550   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0      22.673 -19.250   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0       6.668 -14.630   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0      22.673 -25.410   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0      13.337 -12.320   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0      24.006 -18.480   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0       5.335 -13.860   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0      24.006 -26.180   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0      13.337 -13.860   0.000  0.00  0.00           C+0
HETATM   32  C   UNK     0      25.340 -19.250   0.000  0.00  0.00           C+0
HETATM   33  C   UNK     0       4.001 -14.630   0.000  0.00  0.00           C+0
HETATM   34  C   UNK     0      24.006 -27.720   0.000  0.00  0.00           C+0
HETATM   35  C   UNK     0      12.003 -14.630   0.000  0.00  0.00           C+0
HETATM   36  C   UNK     0      25.340 -20.790   0.000  0.00  0.00           C+0
HETATM   37  C   UNK     0       4.001 -16.170   0.000  0.00  0.00           C+0
HETATM   38  C   UNK     0      22.673 -28.490   0.000  0.00  0.00           C+0
HETATM   39  C   UNK     0       6.668 -19.250   0.000  0.00  0.00           C+0
HETATM   40  C   UNK     0      18.672 -27.720   0.000  0.00  0.00           C+0
HETATM   41  C   UNK     0      10.669 -13.860   0.000  0.00  0.00           C+0
HETATM   42  C   UNK     0      24.006 -21.560   0.000  0.00  0.00           C+0
HETATM   43  C   UNK     0       5.335 -16.940   0.000  0.00  0.00           C+0
HETATM   44  C   UNK     0      21.339 -27.720   0.000  0.00  0.00           C+0
HETATM   45  O   UNK     0      13.337  -9.240   0.000  0.00  0.00           O+0
HETATM   46  O   UNK     0      21.339 -16.940   0.000  0.00  0.00           O+0
HETATM   47  O   UNK     0      14.670 -11.550   0.000  0.00  0.00           O+0
HETATM   48  O   UNK     0      24.006 -16.940   0.000  0.00  0.00           O+0
HETATM   49  O   UNK     0       5.335 -12.320   0.000  0.00  0.00           O+0
HETATM   50  O   UNK     0      25.340 -25.410   0.000  0.00  0.00           O+0
HETATM   51  O   UNK     0      14.670 -14.630   0.000  0.00  0.00           O+0
HETATM   52  O   UNK     0      26.674 -18.480   0.000  0.00  0.00           O+0
HETATM   53  O   UNK     0       2.667 -13.860   0.000  0.00  0.00           O+0
HETATM   54  O   UNK     0      25.340 -28.490   0.000  0.00  0.00           O+0
HETATM   55  O   UNK     0      12.003 -16.170   0.000  0.00  0.00           O+0
HETATM   56  O   UNK     0      26.674 -21.560   0.000  0.00  0.00           O+0
HETATM   57  O   UNK     0       2.667 -16.940   0.000  0.00  0.00           O+0
HETATM   58  O   UNK     0      22.673 -30.030   0.000  0.00  0.00           O+0
HETATM   59  O   UNK     0       6.668 -20.790   0.000  0.00  0.00           O+0
HETATM   60  O   UNK     0      18.672 -26.180   0.000  0.00  0.00           O+0
HETATM   61  O   UNK     0       9.336 -14.630   0.000  0.00  0.00           O+0
HETATM   62  O   UNK     0      24.006 -23.100   0.000  0.00  0.00           O+0
HETATM   63  O   UNK     0      10.669 -12.320   0.000  0.00  0.00           O+0
HETATM   64  O   UNK     0      22.673 -20.790   0.000  0.00  0.00           O+0
HETATM   65  O   UNK     0       6.668 -16.170   0.000  0.00  0.00           O+0
HETATM   66  O   UNK     0      21.339 -26.180   0.000  0.00  0.00           O+0
HETATM   67  O   UNK     0       5.335 -18.480   0.000  0.00  0.00           O+0
HETATM   68  O   UNK     0      20.005 -28.490   0.000  0.00  0.00           O+0
HETATM   69  H   UNK     0       8.002 -26.180   0.000  0.00  0.00           H+0
HETATM   70  H   UNK     0      12.003 -25.410   0.000  0.00  0.00           H+0
HETATM   71  H   UNK     0      10.669 -21.560   0.000  0.00  0.00           H+0
HETATM   72  H   UNK     0      14.670 -30.030   0.000  0.00  0.00           H+0
HETATM   73  H   UNK     0      10.669 -23.100   0.000  0.00  0.00           H+0
HETATM   74  H   UNK     0       9.336 -28.490   0.000  0.00  0.00           H+0
HETATM   75  H   UNK     0       6.668 -22.330   0.000  0.00  0.00           H+0
HETATM   76  H   UNK     0      13.337 -26.180   0.000  0.00  0.00           H+0
HETATM   77  H   UNK     0      10.669 -18.480   0.000  0.00  0.00           H+0
HETATM   78  H   UNK     0      16.004 -26.180   0.000  0.00  0.00           H+0
CONECT    1   19                                                            
CONECT    2   20                                                            
CONECT    3   21                                                            
CONECT    4   22                                                            
CONECT    5   69    6    9                                                  
CONECT    6    5   70   10                                                  
CONECT    7   71   11   13                                                  
CONECT    8   72   12   14                                                  
CONECT    9    5   73   19                                                  
CONECT   10    6   74   20                                                  
CONECT   11    7   75   19                                                  
CONECT   12    8   76   20                                                  
CONECT   13    7   77   21                                                  
CONECT   14    8   78   22                                                  
CONECT   15   23   45                                                       
CONECT   16   24   46                                                       
CONECT   17   25   61                                                       
CONECT   18   26   62                                                       
CONECT   19    1    9   11                                                  
CONECT   20    2   10   12                                                  
CONECT   21    3   13   39                                                  
CONECT   22    4   14   40                                                  
CONECT   23   15   27   63                                                  
CONECT   24   16   28   64                                                  
CONECT   25   17   29   65                                                  
CONECT   26   18   30   66                                                  
CONECT   27   23   31   47                                                  
CONECT   28   24   32   48                                                  
CONECT   29   25   33   49                                                  
CONECT   30   26   34   50                                                  
CONECT   31   27   35   51                                                  
CONECT   32   28   36   52                                                  
CONECT   33   29   37   53                                                  
CONECT   34   30   38   54                                                  
CONECT   35   31   41   55                                                  
CONECT   36   32   42   56                                                  
CONECT   37   33   43   57                                                  
CONECT   38   34   44   58                                                  
CONECT   39   21   59   67                                                  
CONECT   40   22   60   68                                                  
CONECT   41   35   61   63                                                  
CONECT   42   36   62   64                                                  
CONECT   43   37   65   67                                                  
CONECT   44   38   66   68                                                  
CONECT   45   15                                                            
CONECT   46   16                                                            
CONECT   47   27                                                            
CONECT   48   28                                                            
CONECT   49   29                                                            
CONECT   50   30                                                            
CONECT   51   31                                                            
CONECT   52   32                                                            
CONECT   53   33                                                            
CONECT   54   34                                                            
CONECT   55   35                                                            
CONECT   56   36                                                            
CONECT   57   37                                                            
CONECT   58   38                                                            
CONECT   59   39                                                            
CONECT   60   40                                                            
CONECT   61   17   41                                                       
CONECT   62   18   42                                                       
CONECT   63   23   41                                                       
CONECT   64   24   42                                                       
CONECT   65   25   43                                                       
CONECT   66   26   44                                                       
CONECT   67   39   43                                                       
CONECT   68   40   44                                                       
CONECT   69    5                                                            
CONECT   70    6                                                            
CONECT   71    7                                                            
CONECT   72    8                                                            
CONECT   73    9                                                            
CONECT   74   10                                                            
CONECT   75   11                                                            
CONECT   76   12                                                            
CONECT   77   13                                                            
CONECT   78   14                                                            
MASTER        0    0    0    0    0    0    0    0   78    0  162    0
END

Download
3D PDB for NP0333972 (alpha-Crocin)
Download
SMILES for NP0333972 (alpha-Crocin)
[H]\C(=C(\[H])/C(/[H])=C(/C)\C(\[H])=C(/[H])\C(\[H])=C(/C)C(=O)OC1OC(COC2OC(CO)C(O)C(O)C2O)C(O)C(O)C1O)\C(\[H])=C(/C)C([H])=C([H])C(\[H])=C(\C)C(=O)OC1OC(COC2OC(CO)C(O)C(O)C2O)C(O)C(O)C1O
Download
INCHI for NP0333972 (alpha-Crocin)
InChI=1/C44H64O24/c1-19(11-7-13-21(3)39(59)67-43-37(57)33(53)29(49)25(65-43)17-61-41-35(55)31(51)27(47)23(15-45)63-41)9-5-6-10-20(2)12-8-14-22(4)40(60)68-44-38(58)34(54)30(50)26(66-44)18-62-42-36(56)32(52)28(48)24(16-46)64-42/h5-14,23-38,41-58H,15-18H2,1-4H3/b6-5+,11-7+,12-8+,19-9-,20-10+,21-13+,22-14-
Download
View in JSmol
Synonyms
ValueSource
a-CrocinGenerator
Α-crocinGenerator
Chemical FormulaC44H64O24
Average Mass976.9720 Da
Monoisotopic Mass976.37875 Da
IUPAC Namebis[3,4,5-trihydroxy-6-({[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}methyl)oxan-2-yl] (2Z,6E,8E,10Z,12E,14E)-2,6,11,15-tetramethylhexadeca-2,4,6,8,10,12,14-heptaenedioate
Traditional Namebis[3,4,5-trihydroxy-6-({[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}methyl)oxan-2-yl] (2Z,6E,8E,10Z,12E,14E)-2,6,11,15-tetramethylhexadeca-2,4,6,8,10,12,14-heptaenedioate
CAS Registry NumberNot Available
SMILES
[H]\C(=C(\[H])/C(/[H])=C(/C)\C(\[H])=C(/[H])\C(\[H])=C(/C)C(=O)OC1OC(COC2OC(CO)C(O)C(O)C2O)C(O)C(O)C1O)\C(\[H])=C(/C)C([H])=C([H])C(\[H])=C(\C)C(=O)OC1OC(COC2OC(CO)C(O)C(O)C2O)C(O)C(O)C1O
InChI Identifier
InChI=1/C44H64O24/c1-19(11-7-13-21(3)39(59)67-43-37(57)33(53)29(49)25(65-43)17-61-41-35(55)31(51)27(47)23(15-45)63-41)9-5-6-10-20(2)12-8-14-22(4)40(60)68-44-38(58)34(54)30(50)26(66-44)18-62-42-36(56)32(52)28(48)24(16-46)64-42/h5-14,23-38,41-58H,15-18H2,1-4H3/b6-5+,11-7+,12-8+,19-9-,20-10+,21-13+,22-14-
InChI KeySEBIKDIMAPSUBY-WOPHWFRHNA-N
Experimental Spectra
Not Available
Predicted Spectra
Not Available
Chemical Shift Submissions
Not Available
Species
Species of OriginNot Available
Chemical Taxonomy
DescriptionThis compound belongs to the class of organic compounds known as diterpenoids. These are terpene compounds formed by four isoprene units.
KingdomOrganic compounds  
Super ClassLipids and lipid-like molecules  
ClassPrenol lipids  
Sub ClassDiterpenoids  
Direct ParentDiterpenoids  
Alternative Parents
Substituents
  • Diterpenoid
    • 

  • Fatty acyl glycoside of mono- or disaccharide
    • 

  • Fatty acyl glycoside
    • 

  • Alkyl glycoside
    • 

  • Fatty alcohol
    • 

  • Fatty acid ester
    • 

  • Fatty acyl
    • 

  • Oxane
    • 

  • Monosaccharide
    • 

  • Dicarboxylic acid or derivatives
    • 

  • Alpha,beta-unsaturated carboxylic ester
    • 

  • Enoate ester
    • 

  • Secondary alcohol
    • 

  • Carboxylic acid ester
    • 

  • Oxacycle
    • 

  • Organoheterocyclic compound
    • 

  • Carboxylic acid derivative
    • 

  • Organic oxygen compound
    • 

  • Organic oxide
    • 

  • Hydrocarbon derivative
    • 

  • Organooxygen compound
    • 

  • Alcohol
    • 

  • Aliphatic heteromonocyclic compound
Molecular FrameworkAliphatic heteromonocyclic compounds
External DescriptorsNot Available
Physical Properties
StateNot Available
Experimental Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Predicted Properties
PropertyValueSource
logP-3.2ChemAxon
pKa (Strongest Acidic)11.67ChemAxon
pKa (Strongest Basic)-3.7ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count22ChemAxon
Hydrogen Donor Count14ChemAxon
Polar Surface Area391.2 ŲChemAxon
Rotatable Bond Count20ChemAxon
Refractivity233.49 m³·mol⁻¹ChemAxon
Polarizability100.98 ųChemAxon
Number of Rings4ChemAxon
BioavailabilityNoChemAxon
Rule of FiveNoChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleYesChemAxon
HMDB IDNot Available
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
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References
General References
  1. Abedi AH, Adhami HR, Mousavi Ghahfarrokhi SS, Mirmasoumi M, Amin M: Bacillus subtilis stimulates plant growth and production of bioactive components in saffron. Nat Prod Res. 2024 Apr 10:1-6. doi: 10.1080/14786419.2024.2340045. [PubMed:38598323  ] 
  2. Yadav S, Parijat P, Krishnan V: Crystal structure of the pilus-specific sortase from early colonizing oral Streptococcus sanguinis captures an active open-lid conformation. Int J Biol Macromol. 2023 Jul 15;243:125183. doi: 10.1016/j.ijbiomac.2023.125183.  Epub 2023 Jun 3. [PubMed:37276901  ] 
  3. Bathaie SZ, Shams A, Moghadas Zadeh Kermani F: Crocin Bleaching Assay Using Purified Di-gentiobiosyl Crocin (-crocin) from Iranian Saffron. Iran J Basic Med Sci. 2011 Sep;14(5):399-406. [PubMed:23493090  ] 
  4. Hadizadeh F, Mohajeri SA, Seifi M: Extraction and purification of crocin from saffron stigmas employing a simple and efficient crystallization method. Pak J Biol Sci. 2010 Jul 15;13(14):691-8. doi: 10.3923/pjbs.2010.691.698. [PubMed:21848061  ]