Np mrd loader

Showing NP-Card for crocin (NP0024939)

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Record Information
Version2.0
Created at2021-06-19 17:11:34 UTC
Updated at2021-06-29 23:49:34 UTC
NP-MRD IDNP0024939
Secondary Accession NumbersNone
Natural Product Identification
Common Namecrocin
Provided ByJEOL DatabaseJEOL Logo
Description crocin is found in Crocus sativa, Gardenia jasminoides , Gardenia spp. , Gardenia Yellow, Safran naturalis and Verbascum phlomoides . crocin was first documented in 2007 (Uekura, Y., et al.).
Structure
Thumb
MOL3D MOLSDF3D SDFPDBSMILESInChI

MOL for NP0024939 (crocin)


  Mrv1652306192119113D          

132135  0  0  0  0            999 V2000
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M  END
Download

3D MOL for NP0024939 (crocin)

     RDKit          3D

132135  0  0  0  0  0  0  0  0999 V2000
    2.3585   -0.0120   -1.7810 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5404   -0.1316   -0.2875 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7186   -0.8639    0.1913 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.6638   -1.4476   -0.5658 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.7929   -2.1541    0.0091 C   0  0  0  0  0  0  0  0  0  0  0  0
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M  END
Download

3D SDF for NP0024939 (crocin)


  Mrv1652306192119113D          

132135  0  0  0  0            999 V2000
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    0.4822    1.1413    0.3918 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2853    1.6139    1.3884 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5005    2.3682    1.1491 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3428    2.8877    2.0684 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1593    2.7690    3.5618 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5213    3.6200    1.5902 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4651    4.2050    2.3482 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.5961    4.9099    1.7746 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.5942    5.5183    2.4471 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.7645    5.5858    3.9368 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.6377    6.1766    1.6055 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.6996    6.1166    0.3852 O   0  0  0  0  0  0  0  0  0  0  0  0
   -8.5009    6.8763    2.3739 O   0  0  0  0  0  0  0  0  0  0  0  0
   -9.6137    7.4728    1.6853 C   0  0  1  0  0  0  0  0  0  0  0  0
  -10.6142    7.7110    2.6831 O   0  0  0  0  0  0  0  0  0  0  0  0
  -11.8197    8.2862    2.1563 C   0  0  1  0  0  0  0  0  0  0  0  0
  -12.8648    8.3733    3.2818 C   0  0  1  0  0  0  0  0  0  0  0  0
  -13.2572    7.0585    3.7028 O   0  0  0  0  0  0  0  0  0  0  0  0
  -12.5549    6.6147    4.8708 C   0  0  1  0  0  0  0  0  0  0  0  0
  -12.9672    7.3548    6.0157 O   0  0  0  0  0  0  0  0  0  0  0  0
  -12.2972    6.9377    7.2191 C   0  0  1  0  0  0  0  0  0  0  0  0
  -12.7801    7.8276    8.3751 C   0  0  2  0  0  0  0  0  0  0  0  0
  -14.1637    7.6124    8.6526 O   0  0  0  0  0  0  0  0  0  0  0  0
  -12.5357    5.4478    7.5152 C   0  0  2  0  0  0  0  0  0  0  0  0
  -11.7249    5.0143    8.6153 O   0  0  0  0  0  0  0  0  0  0  0  0
  -12.1812    4.6017    6.2909 C   0  0  1  0  0  0  0  0  0  0  0  0
  -12.5406    3.2321    6.5378 O   0  0  0  0  0  0  0  0  0  0  0  0
  -12.8941    5.1258    5.0505 C   0  0  2  0  0  0  0  0  0  0  0  0
  -12.4801    4.3493    3.9129 O   0  0  0  0  0  0  0  0  0  0  0  0
  -11.5119    9.6711    1.5783 C   0  0  2  0  0  0  0  0  0  0  0  0
  -12.6754   10.2636    1.0001 O   0  0  0  0  0  0  0  0  0  0  0  0
  -10.4359    9.5413    0.5014 C   0  0  1  0  0  0  0  0  0  0  0  0
  -10.0771   10.8553    0.0418 O   0  0  0  0  0  0  0  0  0  0  0  0
   -9.1959    8.8048    1.0137 C   0  0  2  0  0  0  0  0  0  0  0  0
   -8.3118    8.6750   -0.1137 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4662    0.5445   -2.0743 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.2120    0.5080   -2.2304 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2711   -1.0045   -2.2370 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.8200   -0.9285    1.2754 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.5949   -1.4045   -1.6469 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.7981   -2.1962    1.1004 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.8227   -3.7970   -2.5346 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.3149   -2.1138   -2.6892 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.0065   -2.4754   -2.4131 H   0  0  0  0  0  0  0  0  0  0  0  0
    9.3623   -5.1380    1.1356 H   0  0  0  0  0  0  0  0  0  0  0  0
   12.5607   -3.9611    1.0293 H   0  0  0  0  0  0  0  0  0  0  0  0
   12.7714   -3.3896   -1.4029 H   0  0  0  0  0  0  0  0  0  0  0  0
   13.9675   -4.5608   -0.7796 H   0  0  0  0  0  0  0  0  0  0  0  0
   14.4088   -5.4726   -2.7833 H   0  0  0  0  0  0  0  0  0  0  0  0
   15.1004   -4.2950   -4.7825 H   0  0  0  0  0  0  0  0  0  0  0  0
   14.0561   -2.0173   -5.0914 H   0  0  0  0  0  0  0  0  0  0  0  0
   12.8958   -2.7201   -6.2092 H   0  0  0  0  0  0  0  0  0  0  0  0
   14.8644   -3.5452   -7.3426 H   0  0  0  0  0  0  0  0  0  0  0  0
   12.6209   -5.2324   -6.3502 H   0  0  0  0  0  0  0  0  0  0  0  0
   14.3057   -6.2684   -7.5769 H   0  0  0  0  0  0  0  0  0  0  0  0
   14.8344   -6.8948   -5.0330 H   0  0  0  0  0  0  0  0  0  0  0  0
   13.2587   -8.5199   -5.4869 H   0  0  0  0  0  0  0  0  0  0  0  0
   11.9004   -6.6008   -4.1775 H   0  0  0  0  0  0  0  0  0  0  0  0
   12.7633   -7.7173   -2.3417 H   0  0  0  0  0  0  0  0  0  0  0  0
   13.0871   -6.4675    0.7253 H   0  0  0  0  0  0  0  0  0  0  0  0
   11.2819   -5.2011    2.4132 H   0  0  0  0  0  0  0  0  0  0  0  0
   10.6147   -7.6316    0.8432 H   0  0  0  0  0  0  0  0  0  0  0  0
   11.0129   -8.4953   -1.1004 H   0  0  0  0  0  0  0  0  0  0  0  0
   10.2335   -6.0000   -1.6771 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.0903   -6.5176   -1.1186 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9281    0.2401    1.6875 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1870    1.3277   -0.6356 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0102    1.4275    2.4157 H   0  0  0  0  0  0  0  0  0  0  0  0
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   -2.0711    3.7618    4.0171 H   0  0  0  0  0  0  0  0  0  0  0  0
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  -13.7723    8.8602    2.9107 H   0  0  0  0  0  0  0  0  0  0  0  0
  -11.4770    6.7340    4.7150 H   0  0  0  0  0  0  0  0  0  0  0  0
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   -9.2713   10.7222   -0.5000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -8.6660    9.4320    1.7407 H   0  0  0  0  0  0  0  0  0  0  0  0
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M  END
> <DATABASE_ID>
NP0024939

> <DATABASE_NAME>
NP-MRD

> <SMILES>
[H]OC([H])([H])[C@]1([H])O[C@]([H])(OC([H])([H])[C@]2([H])O[C@]([H])(OC(=O)C(=C(/[H])\C(\[H])=C(/[H])\C(=C(/[H])\C(\[H])=C(/[H])\C(\[H])=C(\C(\[H])=C(/[H])\C(\[H])=C(\C(=O)O[C@]3([H])O[C@]([H])(C([H])([H])O[C@]4([H])O[C@]([H])(C([H])([H])O[H])[C@@]([H])(O[H])[C@]([H])(O[H])[C@@]4([H])O[H])[C@@]([H])(O[H])[C@]([H])(O[H])[C@@]3([H])O[H])C([H])([H])[H])/C([H])([H])[H])\C([H])([H])[H])\C([H])([H])[H])[C@@]([H])(O[H])[C@]([H])(O[H])[C@@]2([H])O[H])[C@@]([H])(O[H])[C@]([H])(O[H])[C@@]1([H])O[H]

> <INCHI_IDENTIFIER>
InChI=1S/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+/t23-,24+,25-,26+,27-,28+,29-,30+,31+,32-,33+,34-,35-,36+,37-,38+,41-,42+,43+,44-

> <INCHI_KEY>
SEBIKDIMAPSUBY-NUEBZELJSA-N

> <FORMULA>
C44H64O24

> <MOLECULAR_WEIGHT>
976.972

> <EXACT_MASS>
976.378752941

> <JCHEM_ACCEPTOR_COUNT>
22

> <JCHEM_ATOM_COUNT>
132

> <JCHEM_AVERAGE_POLARIZABILITY>
102.48725576548357

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
14

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

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

> <ALOGPS_LOGP>
-0.02

> <JCHEM_LOGP>
-3.210937580666667

> <ALOGPS_LOGS>
-3.24

> <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>
-3.678613072130494

> <JCHEM_POLAR_SURFACE_AREA>
391.20000000000005

> <JCHEM_REFRACTIVITY>
233.48580000000018

> <JCHEM_ROTATABLE_BOND_COUNT>
20

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
5.67e-01 g/l

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

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for NP0024939 (crocin)

     RDKit          3D

132135  0  0  0  0  0  0  0  0999 V2000
    2.3585   -0.0120   -1.7810 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5404   -0.1316   -0.2875 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7186   -0.8639    0.1913 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.6638   -1.4476   -0.5658 C   0  0  0  0  0  0  0  0  0  0  0  0
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M  END
Download

PDB for NP0024939 (crocin)

HEADER    PROTEIN                                 19-JUN-21   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   19-JUN-21         0                                  
HETATM    1  C   UNK     0       2.358  -0.012  -1.781  0.00  0.00           C+0
HETATM    2  C   UNK     0       2.540  -0.132  -0.288  0.00  0.00           C+0
HETATM    3  C   UNK     0       3.719  -0.864   0.191  0.00  0.00           C+0
HETATM    4  C   UNK     0       4.664  -1.448  -0.566  0.00  0.00           C+0
HETATM    5  C   UNK     0       5.793  -2.154   0.009  0.00  0.00           C+0
HETATM    6  C   UNK     0       6.797  -2.752  -0.664  0.00  0.00           C+0
HETATM    7  C   UNK     0       6.989  -2.785  -2.151  0.00  0.00           C+0
HETATM    8  C   UNK     0       7.837  -3.419   0.179  0.00  0.00           C+0
HETATM    9  O   UNK     0       7.979  -3.235   1.378  0.00  0.00           O+0
HETATM   10  O   UNK     0       8.566  -4.270  -0.583  0.00  0.00           O+0
HETATM   11  C   UNK     0       9.659  -4.904   0.105  0.00  0.00           C+0
HETATM   12  O   UNK     0      10.776  -4.017   0.110  0.00  0.00           O+0
HETATM   13  C   UNK     0      12.082  -4.594   0.271  0.00  0.00           C+0
HETATM   14  C   UNK     0      12.908  -4.405  -1.014  0.00  0.00           C+0
HETATM   15  O   UNK     0      12.501  -5.337  -2.006  0.00  0.00           O+0
HETATM   16  C   UNK     0      13.373  -5.374  -3.135  0.00  0.00           C+0
HETATM   17  O   UNK     0      13.222  -4.185  -3.907  0.00  0.00           O+0
HETATM   18  C   UNK     0      14.048  -4.189  -5.079  0.00  0.00           C+0
HETATM   19  C   UNK     0      13.904  -2.840  -5.798  0.00  0.00           C+0
HETATM   20  O   UNK     0      14.850  -2.695  -6.852  0.00  0.00           O+0
HETATM   21  C   UNK     0      13.655  -5.353  -6.005  0.00  0.00           C+0
HETATM   22  O   UNK     0      14.485  -5.393  -7.172  0.00  0.00           O+0
HETATM   23  C   UNK     0      13.781  -6.672  -5.242  0.00  0.00           C+0
HETATM   24  O   UNK     0      13.318  -7.742  -6.080  0.00  0.00           O+0
HETATM   25  C   UNK     0      12.973  -6.620  -3.948  0.00  0.00           C+0
HETATM   26  O   UNK     0      13.210  -7.832  -3.214  0.00  0.00           O+0
HETATM   27  C   UNK     0      12.078  -6.045   0.789  0.00  0.00           C+0
HETATM   28  O   UNK     0      11.754  -6.026   2.198  0.00  0.00           O+0
HETATM   29  C   UNK     0      11.065  -6.971   0.090  0.00  0.00           C+0
HETATM   30  O   UNK     0      11.712  -7.859  -0.845  0.00  0.00           O+0
HETATM   31  C   UNK     0       9.956  -6.209  -0.640  0.00  0.00           C+0
HETATM   32  O   UNK     0       8.800  -7.062  -0.728  0.00  0.00           O+0
HETATM   33  C   UNK     0       1.697   0.387   0.631  0.00  0.00           C+0
HETATM   34  C   UNK     0       0.482   1.141   0.392  0.00  0.00           C+0
HETATM   35  C   UNK     0      -0.285   1.614   1.388  0.00  0.00           C+0
HETATM   36  C   UNK     0      -1.500   2.368   1.149  0.00  0.00           C+0
HETATM   37  C   UNK     0      -2.343   2.888   2.068  0.00  0.00           C+0
HETATM   38  C   UNK     0      -2.159   2.769   3.562  0.00  0.00           C+0
HETATM   39  C   UNK     0      -3.521   3.620   1.590  0.00  0.00           C+0
HETATM   40  C   UNK     0      -4.465   4.205   2.348  0.00  0.00           C+0
HETATM   41  C   UNK     0      -5.596   4.910   1.775  0.00  0.00           C+0
HETATM   42  C   UNK     0      -6.594   5.518   2.447  0.00  0.00           C+0
HETATM   43  C   UNK     0      -6.765   5.586   3.937  0.00  0.00           C+0
HETATM   44  C   UNK     0      -7.638   6.177   1.605  0.00  0.00           C+0
HETATM   45  O   UNK     0      -7.700   6.117   0.385  0.00  0.00           O+0
HETATM   46  O   UNK     0      -8.501   6.876   2.374  0.00  0.00           O+0
HETATM   47  C   UNK     0      -9.614   7.473   1.685  0.00  0.00           C+0
HETATM   48  O   UNK     0     -10.614   7.711   2.683  0.00  0.00           O+0
HETATM   49  C   UNK     0     -11.820   8.286   2.156  0.00  0.00           C+0
HETATM   50  C   UNK     0     -12.865   8.373   3.282  0.00  0.00           C+0
HETATM   51  O   UNK     0     -13.257   7.059   3.703  0.00  0.00           O+0
HETATM   52  C   UNK     0     -12.555   6.615   4.871  0.00  0.00           C+0
HETATM   53  O   UNK     0     -12.967   7.355   6.016  0.00  0.00           O+0
HETATM   54  C   UNK     0     -12.297   6.938   7.219  0.00  0.00           C+0
HETATM   55  C   UNK     0     -12.780   7.828   8.375  0.00  0.00           C+0
HETATM   56  O   UNK     0     -14.164   7.612   8.653  0.00  0.00           O+0
HETATM   57  C   UNK     0     -12.536   5.448   7.515  0.00  0.00           C+0
HETATM   58  O   UNK     0     -11.725   5.014   8.615  0.00  0.00           O+0
HETATM   59  C   UNK     0     -12.181   4.602   6.291  0.00  0.00           C+0
HETATM   60  O   UNK     0     -12.541   3.232   6.538  0.00  0.00           O+0
HETATM   61  C   UNK     0     -12.894   5.126   5.051  0.00  0.00           C+0
HETATM   62  O   UNK     0     -12.480   4.349   3.913  0.00  0.00           O+0
HETATM   63  C   UNK     0     -11.512   9.671   1.578  0.00  0.00           C+0
HETATM   64  O   UNK     0     -12.675  10.264   1.000  0.00  0.00           O+0
HETATM   65  C   UNK     0     -10.436   9.541   0.501  0.00  0.00           C+0
HETATM   66  O   UNK     0     -10.077  10.855   0.042  0.00  0.00           O+0
HETATM   67  C   UNK     0      -9.196   8.805   1.014  0.00  0.00           C+0
HETATM   68  O   UNK     0      -8.312   8.675  -0.114  0.00  0.00           O+0
HETATM   69  H   UNK     0       1.466   0.545  -2.074  0.00  0.00           H+0
HETATM   70  H   UNK     0       3.212   0.508  -2.230  0.00  0.00           H+0
HETATM   71  H   UNK     0       2.271  -1.004  -2.237  0.00  0.00           H+0
HETATM   72  H   UNK     0       3.820  -0.929   1.275  0.00  0.00           H+0
HETATM   73  H   UNK     0       4.595  -1.405  -1.647  0.00  0.00           H+0
HETATM   74  H   UNK     0       5.798  -2.196   1.100  0.00  0.00           H+0
HETATM   75  H   UNK     0       6.823  -3.797  -2.535  0.00  0.00           H+0
HETATM   76  H   UNK     0       6.315  -2.114  -2.689  0.00  0.00           H+0
HETATM   77  H   UNK     0       8.007  -2.475  -2.413  0.00  0.00           H+0
HETATM   78  H   UNK     0       9.362  -5.138   1.136  0.00  0.00           H+0
HETATM   79  H   UNK     0      12.561  -3.961   1.029  0.00  0.00           H+0
HETATM   80  H   UNK     0      12.771  -3.390  -1.403  0.00  0.00           H+0
HETATM   81  H   UNK     0      13.967  -4.561  -0.780  0.00  0.00           H+0
HETATM   82  H   UNK     0      14.409  -5.473  -2.783  0.00  0.00           H+0
HETATM   83  H   UNK     0      15.100  -4.295  -4.782  0.00  0.00           H+0
HETATM   84  H   UNK     0      14.056  -2.017  -5.091  0.00  0.00           H+0
HETATM   85  H   UNK     0      12.896  -2.720  -6.209  0.00  0.00           H+0
HETATM   86  H   UNK     0      14.864  -3.545  -7.343  0.00  0.00           H+0
HETATM   87  H   UNK     0      12.621  -5.232  -6.350  0.00  0.00           H+0
HETATM   88  H   UNK     0      14.306  -6.268  -7.577  0.00  0.00           H+0
HETATM   89  H   UNK     0      14.834  -6.895  -5.033  0.00  0.00           H+0
HETATM   90  H   UNK     0      13.259  -8.520  -5.487  0.00  0.00           H+0
HETATM   91  H   UNK     0      11.900  -6.601  -4.178  0.00  0.00           H+0
HETATM   92  H   UNK     0      12.763  -7.717  -2.342  0.00  0.00           H+0
HETATM   93  H   UNK     0      13.087  -6.468   0.725  0.00  0.00           H+0
HETATM   94  H   UNK     0      11.282  -5.201   2.413  0.00  0.00           H+0
HETATM   95  H   UNK     0      10.615  -7.632   0.843  0.00  0.00           H+0
HETATM   96  H   UNK     0      11.013  -8.495  -1.100  0.00  0.00           H+0
HETATM   97  H   UNK     0      10.233  -6.000  -1.677  0.00  0.00           H+0
HETATM   98  H   UNK     0       8.090  -6.518  -1.119  0.00  0.00           H+0
HETATM   99  H   UNK     0       1.928   0.240   1.688  0.00  0.00           H+0
HETATM  100  H   UNK     0       0.187   1.328  -0.636  0.00  0.00           H+0
HETATM  101  H   UNK     0       0.010   1.428   2.416  0.00  0.00           H+0
HETATM  102  H   UNK     0      -1.732   2.515   0.093  0.00  0.00           H+0
HETATM  103  H   UNK     0      -2.071   3.762   4.017  0.00  0.00           H+0
HETATM  104  H   UNK     0      -3.012   2.250   4.013  0.00  0.00           H+0
HETATM  105  H   UNK     0      -1.267   2.212   3.855  0.00  0.00           H+0
HETATM  106  H   UNK     0      -3.623   3.684   0.506  0.00  0.00           H+0
HETATM  107  H   UNK     0      -4.394   4.161   3.429  0.00  0.00           H+0
HETATM  108  H   UNK     0      -5.608   4.935   0.683  0.00  0.00           H+0
HETATM  109  H   UNK     0      -6.018   5.009   4.487  0.00  0.00           H+0
HETATM  110  H   UNK     0      -6.691   6.623   4.282  0.00  0.00           H+0
HETATM  111  H   UNK     0      -7.744   5.189   4.228  0.00  0.00           H+0
HETATM  112  H   UNK     0     -10.014   6.760   0.953  0.00  0.00           H+0
HETATM  113  H   UNK     0     -12.216   7.616   1.382  0.00  0.00           H+0
HETATM  114  H   UNK     0     -12.489   8.961   4.128  0.00  0.00           H+0
HETATM  115  H   UNK     0     -13.772   8.860   2.911  0.00  0.00           H+0
HETATM  116  H   UNK     0     -11.477   6.734   4.715  0.00  0.00           H+0
HETATM  117  H   UNK     0     -11.222   7.126   7.094  0.00  0.00           H+0
HETATM  118  H   UNK     0     -12.660   8.883   8.108  0.00  0.00           H+0
HETATM  119  H   UNK     0     -12.212   7.625   9.288  0.00  0.00           H+0
HETATM  120  H   UNK     0     -14.415   8.247   9.345  0.00  0.00           H+0
HETATM  121  H   UNK     0     -13.582   5.263   7.786  0.00  0.00           H+0
HETATM  122  H   UNK     0     -11.867   4.047   8.661  0.00  0.00           H+0
HETATM  123  H   UNK     0     -11.095   4.593   6.135  0.00  0.00           H+0
HETATM  124  H   UNK     0     -12.497   2.798   5.662  0.00  0.00           H+0
HETATM  125  H   UNK     0     -13.977   4.982   5.148  0.00  0.00           H+0
HETATM  126  H   UNK     0     -12.866   4.816   3.144  0.00  0.00           H+0
HETATM  127  H   UNK     0     -11.158  10.347   2.367  0.00  0.00           H+0
HETATM  128  H   UNK     0     -12.349  11.044   0.506  0.00  0.00           H+0
HETATM  129  H   UNK     0     -10.845   9.027  -0.378  0.00  0.00           H+0
HETATM  130  H   UNK     0      -9.271  10.722  -0.500  0.00  0.00           H+0
HETATM  131  H   UNK     0      -8.666   9.432   1.741  0.00  0.00           H+0
HETATM  132  H   UNK     0      -8.026   7.740  -0.197  0.00  0.00           H+0
CONECT    1    2   69   70   71                                             
CONECT    2    3   33    1                                                  
CONECT    3    4    2   72                                                  
CONECT    4    5    3   73                                                  
CONECT    5    6    4   74                                                  
CONECT    6    8    5    7                                                  
CONECT    7    6   75   76   77                                             
CONECT    8    6   10    9                                                  
CONECT    9    8                                                            
CONECT   10    8   11                                                       
CONECT   11   31   12   10   78                                             
CONECT   12   11   13                                                       
CONECT   13   12   27   14   79                                             
CONECT   14   15   13   80   81                                             
CONECT   15   14   16                                                       
CONECT   16   25   17   15   82                                             
CONECT   17   16   18                                                       
CONECT   18   17   21   19   83                                             
CONECT   19   20   18   84   85                                             
CONECT   20   19   86                                                       
CONECT   21   18   23   22   87                                             
CONECT   22   21   88                                                       
CONECT   23   25   21   24   89                                             
CONECT   24   23   90                                                       
CONECT   25   23   16   26   91                                             
CONECT   26   25   92                                                       
CONECT   27   13   29   28   93                                             
CONECT   28   27   94                                                       
CONECT   29   31   27   30   95                                             
CONECT   30   29   96                                                       
CONECT   31   32   29   11   97                                             
CONECT   32   31   98                                                       
CONECT   33    2   34   99                                                  
CONECT   34   33   35  100                                                  
CONECT   35   34   36  101                                                  
CONECT   36   35   37  102                                                  
CONECT   37   36   39   38                                                  
CONECT   38   37  103  104  105                                             
CONECT   39   37   40  106                                                  
CONECT   40   39   41  107                                                  
CONECT   41   40   42  108                                                  
CONECT   42   41   44   43                                                  
CONECT   43   42  109  110  111                                             
CONECT   44   42   46   45                                                  
CONECT   45   44                                                            
CONECT   46   47   44                                                       
CONECT   47   67   48   46  112                                             
CONECT   48   47   49                                                       
CONECT   49   48   63   50  113                                             
CONECT   50   51   49  114  115                                             
CONECT   51   50   52                                                       
CONECT   52   61   53   51  116                                             
CONECT   53   52   54                                                       
CONECT   54   53   57   55  117                                             
CONECT   55   56   54  118  119                                             
CONECT   56   55  120                                                       
CONECT   57   54   59   58  121                                             
CONECT   58   57  122                                                       
CONECT   59   61   57   60  123                                             
CONECT   60   59  124                                                       
CONECT   61   62   59   52  125                                             
CONECT   62   61  126                                                       
CONECT   63   49   65   64  127                                             
CONECT   64   63  128                                                       
CONECT   65   67   63   66  129                                             
CONECT   66   65  130                                                       
CONECT   67   65   47   68  131                                             
CONECT   68   67  132                                                       
CONECT   69    1                                                            
CONECT   70    1                                                            
CONECT   71    1                                                            
CONECT   72    3                                                            
CONECT   73    4                                                            
CONECT   74    5                                                            
CONECT   75    7                                                            
CONECT   76    7                                                            
CONECT   77    7                                                            
CONECT   78   11                                                            
CONECT   79   13                                                            
CONECT   80   14                                                            
CONECT   81   14                                                            
CONECT   82   16                                                            
CONECT   83   18                                                            
CONECT   84   19                                                            
CONECT   85   19                                                            
CONECT   86   20                                                            
CONECT   87   21                                                            
CONECT   88   22                                                            
CONECT   89   23                                                            
CONECT   90   24                                                            
CONECT   91   25                                                            
CONECT   92   26                                                            
CONECT   93   27                                                            
CONECT   94   28                                                            
CONECT   95   29                                                            
CONECT   96   30                                                            
CONECT   97   31                                                            
CONECT   98   32                                                            
CONECT   99   33                                                            
CONECT  100   34                                                            
CONECT  101   35                                                            
CONECT  102   36                                                            
CONECT  103   38                                                            
CONECT  104   38                                                            
CONECT  105   38                                                            
CONECT  106   39                                                            
CONECT  107   40                                                            
CONECT  108   41                                                            
CONECT  109   43                                                            
CONECT  110   43                                                            
CONECT  111   43                                                            
CONECT  112   47                                                            
CONECT  113   49                                                            
CONECT  114   50                                                            
CONECT  115   50                                                            
CONECT  116   52                                                            
CONECT  117   54                                                            
CONECT  118   55                                                            
CONECT  119   55                                                            
CONECT  120   56                                                            
CONECT  121   57                                                            
CONECT  122   58                                                            
CONECT  123   59                                                            
CONECT  124   60                                                            
CONECT  125   61                                                            
CONECT  126   62                                                            
CONECT  127   63                                                            
CONECT  128   64                                                            
CONECT  129   65                                                            
CONECT  130   66                                                            
CONECT  131   67                                                            
CONECT  132   68                                                            
MASTER        0    0    0    0    0    0    0    0  132    0  270    0
END
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3D PDB for NP0024939 (crocin)

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SMILES for NP0024939 (crocin)
[H]OC([H])([H])[C@]1([H])O[C@]([H])(OC([H])([H])[C@]2([H])O[C@]([H])(OC(=O)C(=C(/[H])\C(\[H])=C(/[H])\C(=C(/[H])\C(\[H])=C(/[H])\C(\[H])=C(\C(\[H])=C(/[H])\C(\[H])=C(\C(=O)O[C@]3([H])O[C@]([H])(C([H])([H])O[C@]4([H])O[C@]([H])(C([H])([H])O[H])[C@@]([H])(O[H])[C@]([H])(O[H])[C@@]4([H])O[H])[C@@]([H])(O[H])[C@]([H])(O[H])[C@@]3([H])O[H])C([H])([H])[H])/C([H])([H])[H])\C([H])([H])[H])\C([H])([H])[H])[C@@]([H])(O[H])[C@]([H])(O[H])[C@@]2([H])O[H])[C@@]([H])(O[H])[C@]([H])(O[H])[C@@]1([H])O[H]
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INCHI for NP0024939 (crocin)
InChI=1S/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+/t23-,24+,25-,26+,27-,28+,29-,30+,31+,32-,33+,34-,35-,36+,37-,38+,41-,42+,43+,44-
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View in JSmol
Synonyms
ValueSource
(2S,3R,4S,5S,6R)-3,4,5-Trihydroxy-6-({[(2R,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}methyl)oxan-2-yl (2R,3S,4R,5R,6S)-3,4,5-trihydroxy-6-({[(2S,3S,4R,5R,6S)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}methyl)oxan-2-yl (2E,4E,6E,8E,10E,12E,14E)-2,6,11,15-tetramethylhexadeca-2,4,6,8,10,12,14-heptaenedioic acidGenerator
Chemical FormulaC44H64O24
Average Mass976.9720 Da
Monoisotopic Mass976.37875 Da
IUPAC Name(2S,3R,4S,5S,6R)-3,4,5-trihydroxy-6-({[(2R,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}methyl)oxan-2-yl (2R,3S,4R,5R,6S)-3,4,5-trihydroxy-6-({[(2S,3S,4R,5R,6S)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}methyl)oxan-2-yl (2E,4E,6E,8E,10E,12E,14E)-2,6,11,15-tetramethylhexadeca-2,4,6,8,10,12,14-heptaenedioate
Traditional Name(2S,3R,4S,5S,6R)-3,4,5-trihydroxy-6-({[(2R,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}methyl)oxan-2-yl (2R,3S,4R,5R,6S)-3,4,5-trihydroxy-6-({[(2S,3S,4R,5R,6S)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}methyl)oxan-2-yl (2E,4E,6E,8E,10E,12E,14E)-2,6,11,15-tetramethylhexadeca-2,4,6,8,10,12,14-heptaenedioate
CAS Registry NumberNot Available
SMILES
[H]OC([H])([H])[C@]1([H])O[C@]([H])(OC([H])([H])[C@]2([H])O[C@]([H])(OC(=O)C(=C(/[H])\C(\[H])=C(/[H])\C(=C(/[H])\C(\[H])=C(/[H])\C(\[H])=C(\C(\[H])=C(/[H])\C(\[H])=C(\C(=O)O[C@]3([H])O[C@]([H])(C([H])([H])O[C@]4([H])O[C@]([H])(C([H])([H])O[H])[C@@]([H])(O[H])[C@]([H])(O[H])[C@@]4([H])O[H])[C@@]([H])(O[H])[C@]([H])(O[H])[C@@]3([H])O[H])C([H])([H])[H])/C([H])([H])[H])\C([H])([H])[H])\C([H])([H])[H])[C@@]([H])(O[H])[C@]([H])(O[H])[C@@]2([H])O[H])[C@@]([H])(O[H])[C@]([H])(O[H])[C@@]1([H])O[H]
InChI Identifier
InChI=1S/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+/t23-,24+,25-,26+,27-,28+,29-,30+,31+,32-,33+,34-,35-,36+,37-,38+,41-,42+,43+,44-
InChI KeySEBIKDIMAPSUBY-NUEBZELJSA-N
Experimental Spectra
Spectrum TypeDescriptionDepositor EmailDepositor OrganizationDepositorDeposition DateView
1D NMR13C NMR Spectrum (1D, 800 MHz, DMSO-d6/D2O (9:1), simulated)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 800 MHz, DMSO-d6/D2O (9:1), simulated)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 100 MHz, DMSO-d6/D2O (9:1), simulated)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 100 MHz, DMSO-d6/D2O (9:1), simulated)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 200 MHz, DMSO-d6/D2O (9:1), simulated)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 200 MHz, DMSO-d6/D2O (9:1), simulated)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 300 MHz, DMSO-d6/D2O (9:1), simulated)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 300 MHz, DMSO-d6/D2O (9:1), simulated)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 400 MHz, DMSO-d6/D2O (9:1), simulated)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 400 MHz, DMSO-d6/D2O (9:1), simulated)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 500 MHz, DMSO-d6/D2O (9:1), simulated)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 500 MHz, DMSO-d6/D2O (9:1), simulated)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 600 MHz, DMSO-d6/D2O (9:1), simulated)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 600 MHz, DMSO-d6/D2O (9:1), simulated)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 700 MHz, DMSO-d6/D2O (9:1), simulated)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 700 MHz, DMSO-d6/D2O (9:1), simulated)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 900 MHz, DMSO-d6/D2O (9:1), simulated)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 900 MHz, DMSO-d6/D2O (9:1), simulated)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 1000 MHz, DMSO-d6/D2O (9:1), simulated)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 1000 MHz, DMSO-d6/D2O (9:1), simulated)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
Predicted Spectra
Not Available
Chemical Shift Submissions
Not Available
Species
Species of Origin
Species NameSourceReference
Crocus sativaPlant
Crocus sativusFooDB
Gardenia jasminoidesPlant
Gardenia spp.Plant
Gardenia YellowJEOL database
    • Uekura, Y., et al, Chem. Pharm. Bull. 55, 1643 (2007)
Safran naturalis-
Verbascum phlomoidesPlant
Chemical Taxonomy
Description 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
    • 

  • O-glycosyl compound
    • 

  • Glycosyl compound
    • 

  • Disaccharide
    • 

  • Fatty acid ester
    • 

  • Fatty acyl
    • 

  • Oxane
    • 

  • Dicarboxylic acid or derivatives
    • 

  • Alpha,beta-unsaturated carboxylic ester
    • 

  • Enoate ester
    • 

  • Secondary alcohol
    • 

  • Carboxylic acid ester
    • 

  • Oxacycle
    • 

  • Organoheterocyclic compound
    • 

  • Polyol
    • 

  • Carboxylic acid derivative
    • 

  • Acetal
    • 

  • Organic oxygen compound
    • 

  • Organic oxide
    • 

  • Hydrocarbon derivative
    • 

  • Primary alcohol
    • 

  • Organooxygen compound
    • 

  • Carbonyl group
    • 

  • 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-0.02ALOGPS
logP-3.2ChemAxon
logS-3.2ALOGPS
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
Polarizability102.49 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
FoodDB IDNot Available
KNApSAcK IDNot Available
Chemspider ID32674239  
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem CompoundNot Available
PDB IDNot Available
ChEBI IDNot Available
Good Scents IDNot Available
References
General References
  1. Uekura, Y., et al. (2007). Uekura, Y., et al, Chem. Pharm. Bull. 55, 1643 (2007). Chem. Pharm. Bull..