NP-MRD: Showing NP-Card for 1-methyl (2s,3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl (2e,4e,6e,8e,10e,12e,14e)-2,6,11,15-tetramethylhexadeca-2,4,6,8,10,12,14-heptaenedioate (NP0227625)

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Record Information

Version

2.0

Created at

2022-09-06 07:00:39 UTC

Updated at

2022-09-06 07:00:39 UTC

NP-MRD ID

NP0227625

Secondary Accession Numbers

None

Natural Product Identification

Common Name

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

Description

Crocin-4 belongs to the class of organic compounds known as diterpenoids. These are terpene compounds formed by four isoprene units. 1-methyl (2s,3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl (2e,4e,6e,8e,10e,12e,14e)-2,6,11,15-tetramethylhexadeca-2,4,6,8,10,12,14-heptaenedioate is found in Crocus sativus. 1-methyl (2s,3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl (2e,4e,6e,8e,10e,12e,14e)-2,6,11,15-tetramethylhexadeca-2,4,6,8,10,12,14-heptaenedioate was first documented in 2020 (PMID: 33097779). Based on a literature review very few articles have been published on Crocin-4.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652309062209002D          

 36 36  0  0  1  0            999 V2000
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M  END

     RDKit          3D

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M  END


  Mrv1652309062209002D          

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 18 19  2  0  0  0  0
 19 20  1  0  0  0  0
 20 21  2  0  0  0  0
 21 22  1  0  0  0  0
 21 23  1  0  0  0  0
 23 24  2  0  0  0  0
 23 25  1  0  0  0  0
 26 25  1  6  0  0  0
 26 27  1  0  0  0  0
 27 28  1  0  0  0  0
 28 29  1  6  0  0  0
 29 30  1  0  0  0  0
 28 31  1  0  0  0  0
 31 32  1  1  0  0  0
 31 33  1  0  0  0  0
 33 34  1  6  0  0  0
 33 35  1  0  0  0  0
 26 35  1  0  0  0  0
 35 36  1  1  0  0  0
M  END
> <DATABASE_ID>
NP0227625

> <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)O[C@@H]1O[C@H](CO)[C@@H](O)[C@H](O)[C@H]1O

> <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+/t21-,22-,23+,24-,27+/m1/s1

> <INCHI_KEY>
ATQIQIBBBWQWOT-OMNKTTJZSA-N

> <FORMULA>
C27H36O9

> <MOLECULAR_WEIGHT>
504.576

> <EXACT_MASS>
504.235932739

> <JCHEM_ACCEPTOR_COUNT>
7

> <JCHEM_ATOM_COUNT>
72

> <JCHEM_AVERAGE_POLARIZABILITY>
55.25146205430807

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

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

> <JCHEM_LOGP>
2.744695860000001

> <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>
142.75000000000003

> <JCHEM_REFRACTIVITY>
140.99710000000002

> <JCHEM_ROTATABLE_BOND_COUNT>
12

> <JCHEM_RULE_OF_FIVE>
0

> <JCHEM_TRADITIONAL_IUPAC>
1-methyl (2S,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)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

$$$$

HEADER    PROTEIN                                 06-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   06-SEP-22         0                                  
HETATM    1  C   UNK     0      10.669  24.640   0.000  0.00  0.00           C+0
HETATM    2  O   UNK     0      10.669  23.100   0.000  0.00  0.00           O+0
HETATM    3  C   UNK     0       9.336  22.330   0.000  0.00  0.00           C+0
HETATM    4  O   UNK     0       8.002  23.100   0.000  0.00  0.00           O+0
HETATM    5  C   UNK     0       9.336  20.790   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      10.669  20.020   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       8.002  20.020   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       8.002  18.480   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       6.668  17.710   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       6.668  16.170   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       8.002  15.400   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       5.335  15.400   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       5.335  13.860   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       4.001  13.090   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       4.001  11.550   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       2.667  10.780   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       1.334  11.550   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       1.334   8.470   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       1.334   6.930   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0       0.000   6.160   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0      -1.334   6.930   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0       0.000   4.620   0.000  0.00  0.00           C+0
HETATM   24  O   UNK     0      -1.334   3.850   0.000  0.00  0.00           O+0
HETATM   25  O   UNK     0       1.334   3.850   0.000  0.00  0.00           O+0
HETATM   26  C   UNK     0       1.334   2.310   0.000  0.00  0.00           C+0
HETATM   27  O   UNK     0       2.667   1.540   0.000  0.00  0.00           O+0
HETATM   28  C   UNK     0       2.667  -0.000   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0       4.001  -0.770   0.000  0.00  0.00           C+0
HETATM   30  O   UNK     0       4.001  -2.310   0.000  0.00  0.00           O+0
HETATM   31  C   UNK     0       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM   32  O   UNK     0       1.334  -2.310   0.000  0.00  0.00           O+0
HETATM   33  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM   34  O   UNK     0      -1.334  -0.770   0.000  0.00  0.00           O+0
HETATM   35  C   UNK     0       0.000   1.540   0.000  0.00  0.00           C+0
HETATM   36  O   UNK     0      -1.334   2.310   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4    5                                                  
CONECT    4    3                                                            
CONECT    5    3    6    7                                                  
CONECT    6    5                                                            
CONECT    7    5    8                                                       
CONECT    8    7    9                                                       
CONECT    9    8   10                                                       
CONECT   10    9   11   12                                                  
CONECT   11   10                                                            
CONECT   12   10   13                                                       
CONECT   13   12   14                                                       
CONECT   14   13   15                                                       
CONECT   15   14   16                                                       
CONECT   16   15   17   18                                                  
CONECT   17   16                                                            
CONECT   18   16   19                                                       
CONECT   19   18   20                                                       
CONECT   20   19   21                                                       
CONECT   21   20   22   23                                                  
CONECT   22   21                                                            
CONECT   23   21   24   25                                                  
CONECT   24   23                                                            
CONECT   25   23   26                                                       
CONECT   26   25   27   35                                                  
CONECT   27   26   28                                                       
CONECT   28   27   29   31                                                  
CONECT   29   28   30                                                       
CONECT   30   29                                                            
CONECT   31   28   32   33                                                  
CONECT   32   31                                                            
CONECT   33   31   34   35                                                  
CONECT   34   33                                                            
CONECT   35   33   26   36                                                  
CONECT   36   35                                                            
MASTER        0    0    0    0    0    0    0    0   36    0   72    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₂₇H₃₆O₉

Average Mass

504.5760 Da

Monoisotopic Mass

504.23593 Da

IUPAC Name

1-methyl (2S,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)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

1-methyl (2S,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)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 Number

Not Available

SMILES

COC(=O)C(\C)=C\C=C\C(\C)=C\C=C\C=C(/C)\C=C\C=C(/C)C(=O)O[C@@H]1O[C@H](CO)[C@@H](O)[C@H](O)[C@H]1O

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+/t21-,22-,23+,24-,27+/m1/s1

InChI Key

ATQIQIBBBWQWOT-OMNKTTJZSA-N

Experimental Spectra

Not Available

Predicted Spectra

Spectrum Type	Description	Depositor ID	Depositor Organization	Depositor	Deposition Date	View
1D NMR	¹³C NMR Spectrum (1D, 25 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 252 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 50 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 75 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 101 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 126 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 151 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 176 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 201 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 226 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum

Chemical Shift Submissions

Not Available

Species

Species of Origin

Species Name	Source	Reference
Crocus sativus	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	2.74	ChemAxon
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	55.25 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

Not Available

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

Not Available

KNApSAcK ID

C00054688

Chemspider ID

59700327

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

101606290

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Koulakiotis NS, Purhonen P, Gikas E, Hebert H, Tsarbopoulos A: Crocus-derived compounds alter the aggregation pathway of Alzheimer's Disease: associated beta amyloid protein. Sci Rep. 2020 Oct 23;10(1):18150. doi: 10.1038/s41598-020-74770-x. [PubMed:33097779 ]
LOTUS database [Link]

Showing NP-Card for 1-methyl (2s,3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl (2e,4e,6e,8e,10e,12e,14e)-2,6,11,15-tetramethylhexadeca-2,4,6,8,10,12,14-heptaenedioate (NP0227625)

MOL for NP0227625 (1-methyl (2s,3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl (2e,4e,6e,8e,10e,12e,14e)-2,6,11,15-tetramethylhexadeca-2,4,6,8,10,12,14-heptaenedioate)

3D MOL for NP0227625 (1-methyl (2s,3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl (2e,4e,6e,8e,10e,12e,14e)-2,6,11,15-tetramethylhexadeca-2,4,6,8,10,12,14-heptaenedioate)

3D SDF for NP0227625 (1-methyl (2s,3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl (2e,4e,6e,8e,10e,12e,14e)-2,6,11,15-tetramethylhexadeca-2,4,6,8,10,12,14-heptaenedioate)

3D-SDF for NP0227625 (1-methyl (2s,3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl (2e,4e,6e,8e,10e,12e,14e)-2,6,11,15-tetramethylhexadeca-2,4,6,8,10,12,14-heptaenedioate)

PDB for NP0227625 (1-methyl (2s,3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl (2e,4e,6e,8e,10e,12e,14e)-2,6,11,15-tetramethylhexadeca-2,4,6,8,10,12,14-heptaenedioate)

3D PDB for NP0227625 (1-methyl (2s,3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl (2e,4e,6e,8e,10e,12e,14e)-2,6,11,15-tetramethylhexadeca-2,4,6,8,10,12,14-heptaenedioate)

SMILES for NP0227625 (1-methyl (2s,3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl (2e,4e,6e,8e,10e,12e,14e)-2,6,11,15-tetramethylhexadeca-2,4,6,8,10,12,14-heptaenedioate)

INCHI for NP0227625 (1-methyl (2s,3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl (2e,4e,6e,8e,10e,12e,14e)-2,6,11,15-tetramethylhexadeca-2,4,6,8,10,12,14-heptaenedioate)

Structure for NP0227625 (1-methyl (2s,3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl (2e,4e,6e,8e,10e,12e,14e)-2,6,11,15-tetramethylhexadeca-2,4,6,8,10,12,14-heptaenedioate)

3D Structure for NP0227625 (1-methyl (2s,3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl (2e,4e,6e,8e,10e,12e,14e)-2,6,11,15-tetramethylhexadeca-2,4,6,8,10,12,14-heptaenedioate)