NP-MRD: Showing NP-Card for Retrocalamin (NP0049040)

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Record Information

Version

2.0

Created at

2022-03-17 21:06:10 UTC

Updated at

2022-03-17 21:06:10 UTC

NP-MRD ID

NP0049040

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Retrocalamin

Description

Retrocalamin belongs to the class of organic compounds known as naphthopyrans. Naphthopyrans are compounds containing a pyran ring fused to a naphthalene moiety. Furan is a 6 membered-ring non-aromatic ring with five carbon and one oxygen atoms. Naphthalene is a polycyclic aromatic hydrocarbon made up of two fused benzene rings. Retrocalamin is an extremely weak basic (essentially neutral) compound (based on its pKa). Outside of the human body, retrocalamin has been detected, but not quantified in, citrus and mandarin orange (clementine, tangerine). Retrocalamin is found in Skimmia japonica. This could make retrocalamin a potential biomarker for the consumption of these foods.

Structure

MOL SDF PDB SMILES InChI


  Mrv0541 01251306392D          

 33 37  0  0  0  0            999 V2000
   -4.9381   -7.4949    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.6525   -7.9074    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.6525   -8.7325    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9381   -9.1450    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -4.2236   -8.7325    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -4.2236   -7.9074    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -3.5091   -7.4949    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -3.5091   -9.1450    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.7947   -8.7325    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7947   -7.9074    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -6.3670   -9.1450    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -6.3670   -9.9700    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.6525  -10.3825    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9381   -9.9700    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2236   -7.0824    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0802   -9.1449    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2236   -9.5575    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9381   -8.3200    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2236  -10.3825    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -6.3670   -8.3199    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0966   -5.4004    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9216   -5.4004    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1766   -6.1850    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5091   -6.6699    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8417   -6.1850    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.0815   -8.7324    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -7.7959   -9.1450    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.7959   -9.9700    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.0814   -7.9074    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.6525  -11.2075    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -8.5104  -10.3825    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -7.0814  -10.3825    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -7.0814  -11.2075    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  4  5  1  0  0  0  0
  1  6  1  0  0  0  0
  7  6  1  0  0  0  0
  6  5  1  0  0  0  0
  5  8  1  0  0  0  0
  8  9  1  0  0  0  0
  9 10  1  0  0  0  0
  7 10  1  0  0  0  0
 14  4  1  0  0  0  0
  3  4  1  0  0  0  0
  3 11  1  0  0  0  0
 12 13  1  0  0  0  0
 13 14  1  0  0  0  0
  7 24  1  6  0  0  0
  6 15  1  6  0  0  0
  9 16  2  0  0  0  0
  8 17  1  1  0  0  0
  5 17  1  1  0  0  0
  4 18  1  1  0  0  0
 14 19  1  0  0  0  0
 11 20  1  1  0  0  0
 21 22  1  0  0  0  0
 22 23  2  0  0  0  0
 23 24  1  0  0  0  0
 24 25  2  0  0  0  0
 21 25  1  0  0  0  0
 12 11  1  0  0  0  0
 26 11  1  0  0  0  0
 26 27  1  0  0  0  0
 27 28  1  0  0  0  0
 26 29  1  6  0  0  0
 13 30  2  0  0  0  0
 28 31  2  0  0  0  0
 28 32  1  0  0  0  0
 32 33  1  0  0  0  0
M  END


  Mrv0541 01251306392D          

 33 37  0  0  0  0            999 V2000
   -4.9381   -7.4949    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.6525   -7.9074    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.6525   -8.7325    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9381   -9.1450    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -4.2236   -8.7325    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -4.2236   -7.9074    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -3.5091   -7.4949    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -3.5091   -9.1450    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.7947   -8.7325    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7947   -7.9074    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -6.3670   -9.1450    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -6.3670   -9.9700    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.6525  -10.3825    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9381   -9.9700    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2236   -7.0824    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0802   -9.1449    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2236   -9.5575    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9381   -8.3200    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2236  -10.3825    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -6.3670   -8.3199    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0966   -5.4004    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9216   -5.4004    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1766   -6.1850    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5091   -6.6699    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8417   -6.1850    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.0815   -8.7324    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -7.7959   -9.1450    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.7959   -9.9700    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.0814   -7.9074    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.6525  -11.2075    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -8.5104  -10.3825    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -7.0814  -10.3825    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -7.0814  -11.2075    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  4  5  1  0  0  0  0
  1  6  1  0  0  0  0
  7  6  1  0  0  0  0
  6  5  1  0  0  0  0
  5  8  1  0  0  0  0
  8  9  1  0  0  0  0
  9 10  1  0  0  0  0
  7 10  1  0  0  0  0
 14  4  1  0  0  0  0
  3  4  1  0  0  0  0
  3 11  1  0  0  0  0
 12 13  1  0  0  0  0
 13 14  1  0  0  0  0
  7 24  1  6  0  0  0
  6 15  1  6  0  0  0
  9 16  2  0  0  0  0
  8 17  1  1  0  0  0
  5 17  1  1  0  0  0
  4 18  1  1  0  0  0
 14 19  1  0  0  0  0
 11 20  1  1  0  0  0
 21 22  1  0  0  0  0
 22 23  2  0  0  0  0
 23 24  1  0  0  0  0
 24 25  2  0  0  0  0
 21 25  1  0  0  0  0
 12 11  1  0  0  0  0
 26 11  1  0  0  0  0
 26 27  1  0  0  0  0
 27 28  1  0  0  0  0
 26 29  1  6  0  0  0
 13 30  2  0  0  0  0
 28 31  2  0  0  0  0
 28 32  1  0  0  0  0
 32 33  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0049040

> <DATABASE_NAME>
NP-MRD

> <SMILES>
COC(=O)C[C@H](O)[C@@]1(C)CC(=O)C(O)[C@]2(C)C1CC[C@@]1(C)[C@@H](OC(=O)[C@H]3O[C@@]213)C1=COC=C1

> <INCHI_IDENTIFIER>
InChI=1S/C24H30O9/c1-21(15(26)9-16(27)30-4)10-13(25)17(28)23(3)14(21)5-7-22(2)18(12-6-8-31-11-12)32-20(29)19-24(22,23)33-19/h6,8,11,14-15,17-19,26,28H,5,7,9-10H2,1-4H3/t14?,15-,17?,18-,19+,21-,22-,23-,24+/m0/s1

> <INCHI_KEY>
HMNKPIJMXBZMJF-IHGWNHGOSA-N

> <FORMULA>
C24H30O9

> <MOLECULAR_WEIGHT>
462.4896

> <EXACT_MASS>
462.188982558

> <JCHEM_ACCEPTOR_COUNT>
6

> <JCHEM_AVERAGE_POLARIZABILITY>
46.50843394569763

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
methyl (3S)-3-[(1R,2S,6S,10S,11R,14S)-11-(furan-3-yl)-3-hydroxy-2,6,10-trimethyl-4,13-dioxo-12,15-dioxatetracyclo[8.5.0.0¹,¹⁴.0²,⁷]pentadecan-6-yl]-3-hydroxypropanoate

> <ALOGPS_LOGP>
1.51

> <JCHEM_LOGP>
1.2051429293333338

> <ALOGPS_LOGS>
-3.35

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
5

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
14.427936520358564

> <JCHEM_PKA_STRONGEST_ACIDIC>
12.859083527018669

> <JCHEM_PKA_STRONGEST_BASIC>
-3.0538626234323525

> <JCHEM_POLAR_SURFACE_AREA>
135.79999999999998

> <JCHEM_REFRACTIVITY>
110.54499999999999

> <JCHEM_ROTATABLE_BOND_COUNT>
5

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
2.05e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
methyl (3S)-3-[(1R,2S,6S,10S,11R,14S)-11-(furan-3-yl)-3-hydroxy-2,6,10-trimethyl-4,13-dioxo-12,15-dioxatetracyclo[8.5.0.0¹,¹⁴.0²,⁷]pentadecan-6-yl]-3-hydroxypropanoate

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 25-JAN-13   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   25-JAN-13         0                                  
HETATM    1  C   UNK     0      -9.218 -13.990   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0     -10.551 -14.760   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0     -10.551 -16.301   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -9.218 -17.071   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      -7.884 -16.301   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      -7.884 -14.760   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      -6.550 -13.990   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      -6.550 -17.071   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      -5.217 -16.301   0.000  0.00  0.00           C+0
HETATM   10  O   UNK     0      -5.217 -14.760   0.000  0.00  0.00           O+0
HETATM   11  C   UNK     0     -11.885 -17.071   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0     -11.885 -18.611   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0     -10.551 -19.381   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      -9.218 -18.611   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0      -7.884 -13.220   0.000  0.00  0.00           C+0
HETATM   16  O   UNK     0      -3.883 -17.070   0.000  0.00  0.00           O+0
HETATM   17  O   UNK     0      -7.884 -17.841   0.000  0.00  0.00           O+0
HETATM   18  C   UNK     0      -9.218 -15.531   0.000  0.00  0.00           C+0
HETATM   19  O   UNK     0      -7.884 -19.381   0.000  0.00  0.00           O+0
HETATM   20  C   UNK     0     -11.885 -15.530   0.000  0.00  0.00           C+0
HETATM   21  O   UNK     0      -5.780 -10.081   0.000  0.00  0.00           O+0
HETATM   22  C   UNK     0      -7.320 -10.081   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0      -7.796 -11.545   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0      -6.550 -12.450   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0      -5.305 -11.545   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0     -13.219 -16.300   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0     -14.552 -17.071   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0     -14.552 -18.611   0.000  0.00  0.00           C+0
HETATM   29  O   UNK     0     -13.219 -14.760   0.000  0.00  0.00           O+0
HETATM   30  O   UNK     0     -10.551 -20.921   0.000  0.00  0.00           O+0
HETATM   31  O   UNK     0     -15.886 -19.381   0.000  0.00  0.00           O+0
HETATM   32  O   UNK     0     -13.219 -19.381   0.000  0.00  0.00           O+0
HETATM   33  C   UNK     0     -13.219 -20.921   0.000  0.00  0.00           C+0
CONECT    1    2    6                                                       
CONECT    2    1    3                                                       
CONECT    3    2    4   11                                                  
CONECT    4    5   14    3   18                                             
CONECT    5    4    6    8   17                                             
CONECT    6    1    7    5   15                                             
CONECT    7    6   10   24                                                  
CONECT    8    5    9   17                                                  
CONECT    9    8   10   16                                                  
CONECT   10    9    7                                                       
CONECT   11    3   20   12   26                                             
CONECT   12   13   11                                                       
CONECT   13   12   14   30                                                  
CONECT   14    4   13   19                                                  
CONECT   15    6                                                            
CONECT   16    9                                                            
CONECT   17    8    5                                                       
CONECT   18    4                                                            
CONECT   19   14                                                            
CONECT   20   11                                                            
CONECT   21   22   25                                                       
CONECT   22   21   23                                                       
CONECT   23   22   24                                                       
CONECT   24    7   23   25                                                  
CONECT   25   24   21                                                       
CONECT   26   11   27   29                                                  
CONECT   27   26   28                                                       
CONECT   28   27   31   32                                                  
CONECT   29   26                                                            
CONECT   30   13                                                            
CONECT   31   28                                                            
CONECT   32   28   33                                                       
CONECT   33   32                                                            
MASTER        0    0    0    0    0    0    0    0   33    0   74    0
END

View in JSmol

Synonyms

Value	Source
Methyl (3S)-3-[(1R,2S,6S,10S,11R,14S)-11-(furan-3-yl)-3-hydroxy-2,6,10-trimethyl-4,13-dioxo-12,15-dioxatetracyclo[8.5.0.0¹,¹⁴.0²,⁷]pentadecan-6-yl]-3-hydroxypropanoic acid	Generator

Chemical Formula

C₂₄H₃₀O₉

Average Mass

462.4896 Da

Monoisotopic Mass

462.18898 Da

IUPAC Name

methyl (3S)-3-[(1R,2S,6S,10S,11R,14S)-11-(furan-3-yl)-3-hydroxy-2,6,10-trimethyl-4,13-dioxo-12,15-dioxatetracyclo[8.5.0.0¹,¹⁴.0²,⁷]pentadecan-6-yl]-3-hydroxypropanoate

Traditional Name

methyl (3S)-3-[(1R,2S,6S,10S,11R,14S)-11-(furan-3-yl)-3-hydroxy-2,6,10-trimethyl-4,13-dioxo-12,15-dioxatetracyclo[8.5.0.0¹,¹⁴.0²,⁷]pentadecan-6-yl]-3-hydroxypropanoate

CAS Registry Number

74729-98-9

SMILES

COC(=O)C[C@H](O)[C@@]1(C)CC(=O)C(O)[C@]2(C)C1CC[C@@]1(C)[C@@H](OC(=O)[C@H]3O[C@@]213)C1=COC=C1

InChI Identifier

InChI=1S/C24H30O9/c1-21(15(26)9-16(27)30-4)10-13(25)17(28)23(3)14(21)5-7-22(2)18(12-6-8-31-11-12)32-20(29)19-24(22,23)33-19/h6,8,11,14-15,17-19,26,28H,5,7,9-10H2,1-4H3/t14?,15-,17?,18-,19+,21-,22-,23-,24+/m0/s1

InChI Key

HMNKPIJMXBZMJF-IHGWNHGOSA-N

Experimental Spectra

Not Available

Predicted Spectra

Not Available

Chemical Shift Submissions

Not Available

Species

Species of Origin

Species Name	Source	Reference
Citrus reticulata	FooDB	Dr. Duke's Phytochemical and Ethnobotanical Databases
Skimmia japonica	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as naphthopyrans. Naphthopyrans are compounds containing a pyran ring fused to a naphthalene moiety. Furan is a 6 membered-ring non-aromatic ring with five carbon and one oxygen atoms. Naphthalene is a polycyclic aromatic hydrocarbon made up of two fused benzene rings.

Kingdom

Organic compounds

Super Class

Organoheterocyclic compounds

Class

Naphthopyrans

Sub Class

Not Available

Direct Parent

Naphthopyrans

Alternative Parents

Substituents

Naphthopyran
Naphthalene
Delta_valerolactone
1,4-dioxepane
Beta-hydroxy acid
Fatty acid ester
Dioxepane
Delta valerolactone
Pyran
Oxane
Dicarboxylic acid or derivatives
Fatty acyl
Hydroxy acid
Furan
Methyl ester
Heteroaromatic compound
Cyclic alcohol
Carboxylic acid ester
Cyclic ketone
Secondary alcohol
Lactone
Ketone
Dialkyl ether
Oxacycle
Carboxylic acid derivative
Oxirane
Ether
Alcohol
Hydrocarbon derivative
Organic oxygen compound
Organooxygen compound
Organic oxide
Carbonyl group
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic heteropolycyclic 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	1.51	ALOGPS
logP	1.21	ChemAxon
logS	-3.4	ALOGPS
pKa (Strongest Acidic)	12.86	ChemAxon
pKa (Strongest Basic)	-3.1	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	6	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	135.8 Å²	ChemAxon
Rotatable Bond Count	5	ChemAxon
Refractivity	110.54 m³·mol⁻¹	ChemAxon
Polarizability	46.51 Å³	ChemAxon
Number of Rings	5	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

External Links

HMDB ID

HMDB0038159

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

FDB017389

KNApSAcK ID

Not Available

Chemspider ID

Not Available

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

131752313

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Not Available

Showing NP-Card for Retrocalamin (NP0049040)

MOL for NP0049040 (Retrocalamin)

3D MOL for NP0049040 (Retrocalamin)

3D SDF for NP0049040 (Retrocalamin)

3D-SDF for NP0049040 (Retrocalamin)

PDB for NP0049040 (Retrocalamin)

3D PDB for NP0049040 (Retrocalamin)

SMILES for NP0049040 (Retrocalamin)

INCHI for NP0049040 (Retrocalamin)

Structure for NP0049040 (Retrocalamin)

3D Structure for NP0049040 (Retrocalamin)