NP-MRD: Showing NP-Card for Micromelin (NP0051454)

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Record Information

Version

2.0

Created at

2022-04-27 22:48:52 UTC

Updated at

2022-04-27 22:48:52 UTC

NP-MRD ID

NP0051454

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Micromelin

Description

Micromelin belongs to the class of organic compounds known as coumarins and derivatives. These are polycyclic aromatic compounds containing a 1-benzopyran moiety with a ketone group at the C2 carbon atom (1-benzopyran-2-one). Micromelin is found in Caesaria graveolens, Casearia graveolens, Micromelum hirsutum, Micromelum integerrimum , Micromelum integrrimum and Micromelum minutum . Micromelin was first documented in 2011 (PMID: 21837101). Based on a literature review very few articles have been published on Micromelin (PMID: 21544717).

Structure

MOL 3D MOL SDF PDB SMILES InChI

     RDKit          3D

 33 36  0  0  0  0  0  0  0  0999 V2000
    1.1941   -3.7145    0.2858 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4420   -2.5350    0.3097 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.9667   -1.2786    0.1436 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3046   -1.0398   -0.0692 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7651    0.2678   -0.2303 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0413    0.5108   -0.4355 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.5213    1.7173   -0.5926 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.7467    1.9387   -0.7891 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.6665    2.7980   -0.5440 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3078    2.6008   -0.3304 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8755    1.3046   -0.1739 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5149    1.0468    0.0441 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0410   -0.2260    0.2043 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3619   -0.5411    0.4288 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.9771   -1.1433   -0.7246 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3322   -1.1276   -0.4351 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1649   -2.0517   -0.7367 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6733    0.1055    0.2686 C   0  0  1  0  0  0  0  0  0  0  0  0
   -4.6539    1.0762   -0.3479 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3125    0.3784    1.5602 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2801    0.6168    0.6611 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.6436   -4.5473   -0.2208 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.1985   -3.6444   -0.1385 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3162   -4.0628    1.3398 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.0290   -1.8398   -0.1180 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.0575    3.7906   -0.6733 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6186    3.4347   -0.2882 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1592    1.8892    0.0837 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5103   -1.3125    1.2291 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.3536    0.5483   -0.9945 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1190    1.8392   -0.9184 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.2487    1.5822    0.4665 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1038    1.6185    0.2702 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3 13  2  0
 13 12  1  0
 12 11  2  0
 11 10  1  0
 10  9  2  0
  9  7  1  0
  7  8  2  0
  7  6  1  0
  6  5  1  0
  5  4  2  0
 13 14  1  0
 14 15  1  0
 15 16  1  0
 16 17  2  0
 16 18  1  0
 18 19  1  6
 18 20  1  0
 20 21  1  0
  4  3  1  0
 21 14  1  0
  5 11  1  0
 21 18  1  0
  1 22  1  0
  1 23  1  0
  1 24  1  0
 12 28  1  0
 10 27  1  0
  9 26  1  0
  4 25  1  0
 14 29  1  1
 19 30  1  0
 19 31  1  0
 19 32  1  0
 21 33  1  6
M  END


  Mrv1652304282200482D          

 21 24  0  0  1  0            999 V2000
   -0.5914   -4.2413    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1435   -4.8544    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8885   -5.6390    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0816   -5.8105    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4705   -5.1974    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2155   -4.4128    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2775   -5.3689    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5324   -6.1536    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9804   -6.7666    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2353   -7.5513    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.1734   -6.5951    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9504   -4.6828    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5025   -5.2959    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8464   -3.4566    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.6310   -3.2017    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.6310   -2.3767    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.8464   -2.1218    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5914   -1.3371    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3614   -2.7892    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9665   -1.6230    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3455   -2.7892    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0  0  0  0
  2  3  1  0  0  0  0
  3  4  2  0  0  0  0
  4  5  1  0  0  0  0
  5  6  2  0  0  0  0
  1  6  1  0  0  0  0
  5  7  1  0  0  0  0
  7  8  2  0  0  0  0
  8  9  1  0  0  0  0
  9 10  2  0  0  0  0
  9 11  1  0  0  0  0
  4 11  1  0  0  0  0
  2 12  1  0  0  0  0
 12 13  1  0  0  0  0
 14  1  1  1  0  0  0
 14 15  1  0  0  0  0
 15 16  1  0  0  0  0
 16 17  1  0  0  0  0
 17 18  2  0  0  0  0
 17 19  1  0  0  0  0
 14 19  1  0  0  0  0
 16 20  1  1  0  0  0
 16 21  1  0  0  0  0
 15 21  1  6  0  0  0
M  END
> <DATABASE_ID>
NP0051454

> <DATABASE_NAME>
NP-MRD

> <SMILES>
COC1=C(C=C2C=CC(=O)OC2=C1)[C@@H]1OC(=O)[C@@]2(C)O[C@@H]12

> <INCHI_IDENTIFIER>
InChI=1S/C15H12O6/c1-15-13(21-15)12(20-14(15)17)8-5-7-3-4-11(16)19-9(7)6-10(8)18-2/h3-6,12-13H,1-2H3/t12-,13-,15-/m0/s1

> <INCHI_KEY>
VIORQNDMAWQQCV-YDHLFZDLSA-N

> <FORMULA>
C15H12O6

> <MOLECULAR_WEIGHT>
288.255

> <EXACT_MASS>
288.063388106

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_ATOM_COUNT>
33

> <JCHEM_AVERAGE_POLARIZABILITY>
27.512391734712743

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
7-methoxy-6-[(1S,2S,5S)-5-methyl-4-oxo-3,6-dioxabicyclo[3.1.0]hexan-2-yl]-2H-chromen-2-one

> <ALOGPS_LOGP>
2.19

> <JCHEM_LOGP>
1.5465488773333331

> <ALOGPS_LOGS>
-3.14

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
4

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_BASIC>
-4.208624931082011

> <JCHEM_POLAR_SURFACE_AREA>
74.36

> <JCHEM_REFRACTIVITY>
70.29360000000001

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
2.10e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
micromelin

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 28-APR-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   28-APR-22         0                                  
HETATM    1  C   UNK     0      -1.104  -7.917   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -2.134  -9.061   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -1.659 -10.526   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -0.152 -10.846   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       0.878  -9.702   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       0.402  -8.237   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       2.385 -10.022   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       2.860 -11.487   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       1.830 -12.631   0.000  0.00  0.00           C+0
HETATM   10  O   UNK     0       2.306 -14.096   0.000  0.00  0.00           O+0
HETATM   11  O   UNK     0       0.324 -12.311   0.000  0.00  0.00           O+0
HETATM   12  O   UNK     0      -3.641  -8.741   0.000  0.00  0.00           O+0
HETATM   13  C   UNK     0      -4.671  -9.886   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      -1.580  -6.452   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0      -3.045  -5.977   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0      -3.045  -4.437   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0      -1.580  -3.961   0.000  0.00  0.00           C+0
HETATM   18  O   UNK     0      -1.104  -2.496   0.000  0.00  0.00           O+0
HETATM   19  O   UNK     0      -0.675  -5.207   0.000  0.00  0.00           O+0
HETATM   20  C   UNK     0      -3.671  -3.030   0.000  0.00  0.00           C+0
HETATM   21  O   UNK     0      -4.378  -5.207   0.000  0.00  0.00           O+0
CONECT    1    2    6   14                                                  
CONECT    2    1    3   12                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5   11                                                  
CONECT    5    4    6    7                                                  
CONECT    6    5    1                                                       
CONECT    7    5    8                                                       
CONECT    8    7    9                                                       
CONECT    9    8   10   11                                                  
CONECT   10    9                                                            
CONECT   11    9    4                                                       
CONECT   12    2   13                                                       
CONECT   13   12                                                            
CONECT   14    1   15   19                                                  
CONECT   15   14   16   21                                                  
CONECT   16   15   17   20   21                                             
CONECT   17   16   18   19                                                  
CONECT   18   17                                                            
CONECT   19   17   14                                                       
CONECT   20   16                                                            
CONECT   21   16   15                                                       
MASTER        0    0    0    0    0    0    0    0   21    0   48    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₁₅H₁₂O₆

Average Mass

288.2550 Da

Monoisotopic Mass

288.06339 Da

IUPAC Name

7-methoxy-6-[(1S,2S,5S)-5-methyl-4-oxo-3,6-dioxabicyclo[3.1.0]hexan-2-yl]-2H-chromen-2-one

Traditional Name

micromelin

CAS Registry Number

Not Available

SMILES

COC1=C(C=C2C=CC(=O)OC2=C1)[C@@H]1OC(=O)[C@@]2(C)O[C@@H]12

InChI Identifier

InChI=1S/C15H12O6/c1-15-13(21-15)12(20-14(15)17)8-5-7-3-4-11(16)19-9(7)6-10(8)18-2/h3-6,12-13H,1-2H3/t12-,13-,15-/m0/s1

InChI Key

VIORQNDMAWQQCV-YDHLFZDLSA-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, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 252 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 50 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 75 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 101 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 126 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 151 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 176 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 201 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 226 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, 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
Caesaria graveolens	-	KNApSAcK
Casearia graveolens	LOTUS Database	35616633
Micromelum hirsutum	LOTUS Database	35616633
Micromelum integerrimum	Plant	KNApSAcK
Micromelum integrrimum	Plant	KNApSAcK
Micromelum minutum	Plant	KNApSAcK

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as coumarins and derivatives. These are polycyclic aromatic compounds containing a 1-benzopyran moiety with a ketone group at the C2 carbon atom (1-benzopyran-2-one).

Kingdom

Organic compounds

Super Class

Phenylpropanoids and polyketides

Class

Coumarins and derivatives

Sub Class

Not Available

Direct Parent

Coumarins and derivatives

Alternative Parents

Substituents

Coumarin
Benzopyran
1-benzopyran
Anisole
Alkyl aryl ether
Pyranone
Para-dioxane
Benzenoid
Pyran
Gamma butyrolactone
Heteroaromatic compound
Tetrahydrofuran
Carboxylic acid ester
Lactone
Ether
Oxirane
Dialkyl ether
Organoheterocyclic compound
Carboxylic acid derivative
Oxacycle
Monocarboxylic acid or derivatives
Organooxygen compound
Organic oxygen compound
Carbonyl group
Hydrocarbon derivative
Organic oxide
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic heteropolycyclic compounds

External Descriptors

coumarins (CHEBI:6929 )
coumarins (C09277 )

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	2.19	ALOGPS
logP	1.55	ChemAxon
logS	-3.1	ALOGPS
pKa (Strongest Basic)	-4.2	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	4	ChemAxon
Hydrogen Donor Count	0	ChemAxon
Polar Surface Area	74.36 Å²	ChemAxon
Rotatable Bond Count	2	ChemAxon
Refractivity	70.29 m³·mol⁻¹	ChemAxon
Polarizability	27.51 Å³	ChemAxon
Number of Rings	4	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

Not Available

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

Not Available

KNApSAcK ID

C00002484

Chemspider ID

65985

KEGG Compound ID

C09277

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

73230

PDB ID

Not Available

ChEBI ID

6929

Good Scents ID

Not Available

References

General References

Fun HK, Siridechakorn I, Laphookhieo S, Chantrapromma S: Absolute configuration of micromelin. Acta Crystallogr Sect E Struct Rep Online. 2011 Jul 1;67(Pt 7):o1706-7. doi: 10.1107/S1600536811022720. Epub 2011 Jun 18. [PubMed:21837101 ]
Lekphrom R, Kanokmedhakul S, Kukongviriyapan V, Kanokmedhakul K: C-7 oxygenated coumarins from the fruits of Micromelum minutum. Arch Pharm Res. 2011 Apr;34(4):527-31. doi: 10.1007/s12272-011-0402-y. Epub 2011 May 5. [PubMed:21544717 ]

Showing NP-Card for Micromelin (NP0051454)

MOL for NP0051454 (Micromelin)

3D MOL for NP0051454 (Micromelin)

3D SDF for NP0051454 (Micromelin)

3D-SDF for NP0051454 (Micromelin)

PDB for NP0051454 (Micromelin)

3D PDB for NP0051454 (Micromelin)

SMILES for NP0051454 (Micromelin)

INCHI for NP0051454 (Micromelin)

Structure for NP0051454 (Micromelin)

3D Structure for NP0051454 (Micromelin)