NP-MRD: Showing NP-Card for Crombenin (NP0055429)

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Record Information

Version

2.0

Created at

2022-04-28 01:29:09 UTC

Updated at

2022-04-28 01:29:09 UTC

NP-MRD ID

NP0055429

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Crombenin

Description

(2S,4'S)-4,4',6,6',7'-pentahydroxy-1',4'-dihydro-3H-spiro[1-benzofuran-2,3'-[2]benzopyran]-3-one belongs to the class of organic compounds known as 2-benzopyrans. These are organic aromatic compounds that 1-benzopyran, a bicyclic compound made up of a benzene ring fused to a pyran, so that the oxygen atom is at the 2-position. Crombenin is found in Acacia crombei. Based on a literature review very few articles have been published on (2S,4'S)-4,4',6,6',7'-pentahydroxy-1',4'-dihydro-3H-spiro[1-benzofuran-2,3'-[2]benzopyran]-3-one.

Structure

MOL 3D MOL SDF PDB SMILES InChI

     RDKit          3D

 36 39  0  0  0  0  0  0  0  0999 V2000
    0.3336   -0.4347    1.9181 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.9448   -0.3813    0.8239 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3942   -0.1361    0.7106 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2996    0.4011    1.5904 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9134    0.8331    2.8513 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.6169    0.5189    1.2272 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.9993    0.0881   -0.0290 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.3279    0.2072   -0.3945 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.0859   -0.4502   -0.9072 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7405   -0.5754   -0.5485 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6469   -1.0670   -1.2213 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.4881   -0.5270   -0.5698 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.2092    0.7015   -1.1358 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7133    1.3442   -0.3135 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9860    0.5818   -0.4018 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1998    1.2754   -0.2970 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3850    0.5774   -0.3779 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.6147    1.1917   -0.2836 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3256   -0.7811   -0.5594 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.5306   -1.4933   -0.6420 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1411   -1.4718   -0.6635 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9250   -0.7786   -0.5836 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6379   -1.5064   -0.6937 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.5818   -2.4000    0.3766 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.9637    0.7661    3.1574 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.3594    0.9381    1.8958 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.6714    1.0394   -0.8506 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.3941   -0.7846   -1.8880 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3499    1.4408    0.7144 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8580    2.3716   -0.7088 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2039    2.3608   -0.1524 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.6620    2.1941   -0.1496 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.4237   -1.0464   -0.5734 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0797   -2.5390   -0.8062 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6186   -2.0804   -1.6391 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1524   -2.0672    1.1247 H   0  0  0  0  0  0  0  0  0  0  0  0
 24 23  1  0
 23 22  1  0
 22 15  2  0
 15 14  1  0
 14 13  1  0
 12 13  1  6
 12 11  1  0
 11 10  1  0
 10  3  2  0
  3  2  1  0
  2  1  2  0
  3  4  1  0
  4  5  1  0
  4  6  2  0
  6  7  1  0
  7  8  1  0
  7  9  2  0
 15 16  1  0
 16 17  2  0
 17 18  1  0
 17 19  1  0
 19 20  1  0
 19 21  2  0
 12 23  1  0
  2 12  1  0
 21 22  1  0
  9 10  1  0
 24 36  1  0
 23 35  1  6
 14 29  1  0
 14 30  1  0
  5 25  1  0
  6 26  1  0
  8 27  1  0
  9 28  1  0
 16 31  1  0
 18 32  1  0
 20 33  1  0
 21 34  1  0
M  END


  Mrv1652304282203292D          

 24 27  0  0  1  0            999 V2000
    4.0483    0.6945    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.1917   -0.1179    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.9670   -0.3999    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.5989    0.1305    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.4554    0.9429    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.6801    1.2249    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.5367    2.0374    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.3742   -0.1515    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.4634   -0.5054    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.8698    0.0675    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    3.2313    0.8091    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8438    1.5375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.3393    0.6994    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.5269    0.5559    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2449   -0.2194    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7754   -0.8512    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5878   -0.7078    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.4325   -0.3628    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0980    0.2691    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1840    1.0444    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9965    1.1878    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3464    1.6762    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9104    0.1256    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.3679    1.5239    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
  6  7  1  0  0  0  0
  4  8  1  0  0  0  0
  2  9  1  0  0  0  0
 10  9  1  1  0  0  0
 10 11  1  0  0  0  0
  1 11  1  0  0  0  0
 11 12  2  0  0  0  0
 10 13  1  0  0  0  0
 13 14  1  0  0  0  0
 14 15  2  0  0  0  0
 15 16  1  0  0  0  0
 16 17  1  0  0  0  0
 10 17  1  0  0  0  0
 15 18  1  0  0  0  0
 18 19  2  0  0  0  0
 19 20  1  0  0  0  0
 20 21  2  0  0  0  0
 14 21  1  0  0  0  0
 20 22  1  0  0  0  0
 19 23  1  0  0  0  0
 13 24  1  6  0  0  0
M  END
> <DATABASE_ID>
NP0055429

> <DATABASE_NAME>
NP-MRD

> <SMILES>
O[C@H]1C2=C(CO[C@]11OC3=C(C1=O)C(O)=CC(O)=C3)C=C(O)C(O)=C2

> <INCHI_IDENTIFIER>
InChI=1S/C16H12O8/c17-7-2-11(20)13-12(3-7)24-16(15(13)22)14(21)8-4-10(19)9(18)1-6(8)5-23-16/h1-4,14,17-21H,5H2/t14-,16-/m0/s1

> <INCHI_KEY>
AZXDUXHNBXWISJ-HOCLYGCPSA-N

> <FORMULA>
C16H12O8

> <MOLECULAR_WEIGHT>
332.264

> <EXACT_MASS>
332.053217346

> <JCHEM_ACCEPTOR_COUNT>
8

> <JCHEM_ATOM_COUNT>
36

> <JCHEM_AVERAGE_POLARIZABILITY>
31.363164331325095

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
5

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
(2S,4'S)-4,4',6,6',7'-pentahydroxy-1',4'-dihydro-3H-spiro[1-benzofuran-2,3'-[2]benzopyran]-3-one

> <ALOGPS_LOGP>
0.75

> <JCHEM_LOGP>
2.173243249

> <ALOGPS_LOGS>
-2.33

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
4

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
8.821252770750007

> <JCHEM_PKA_STRONGEST_ACIDIC>
7.571415919827729

> <JCHEM_PKA_STRONGEST_BASIC>
-3.999792816898201

> <JCHEM_POLAR_SURFACE_AREA>
136.68

> <JCHEM_REFRACTIVITY>
79.45710000000001

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.56e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(2S,4'S)-4,4',6,6',7'-pentahydroxy-1',4'-dihydrospiro[1-benzofuran-2,3'-[2]benzopyran]-3-one

> <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       7.557   1.296   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       7.825  -0.220   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       9.272  -0.747   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      10.451   0.244   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      10.183   1.760   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       8.736   2.287   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0       8.468   3.803   0.000  0.00  0.00           O+0
HETATM    8  O   UNK     0      11.899  -0.283   0.000  0.00  0.00           O+0
HETATM    9  O   UNK     0       6.465  -0.943   0.000  0.00  0.00           O+0
HETATM   10  C   UNK     0       5.357   0.126   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       6.032   1.510   0.000  0.00  0.00           C+0
HETATM   12  O   UNK     0       5.308   2.870   0.000  0.00  0.00           O+0
HETATM   13  C   UNK     0       4.367   1.306   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       2.850   1.038   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       2.324  -0.409   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       3.314  -1.589   0.000  0.00  0.00           C+0
HETATM   17  O   UNK     0       4.831  -1.321   0.000  0.00  0.00           O+0
HETATM   18  C   UNK     0       0.807  -0.677   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0      -0.183   0.502   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       0.344   1.949   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0       1.860   2.217   0.000  0.00  0.00           C+0
HETATM   22  O   UNK     0      -0.647   3.129   0.000  0.00  0.00           O+0
HETATM   23  O   UNK     0      -1.699   0.234   0.000  0.00  0.00           O+0
HETATM   24  O   UNK     0       4.420   2.845   0.000  0.00  0.00           O+0
CONECT    1    2    6   11                                                  
CONECT    2    1    3    9                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5    8                                                  
CONECT    5    4    6                                                       
CONECT    6    5    1    7                                                  
CONECT    7    6                                                            
CONECT    8    4                                                            
CONECT    9    2   10                                                       
CONECT   10    9   11   13   17                                             
CONECT   11   10    1   12                                                  
CONECT   12   11                                                            
CONECT   13   10   14   24                                                  
CONECT   14   13   15   21                                                  
CONECT   15   14   16   18                                                  
CONECT   16   15   17                                                       
CONECT   17   16   10                                                       
CONECT   18   15   19                                                       
CONECT   19   18   20   23                                                  
CONECT   20   19   21   22                                                  
CONECT   21   20   14                                                       
CONECT   22   20                                                            
CONECT   23   19                                                            
CONECT   24   13                                                            
MASTER        0    0    0    0    0    0    0    0   24    0   54    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₁₆H₁₂O₈

Average Mass

332.2640 Da

Monoisotopic Mass

332.05322 Da

IUPAC Name

(2S,4'S)-4,4',6,6',7'-pentahydroxy-1',4'-dihydro-3H-spiro[1-benzofuran-2,3'-[2]benzopyran]-3-one

Traditional Name

(2S,4'S)-4,4',6,6',7'-pentahydroxy-1',4'-dihydrospiro[1-benzofuran-2,3'-[2]benzopyran]-3-one

CAS Registry Number

Not Available

SMILES

O[C@H]1C2=C(CO[C@]11OC3=C(C1=O)C(O)=CC(O)=C3)C=C(O)C(O)=C2

InChI Identifier

InChI=1S/C16H12O8/c17-7-2-11(20)13-12(3-7)24-16(15(13)22)14(21)8-4-10(19)9(18)1-6(8)5-23-16/h1-4,14,17-21H,5H2/t14-,16-/m0/s1

InChI Key

AZXDUXHNBXWISJ-HOCLYGCPSA-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
Acacia crombei	Plant	KNApSAcK

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as 2-benzopyrans. These are organic aromatic compounds that 1-benzopyran, a bicyclic compound made up of a benzene ring fused to a pyran, so that the oxygen atom is at the 2-position.

Kingdom

Organic compounds

Super Class

Organoheterocyclic compounds

Class

Benzopyrans

Sub Class

2-benzopyrans

Direct Parent

2-benzopyrans

Alternative Parents

Substituents

2-benzopyran
Coumaran
Benzofuran
Aryl alkyl ketone
Aryl ketone
1-hydroxy-4-unsubstituted benzenoid
1-hydroxy-2-unsubstituted benzenoid
Ketal
Benzenoid
Vinylogous acid
Secondary alcohol
Ketone
Oxacycle
Polyol
Acetal
Organic oxygen compound
Organic oxide
Hydrocarbon derivative
Organooxygen compound
Alcohol
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	0.75	ALOGPS
logP	2.17	ChemAxon
logS	-2.3	ALOGPS
pKa (Strongest Acidic)	7.57	ChemAxon
pKa (Strongest Basic)	-4	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	8	ChemAxon
Hydrogen Donor Count	5	ChemAxon
Polar Surface Area	136.68 Å²	ChemAxon
Rotatable Bond Count	0	ChemAxon
Refractivity	79.46 m³·mol⁻¹	ChemAxon
Polarizability	31.36 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

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

163089805

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Showing NP-Card for Crombenin (NP0055429)

MOL for NP0055429 (Crombenin)

3D MOL for NP0055429 (Crombenin)

3D SDF for NP0055429 (Crombenin)

3D-SDF for NP0055429 (Crombenin)

PDB for NP0055429 (Crombenin)

3D PDB for NP0055429 (Crombenin)

SMILES for NP0055429 (Crombenin)

INCHI for NP0055429 (Crombenin)

Structure for NP0055429 (Crombenin)

3D Structure for NP0055429 (Crombenin)