NP-MRD: Showing NP-Card for Daedalin A (NP0007400)

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Record Information

Version

2.0

Created at

2020-12-09 04:13:15 UTC

Updated at

2021-07-15 16:57:29 UTC

NP-MRD ID

NP0007400

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Daedalin A

Provided By

NPAtlas

Description

Daedalin A is a secondary metabolite. Secondary metabolites are metabolically or physiologically non-essential metabolites that may serve a role as defense or signalling molecules. In some cases they are simply molecules that arise from the incomplete metabolism of other secondary metabolites. Daedalin A is found in Daedalea dickinsii. Daedalin A was first documented in 2007 (PMID: 17986791). Based on a literature review a small amount of articles have been published on Daedalin A (PMID: 19270380) (PMID: 20036119).

Structure

MOL 3D MOL SDF 3D SDF PDB SMILES InChI


  Mrv1652306242118393D          

 26 27  0  0  0  0            999 V2000
   -2.3269   -0.8086    1.3869 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6313   -0.0313    0.2452 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.6966    0.9083   -0.3328 C   0  0  1  0  0  0  0  0  0  0  0  0
   -3.7513    0.1907   -0.8617 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2125   -1.0107   -0.7701 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0439   -1.1621   -1.1036 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0929   -0.3745   -0.4924 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4241   -0.5343   -0.8451 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4229    0.2191   -0.2598 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.7455    0.0546   -0.6158 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.0708    1.1504    0.6989 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7588    1.3164    1.0549 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7457    0.5610    0.4696 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5662    0.6798    0.7797 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6930   -1.6679    1.6942 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4915   -0.0857    2.2125 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2947   -1.1367    0.9540 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1106    1.5137    0.5105 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2474    1.6156   -1.0516 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8732    0.2725   -1.8200 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9828   -1.6465   -1.2749 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2715   -1.9216   -1.8766 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.6693   -1.2729   -1.6005 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.2974   -0.6373   -0.0856 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.8387    1.7528    1.1715 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4965    2.0550    1.8127 H   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  1  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  2  5  1  0  0  0  0
  5  6  2  0  0  0  0
  6  7  1  0  0  0  0
  7  8  2  0  0  0  0
  8  9  1  0  0  0  0
  9 10  1  0  0  0  0
  9 11  2  0  0  0  0
 11 12  1  0  0  0  0
 12 13  2  0  0  0  0
 13 14  1  0  0  0  0
 14  2  1  0  0  0  0
 13  7  1  0  0  0  0
  1 15  1  0  0  0  0
  1 16  1  0  0  0  0
  1 17  1  0  0  0  0
  3 18  1  0  0  0  0
  3 19  1  0  0  0  0
  4 20  1  0  0  0  0
  5 21  1  0  0  0  0
  6 22  1  0  0  0  0
  8 23  1  0  0  0  0
 10 24  1  0  0  0  0
 11 25  1  0  0  0  0
 12 26  1  0  0  0  0
M  END


  Mrv1652306242118393D          

 26 27  0  0  0  0            999 V2000
   -2.3269   -0.8086    1.3869 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6313   -0.0313    0.2452 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.6966    0.9083   -0.3328 C   0  0  1  0  0  0  0  0  0  0  0  0
   -3.7513    0.1907   -0.8617 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2125   -1.0107   -0.7701 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0439   -1.1621   -1.1036 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0929   -0.3745   -0.4924 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4241   -0.5343   -0.8451 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4229    0.2191   -0.2598 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.7455    0.0546   -0.6158 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.0708    1.1504    0.6989 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7588    1.3164    1.0549 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7457    0.5610    0.4696 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5662    0.6798    0.7797 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6930   -1.6679    1.6942 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4915   -0.0857    2.2125 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2947   -1.1367    0.9540 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1106    1.5137    0.5105 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2474    1.6156   -1.0516 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8732    0.2725   -1.8200 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9828   -1.6465   -1.2749 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2715   -1.9216   -1.8766 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.6693   -1.2729   -1.6005 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.2974   -0.6373   -0.0856 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.8387    1.7528    1.1715 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4965    2.0550    1.8127 H   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  1  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  2  5  1  0  0  0  0
  5  6  2  0  0  0  0
  6  7  1  0  0  0  0
  7  8  2  0  0  0  0
  8  9  1  0  0  0  0
  9 10  1  0  0  0  0
  9 11  2  0  0  0  0
 11 12  1  0  0  0  0
 12 13  2  0  0  0  0
 13 14  1  0  0  0  0
 14  2  1  0  0  0  0
 13  7  1  0  0  0  0
  1 15  1  0  0  0  0
  1 16  1  0  0  0  0
  1 17  1  0  0  0  0
  3 18  1  0  0  0  0
  3 19  1  0  0  0  0
  4 20  1  0  0  0  0
  5 21  1  0  0  0  0
  6 22  1  0  0  0  0
  8 23  1  0  0  0  0
 10 24  1  0  0  0  0
 11 25  1  0  0  0  0
 12 26  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0007400

> <DATABASE_NAME>
NP-MRD

> <SMILES>
[H]OC1=C([H])C([H])=C2O[C@@](C([H])=C([H])C2=C1[H])(C([H])([H])[H])C([H])([H])O[H]

> <INCHI_IDENTIFIER>
InChI=1S/C11H12O3/c1-11(7-12)5-4-8-6-9(13)2-3-10(8)14-11/h2-6,12-13H,7H2,1H3/t11-/m1/s1

> <INCHI_KEY>
LTKJWSBGTNWRNP-LLVKDONJSA-N

> <FORMULA>
C11H12O3

> <MOLECULAR_WEIGHT>
192.214

> <EXACT_MASS>
192.078644246

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_ATOM_COUNT>
26

> <JCHEM_AVERAGE_POLARIZABILITY>
19.937924960338343

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
(2R)-2-(hydroxymethyl)-2-methyl-2H-chromen-6-ol

> <ALOGPS_LOGP>
1.49

> <JCHEM_LOGP>
1.5233939296666665

> <ALOGPS_LOGS>
-1.76

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
14.313419526195265

> <JCHEM_PKA_STRONGEST_ACIDIC>
9.830999613463081

> <JCHEM_PKA_STRONGEST_BASIC>
-3.0991165840269996

> <JCHEM_POLAR_SURFACE_AREA>
49.69

> <JCHEM_REFRACTIVITY>
53.976000000000006

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
3.34e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(2R)-2-(hydroxymethyl)-2-methylchromen-6-ol

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 24-JUN-21   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   24-JUN-21         0                                  
HETATM    1  C   UNK     0      -2.327  -0.809   1.387  0.00  0.00           C+0
HETATM    2  C   UNK     0      -1.631  -0.031   0.245  0.00  0.00           C+0
HETATM    3  C   UNK     0      -2.697   0.908  -0.333  0.00  0.00           C+0
HETATM    4  O   UNK     0      -3.751   0.191  -0.862  0.00  0.00           O+0
HETATM    5  C   UNK     0      -1.212  -1.011  -0.770  0.00  0.00           C+0
HETATM    6  C   UNK     0       0.044  -1.162  -1.104  0.00  0.00           C+0
HETATM    7  C   UNK     0       1.093  -0.375  -0.492  0.00  0.00           C+0
HETATM    8  C   UNK     0       2.424  -0.534  -0.845  0.00  0.00           C+0
HETATM    9  C   UNK     0       3.423   0.219  -0.260  0.00  0.00           C+0
HETATM   10  O   UNK     0       4.745   0.055  -0.616  0.00  0.00           O+0
HETATM   11  C   UNK     0       3.071   1.150   0.699  0.00  0.00           C+0
HETATM   12  C   UNK     0       1.759   1.316   1.055  0.00  0.00           C+0
HETATM   13  C   UNK     0       0.746   0.561   0.470  0.00  0.00           C+0
HETATM   14  O   UNK     0      -0.566   0.680   0.780  0.00  0.00           O+0
HETATM   15  H   UNK     0      -1.693  -1.668   1.694  0.00  0.00           H+0
HETATM   16  H   UNK     0      -2.491  -0.086   2.212  0.00  0.00           H+0
HETATM   17  H   UNK     0      -3.295  -1.137   0.954  0.00  0.00           H+0
HETATM   18  H   UNK     0      -3.111   1.514   0.510  0.00  0.00           H+0
HETATM   19  H   UNK     0      -2.247   1.616  -1.052  0.00  0.00           H+0
HETATM   20  H   UNK     0      -3.873   0.273  -1.820  0.00  0.00           H+0
HETATM   21  H   UNK     0      -1.983  -1.647  -1.275  0.00  0.00           H+0
HETATM   22  H   UNK     0       0.272  -1.922  -1.877  0.00  0.00           H+0
HETATM   23  H   UNK     0       2.669  -1.273  -1.601  0.00  0.00           H+0
HETATM   24  H   UNK     0       5.297  -0.637  -0.086  0.00  0.00           H+0
HETATM   25  H   UNK     0       3.839   1.753   1.172  0.00  0.00           H+0
HETATM   26  H   UNK     0       1.496   2.055   1.813  0.00  0.00           H+0
CONECT    1    2   15   16   17                                             
CONECT    2    1    3    5   14                                             
CONECT    3    2    4   18   19                                             
CONECT    4    3   20                                                       
CONECT    5    2    6   21                                                  
CONECT    6    5    7   22                                                  
CONECT    7    6    8   13                                                  
CONECT    8    7    9   23                                                  
CONECT    9    8   10   11                                                  
CONECT   10    9   24                                                       
CONECT   11    9   12   25                                                  
CONECT   12   11   13   26                                                  
CONECT   13   12   14    7                                                  
CONECT   14   13    2                                                       
CONECT   15    1                                                            
CONECT   16    1                                                            
CONECT   17    1                                                            
CONECT   18    3                                                            
CONECT   19    3                                                            
CONECT   20    4                                                            
CONECT   21    5                                                            
CONECT   22    6                                                            
CONECT   23    8                                                            
CONECT   24   10                                                            
CONECT   25   11                                                            
CONECT   26   12                                                            
MASTER        0    0    0    0    0    0    0    0   26    0   54    0
END

View in JSmol View NMR Assignments

Synonyms

Value	Source
(2R)-6-Hydroxy-2-hydroxymethyl-2-methyl-2H-chromene	MeSH

Chemical Formula

C₁₁H₁₂O₃

Average Mass

192.2140 Da

Monoisotopic Mass

192.07864 Da

IUPAC Name

(2R)-2-(hydroxymethyl)-2-methyl-2H-chromen-6-ol

Traditional Name

(2R)-2-(hydroxymethyl)-2-methylchromen-6-ol

CAS Registry Number

Not Available

SMILES

C[C@@]1(CO)OC2=C(C=C1)C=C(O)C=C2

InChI Identifier

InChI=1S/C11H12O3/c1-11(7-12)5-4-8-6-9(13)2-3-10(8)14-11/h2-6,12-13H,7H2,1H3/t11-/m1/s1

InChI Key

LTKJWSBGTNWRNP-LLVKDONJSA-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
Daedalea dickinsii	NPAtlas	17986791

Chemical Taxonomy

Classification

Not classified

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	1.49	ALOGPS
logP	1.52	ChemAxon
logS	-1.8	ALOGPS
pKa (Strongest Acidic)	9.83	ChemAxon
pKa (Strongest Basic)	-3.1	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	3	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	49.69 Å²	ChemAxon
Rotatable Bond Count	1	ChemAxon
Refractivity	53.98 m³·mol⁻¹	ChemAxon
Polarizability	19.94 Å³	ChemAxon
Number of Rings	2	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

NPAtlas ID

NPA005544

HMDB ID

Not Available

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

Not Available

KNApSAcK ID

Not Available

Chemspider ID

24652728

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

46216805

PDB ID

Not Available

ChEBI ID

65721

Good Scents ID

Not Available

References

General References

Morimura K, Yamazaki C, Hattori Y, Makabe H, Kamo T, Hirota M: A tyrosinase inhibitor, Daedalin A, from mycelial culture of Daedalea dickinsii. Biosci Biotechnol Biochem. 2007 Nov;71(11):2837-40. doi: 10.1271/bbb.70266. Epub 2007 Nov 7. [PubMed:17986791 ]
Morimura K, Hiramatsu K, Yamazaki C, Hattori Y, Makabe H, Hirota M: Daedalin A, a metabolite of Daedalea dickinsii, inhibits melanin synthesis in an in vitro human skin model. Biosci Biotechnol Biochem. 2009 Mar 23;73(3):627-32. doi: 10.1271/bbb.80695. Epub 2009 Mar 7. [PubMed:19270380 ]
Sekimoto M, Hattori Y, Morimura K, Hirota M, Makabe H: Asymmetric syntheses of daedalin A and quercinol and their tyrosinase inhibitory activity. Bioorg Med Chem Lett. 2010 Feb 1;20(3):1063-4. doi: 10.1016/j.bmcl.2009.12.034. Epub 2009 Dec 11. [PubMed:20036119 ]

Showing NP-Card for Daedalin A (NP0007400)

MOL for NP0007400 (Daedalin A)

3D MOL for NP0007400 (Daedalin A)

3D SDF for NP0007400 (Daedalin A)

3D-SDF for NP0007400 (Daedalin A)

PDB for NP0007400 (Daedalin A)

3D PDB for NP0007400 (Daedalin A)

SMILES for NP0007400 (Daedalin A)

INCHI for NP0007400 (Daedalin A)

Structure for NP0007400 (Daedalin A)

3D Structure for NP0007400 (Daedalin A)