NP-MRD: Showing NP-Card for Lucidimine B (NP0014989)

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Record Information

Version

2.0

Created at

2021-01-06 00:08:16 UTC

Updated at

2021-07-15 17:18:44 UTC

NP-MRD ID

NP0014989

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Lucidimine B

Provided By

NPAtlas

Description

Lucidimine B is found in Ganoderma lucidum. It was first documented in 2012 (PMID: 34383397). Based on a literature review very few articles have been published on Lucidimine B (PMID: 26666338) (PMID: 34383398) (PMID: 34383396) (PMID: 30023870).

Structure

MOL 3D MOL SDF 3D SDF PDB SMILES InChI


  Mrv1652306242117123D          

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M  END

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M  END


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M  END
> <DATABASE_ID>
NP0014989

> <DATABASE_NAME>
NP-MRD

> <SMILES>
[H]OC1=C([H])C([H])=C2OC([H])([H])C3=C4C(=C([H])N=C3C2=C1[H])C([H])([H])C([H])([H])C4([H])[H]

> <INCHI_IDENTIFIER>
InChI=1S/C15H13NO2/c17-10-4-5-14-12(6-10)15-13(8-18-14)11-3-1-2-9(11)7-16-15/h4-7,17H,1-3,8H2

> <INCHI_KEY>
NACSDIWKTFLUJA-UHFFFAOYSA-N

> <FORMULA>
C15H13NO2

> <MOLECULAR_WEIGHT>
239.274

> <EXACT_MASS>
239.094628663

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_ATOM_COUNT>
31

> <JCHEM_AVERAGE_POLARIZABILITY>
26.200342973444624

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
8-oxa-17-azatetracyclo[8.7.0.0^{2,7}.0^{11,15}]heptadeca-1(17),2,4,6,10,15-hexaen-4-ol

> <ALOGPS_LOGP>
2.96

> <JCHEM_LOGP>
3.086325331666667

> <ALOGPS_LOGS>
-2.37

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
4

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_ACIDIC>
9.599460530681325

> <JCHEM_PKA_STRONGEST_BASIC>
4.370019588266098

> <JCHEM_POLAR_SURFACE_AREA>
42.35000000000001

> <JCHEM_REFRACTIVITY>
68.54520000000001

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.02e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
8-oxa-17-azatetracyclo[8.7.0.0^{2,7}.0^{11,15}]heptadeca-1(17),2,4,6,10,15-hexaen-4-ol

> <JCHEM_VEBER_RULE>
0

$$$$

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  4 21  1  0
  7 22  1  0
 10 23  1  0
 14 24  1  0
 14 25  1  0
 16 26  1  0
 16 27  1  0
 17 28  1  0
 17 29  1  0
 18 30  1  0
 18 31  1  0
M  END

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  O   UNK     0       4.935  -0.862   1.933  0.00  0.00           O+0
HETATM    2  C   UNK     0       4.063  -0.565   0.868  0.00  0.00           C+0
HETATM    3  C   UNK     0       4.536  -0.344  -0.409  0.00  0.00           C+0
HETATM    4  C   UNK     0       3.689  -0.052  -1.458  0.00  0.00           C+0
HETATM    5  C   UNK     0       2.317   0.027  -1.241  0.00  0.00           C+0
HETATM    6  C   UNK     0       1.840  -0.193   0.034  0.00  0.00           C+0
HETATM    7  C   UNK     0       2.701  -0.481   1.057  0.00  0.00           C+0
HETATM    8  C   UNK     0       0.397  -0.127   0.342  0.00  0.00           C+0
HETATM    9  N   UNK     0      -0.025  -0.350   1.610  0.00  0.00           N+0
HETATM   10  C   UNK     0      -1.345  -0.279   1.843  0.00  0.00           C+0
HETATM   11  C   UNK     0      -2.270   0.011   0.835  0.00  0.00           C+0
HETATM   12  C   UNK     0      -1.809   0.231  -0.433  0.00  0.00           C+0
HETATM   13  C   UNK     0      -0.444   0.163  -0.700  0.00  0.00           C+0
HETATM   14  C   UNK     0       0.023   0.408  -2.092  0.00  0.00           C+0
HETATM   15  O   UNK     0       1.407   0.310  -2.218  0.00  0.00           O+0
HETATM   16  C   UNK     0      -2.955   0.521  -1.343  0.00  0.00           C+0
HETATM   17  C   UNK     0      -4.162   0.133  -0.560  0.00  0.00           C+0
HETATM   18  C   UNK     0      -3.766   0.134   0.892  0.00  0.00           C+0
HETATM   19  H   UNK     0       5.295  -0.068   2.458  0.00  0.00           H+0
HETATM   20  H   UNK     0       5.596  -0.401  -0.598  0.00  0.00           H+0
HETATM   21  H   UNK     0       4.015   0.126  -2.466  0.00  0.00           H+0
HETATM   22  H   UNK     0       2.312  -0.650   2.047  0.00  0.00           H+0
HETATM   23  H   UNK     0      -1.759  -0.448   2.842  0.00  0.00           H+0
HETATM   24  H   UNK     0      -0.431  -0.391  -2.728  0.00  0.00           H+0
HETATM   25  H   UNK     0      -0.373   1.373  -2.449  0.00  0.00           H+0
HETATM   26  H   UNK     0      -2.896  -0.078  -2.275  0.00  0.00           H+0
HETATM   27  H   UNK     0      -3.011   1.597  -1.602  0.00  0.00           H+0
HETATM   28  H   UNK     0      -4.611  -0.842  -0.883  0.00  0.00           H+0
HETATM   29  H   UNK     0      -4.997   0.884  -0.658  0.00  0.00           H+0
HETATM   30  H   UNK     0      -4.179  -0.807   1.343  0.00  0.00           H+0
HETATM   31  H   UNK     0      -4.093   1.018   1.447  0.00  0.00           H+0
CONECT    1    2   19                                                       
CONECT    2    1    3    7                                                  
CONECT    3    2    4   20                                                  
CONECT    4    3    5   21                                                  
CONECT    5    4    6   15                                                  
CONECT    6    5    7    8                                                  
CONECT    7    6    2   22                                                  
CONECT    8    6    9   13                                                  
CONECT    9    8   10                                                       
CONECT   10    9   11   23                                                  
CONECT   11   10   12   18                                                  
CONECT   12   11   13   16                                                  
CONECT   13   12   14    8                                                  
CONECT   14   13   15   24   25                                             
CONECT   15   14    5                                                       
CONECT   16   12   17   26   27                                             
CONECT   17   16   18   28   29                                             
CONECT   18   17   11   30   31                                             
CONECT   19    1                                                            
CONECT   20    3                                                            
CONECT   21    4                                                            
CONECT   22    7                                                            
CONECT   23   10                                                            
CONECT   24   14                                                            
CONECT   25   14                                                            
CONECT   26   16                                                            
CONECT   27   16                                                            
CONECT   28   17                                                            
CONECT   29   17                                                            
CONECT   30   18                                                            
CONECT   31   18                                                            
MASTER        0    0    0    0    0    0    0    0   31    0   68    0
END

RDKit          3D

31 34  0  0  0  0  0  0  0  0999 V2000
    4.9348   -0.8623    1.9325 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.0634   -0.5647    0.8680 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.5361   -0.3443   -0.4086 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6887   -0.0520   -1.4582 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3174    0.0266   -1.2412 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8396   -0.1929    0.0336 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7010   -0.4811    1.0567 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3967   -0.1268    0.3422 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0245   -0.3501    1.6103 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3455   -0.2793    1.8428 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2703    0.0114    0.8349 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8090    0.2311   -0.4329 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4442    0.1634   -0.7000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0233    0.4081   -2.0916 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4067    0.3098   -2.2183 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9547    0.5214   -1.3426 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1618    0.1327   -0.5604 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7664    0.1341    0.8918 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.2951   -0.0680    2.4582 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.5965   -0.4006   -0.5984 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.0153    0.1263   -2.4665 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.3115   -0.6501    2.0475 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7589   -0.4479    2.8419 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4311   -0.3910   -2.7277 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3731    1.3732   -2.4488 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8958   -0.0775   -2.2750 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0106    1.5973   -1.6018 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6109   -0.8416   -0.8829 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9970    0.8839   -0.6583 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1789   -0.8069    1.3432 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0935    1.0179    1.4471 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  2  0
  3  4  1  0
  4  5  2  0
  5  6  1  0
  6  7  2  0
  6  8  1  0
  8  9  2  0
  9 10  1  0
 10 11  2  0
 11 12  1  0
 12 13  2  0
 13 14  1  0
 14 15  1  0
 12 16  1  0
 16 17  1  0
 17 18  1  0
  7  2  1  0
 13  8  1  0
 15  5  1  0
 18 11  1  0
  1 19  1  0
  3 20  1  0
  4 21  1  0
  7 22  1  0
 10 23  1  0
 14 24  1  0
 14 25  1  0
 16 26  1  0
 16 27  1  0
 17 28  1  0
 17 29  1  0
 18 30  1  0
 18 31  1  0
M  END

View in JSmol View NMR Assignments

Synonyms

Not Available

Chemical Formula

C₁₅H₁₃NO₂

Average Mass

239.2740 Da

Monoisotopic Mass

239.09463 Da

IUPAC Name

8-oxa-17-azatetracyclo[8.7.0.0^{2,7}.0^{11,15}]heptadeca-1(17),2,4,6,10,15-hexaen-4-ol

Traditional Name

8-oxa-17-azatetracyclo[8.7.0.0^{2,7}.0^{11,15}]heptadeca-1(17),2,4,6,10,15-hexaen-4-ol

CAS Registry Number

Not Available

SMILES

OC1=CC2=C(OCC3=C4CCCC4=CN=C23)C=C1

InChI Identifier

InChI=1S/C15H13NO2/c17-10-4-5-14-12(6-10)15-13(8-18-14)11-3-1-2-9(11)7-16-15/h4-7,17H,1-3,8H2

InChI Key

NACSDIWKTFLUJA-UHFFFAOYSA-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
Ganoderma lucidum	NPAtlas	26666338

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	2.96	ALOGPS
logP	3.09	ChemAxon
logS	-2.4	ALOGPS
pKa (Strongest Acidic)	9.6	ChemAxon
pKa (Strongest Basic)	4.37	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	3	ChemAxon
Hydrogen Donor Count	1	ChemAxon
Polar Surface Area	42.35 Å²	ChemAxon
Rotatable Bond Count	0	ChemAxon
Refractivity	68.55 m³·mol⁻¹	ChemAxon
Polarizability	26.2 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

NPAtlas ID

NPA001466

HMDB ID

Not Available

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

Not Available

KNApSAcK ID

Not Available

Chemspider ID

78435571

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

139583498

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Zhao ZZ, Chen HP, Feng T, Li ZH, Dong ZJ, Liu JK: Lucidimine A-D, four new alkaloids from the fruiting bodies of Ganoderma lucidum. J Asian Nat Prod Res. 2015;17(12):1160-5. doi: 10.1080/10286020.2015.1119128. Epub 2015 Dec 14. [PubMed:26666338 ]
Mitchell PM: The cost-effectiveness of what in health and care?. 2021 Feb. [PubMed:34383398 ]
Authors unspecified: Ozanimod. 2012. [PubMed:34383397 ]
Authors unspecified: Ponesimod. 2012. [PubMed:34383396 ]
Chen Y, Lan P: Total Syntheses and Biological Evaluation of the Ganoderma lucidum Alkaloids Lucidimines B and C. ACS Omega. 2018 Mar 31;3(3):3471-3481. doi: 10.1021/acsomega.8b00295. Epub 2018 Mar 26. [PubMed:30023870 ]

Showing NP-Card for Lucidimine B (NP0014989)

MOL for NP0014989 (Lucidimine B)

3D MOL for NP0014989 (Lucidimine B)

3D SDF for NP0014989 (Lucidimine B)

3D-SDF for NP0014989 (Lucidimine B)

PDB for NP0014989 (Lucidimine B)

3D PDB for NP0014989 (Lucidimine B)

SMILES for NP0014989 (Lucidimine B)

INCHI for NP0014989 (Lucidimine B)

Structure for NP0014989 (Lucidimine B)

3D Structure for NP0014989 (Lucidimine B)