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Record Information

Version

5.0

Status

Detected but not Quantified

Creation Date

2021-09-11 13:27:11 UTC

Update Date

2021-09-26 23:08:08 UTC

HMDB ID

HMDB0254256

Secondary Accession Numbers

None

Metabolite Identification

Common Name

lycorine

Description

5,7-dioxa-12-azapentacyclo[10.6.1.0²,¹⁰.0⁴,⁸.0¹⁵,¹⁹]nonadeca-2,4(8),9,15-tetraene-17,18-diol belongs to the class of organic compounds known as lycorine-type amaryllidaceae alkaloids. These are amaryllidaceae alkaloids compounds containing the lycorine skeleton, made up of a pyrrolo[d,e]phenanthridine ring system. Based on a literature review very few articles have been published on 5,7-dioxa-12-azapentacyclo[10.6.1.0²,¹⁰.0⁴,⁸.0¹⁵,¹⁹]nonadeca-2,4(8),9,15-tetraene-17,18-diol. This compound has been identified in human blood as reported by (PMID: 31557052 ). Lycorine is not a naturally occurring metabolite and is only found in those individuals exposed to this compound or its derivatives. Technically lycorine is part of the human exposome. The exposome can be defined as the collection of all the exposures of an individual in a lifetime and how those exposures relate to health. An individual's exposure begins before birth and includes insults from environmental and occupational sources.

Structure

MOL 3D MOL SDF 3D SDF PDB 3D PDB SMILES InChI

HMDB0254256
     RDKit          3D
lycorine
 38 42  0  0  0  0  0  0  0  0999 V2000
   -2.7818   -3.2334    0.6012 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2997   -2.2195   -0.2274 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1640   -1.0490   -0.0279 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7565    0.1690    0.2256 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3701    1.5008    0.4648 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2209    2.4697    0.1498 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2148    1.6595   -0.4816 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.1090    2.1715   -0.4059 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1608    1.1551   -0.2216 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4542    1.6532   -0.0289 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5021    0.8057    0.1534 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2557   -0.5431    0.1430 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9669   -1.0518   -0.0487 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9204   -0.2082   -0.2308 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4939   -0.5995   -0.4444 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8299   -1.9780   -0.0377 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1869   -2.8743   -0.9260 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2902    0.4332    0.3276 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.4760   -1.1619    0.3476 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.5180   -0.2000    0.1776 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.8522    1.0478    0.3603 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6433   -3.5316    0.2030 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4877   -2.5820   -1.2768 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2336   -1.2156   -0.0982 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5765    1.6100    1.5490 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2438    1.6821   -0.1680 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5278    3.2532   -0.5471 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7978    2.9112    1.0564 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1673    2.9724    0.3692 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3288    2.6751   -1.3931 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.6448    2.7214   -0.0213 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8055   -2.0996   -0.0508 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7210   -0.4799   -1.5212 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5525   -2.2336    1.0048 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0309   -3.7346   -0.4232 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9418    0.5883    1.3483 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.9207   -0.2102   -0.8365 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.2831   -0.2732    0.9510 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  2  0
  4  5  1  0
  5  6  1  0
  6  7  1  0
  7  8  1  0
  8  9  1  0
  9 10  2  0
 10 11  1  0
 11 12  2  0
 12 13  1  0
 13 14  2  0
 14 15  1  0
 15 16  1  0
 16 17  1  0
 15 18  1  0
 12 19  1  0
 19 20  1  0
 20 21  1  0
 16  2  1  0
 18  4  1  0
 18  7  1  0
 14  9  1  0
 21 11  1  0
  1 22  1  0
  2 23  1  0
  3 24  1  0
  5 25  1  0
  5 26  1  0
  6 27  1  0
  6 28  1  0
  8 29  1  0
  8 30  1  0
 10 31  1  0
 13 32  1  0
 15 33  1  0
 16 34  1  0
 17 35  1  0
 18 36  1  0
 20 37  1  0
 20 38  1  0
M  END


  Mrv1533004161522222D          

 21 25  0  0  0  0            999 V2000
    0.6209   -2.4209    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7925   -1.6139    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1794   -1.0619    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3509   -0.2549    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1340    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3509    1.0799    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1355    0.8250    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.8500    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5645    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2789    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9934    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.7780    1.0799    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.2629    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.7780   -0.2549    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.9934    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2789   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5645    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7486   -0.5520    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5771   -1.3590    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1902   -1.9110    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.1355    0.0000    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
  3  4  2  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  1  0  0  0  0
  7  8  1  0  0  0  0
  8  9  1  0  0  0  0
  9 10  2  0  0  0  0
 10 11  1  0  0  0  0
 11 12  1  0  0  0  0
 12 13  1  0  0  0  0
 13 14  1  0  0  0  0
 14 15  1  0  0  0  0
 11 15  2  0  0  0  0
 15 16  1  0  0  0  0
 16 17  2  0  0  0  0
  9 17  1  0  0  0  0
 17 18  1  0  0  0  0
 18 19  1  0  0  0  0
  2 19  1  0  0  0  0
 19 20  1  0  0  0  0
 18 21  1  0  0  0  0
  4 21  1  0  0  0  0
  7 21  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0254256

> <DATABASE_NAME>
hmdb

> <SMILES>
OC1C=C2CCN3CC4=CC5=C(OCO5)C=C4C(C23)C1O

> <INCHI_IDENTIFIER>
InChI=1S/C16H17NO4/c18-11-3-8-1-2-17-6-9-4-12-13(21-7-20-12)5-10(9)14(15(8)17)16(11)19/h3-5,11,14-16,18-19H,1-2,6-7H2

> <INCHI_KEY>
XGVJWXAYKUHDOO-UHFFFAOYSA-N

> <FORMULA>
C16H17NO4

> <MOLECULAR_WEIGHT>
287.315

> <EXACT_MASS>
287.115758031

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_ATOM_COUNT>
38

> <JCHEM_AVERAGE_POLARIZABILITY>
30.251586065236616

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
5,7-dioxa-12-azapentacyclo[10.6.1.0²,¹⁰.0⁴,⁸.0¹⁵,¹⁹]nonadeca-2,4(8),9,15-tetraene-17,18-diol

> <ALOGPS_LOGP>
0.01

> <JCHEM_LOGP>
0.16233381033333377

> <ALOGPS_LOGS>
-1.59

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
5

> <JCHEM_PHYSIOLOGICAL_CHARGE>
1

> <JCHEM_PKA>
14.900857782201712

> <JCHEM_PKA_STRONGEST_ACIDIC>
13.459854567162708

> <JCHEM_PKA_STRONGEST_BASIC>
7.624193582468524

> <JCHEM_POLAR_SURFACE_AREA>
62.16000000000001

> <JCHEM_REFRACTIVITY>
76.1816

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
7.43e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
lycorine

> <JCHEM_VEBER_RULE>
0

$$$$

HMDB0254256
     RDKit          3D
lycorine
 38 42  0  0  0  0  0  0  0  0999 V2000
   -2.7818   -3.2334    0.6012 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2997   -2.2195   -0.2274 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1640   -1.0490   -0.0279 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7565    0.1690    0.2256 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3701    1.5008    0.4648 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2209    2.4697    0.1498 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2148    1.6595   -0.4816 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.1090    2.1715   -0.4059 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1608    1.1551   -0.2216 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4542    1.6532   -0.0289 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5021    0.8057    0.1534 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2557   -0.5431    0.1430 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9669   -1.0518   -0.0487 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9204   -0.2082   -0.2308 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4939   -0.5995   -0.4444 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8299   -1.9780   -0.0377 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1869   -2.8743   -0.9260 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2902    0.4332    0.3276 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.4760   -1.1619    0.3476 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.5180   -0.2000    0.1776 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.8522    1.0478    0.3603 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6433   -3.5316    0.2030 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4877   -2.5820   -1.2768 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2336   -1.2156   -0.0982 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5765    1.6100    1.5490 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2438    1.6821   -0.1680 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5278    3.2532   -0.5471 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7978    2.9112    1.0564 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1673    2.9724    0.3692 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3288    2.6751   -1.3931 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.6448    2.7214   -0.0213 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8055   -2.0996   -0.0508 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7210   -0.4799   -1.5212 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5525   -2.2336    1.0048 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0309   -3.7346   -0.4232 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9418    0.5883    1.3483 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.9207   -0.2102   -0.8365 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.2831   -0.2732    0.9510 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  2  0
  4  5  1  0
  5  6  1  0
  6  7  1  0
  7  8  1  0
  8  9  1  0
  9 10  2  0
 10 11  1  0
 11 12  2  0
 12 13  1  0
 13 14  2  0
 14 15  1  0
 15 16  1  0
 16 17  1  0
 15 18  1  0
 12 19  1  0
 19 20  1  0
 20 21  1  0
 16  2  1  0
 18  4  1  0
 18  7  1  0
 14  9  1  0
 21 11  1  0
  1 22  1  0
  2 23  1  0
  3 24  1  0
  5 25  1  0
  5 26  1  0
  6 27  1  0
  6 28  1  0
  8 29  1  0
  8 30  1  0
 10 31  1  0
 13 32  1  0
 15 33  1  0
 16 34  1  0
 17 35  1  0
 18 36  1  0
 20 37  1  0
 20 38  1  0
M  END

HEADER    PROTEIN                                 16-APR-15   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   16-APR-15         0                                  
HETATM    1  O   UNK     0       1.159  -4.519   0.000  0.00  0.00           O+0
HETATM    2  C   UNK     0       1.479  -3.013   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       0.335  -1.982   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       0.655  -0.476   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      -0.250   0.770   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       0.655   2.016   0.000  0.00  0.00           C+0
HETATM    7  N   UNK     0       2.120   1.540   0.000  0.00  0.00           N+0
HETATM    8  C   UNK     0       3.453   2.310   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       4.787   1.540   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       6.121   2.310   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       7.454   1.540   0.000  0.00  0.00           C+0
HETATM   12  O   UNK     0       8.919   2.016   0.000  0.00  0.00           O+0
HETATM   13  C   UNK     0       9.824   0.770   0.000  0.00  0.00           C+0
HETATM   14  O   UNK     0       8.919  -0.476   0.000  0.00  0.00           O+0
HETATM   15  C   UNK     0       7.454   0.000   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       6.121  -0.770   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       4.787   0.000   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       3.264  -1.030   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       2.944  -2.537   0.000  0.00  0.00           C+0
HETATM   20  O   UNK     0       4.088  -3.567   0.000  0.00  0.00           O+0
HETATM   21  C   UNK     0       2.120   0.000   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3   19                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5   21                                                  
CONECT    5    4    6                                                       
CONECT    6    5    7                                                       
CONECT    7    6    8   21                                                  
CONECT    8    7    9                                                       
CONECT    9    8   10   17                                                  
CONECT   10    9   11                                                       
CONECT   11   10   12   15                                                  
CONECT   12   11   13                                                       
CONECT   13   12   14                                                       
CONECT   14   13   15                                                       
CONECT   15   14   11   16                                                  
CONECT   16   15   17                                                       
CONECT   17   16    9   18                                                  
CONECT   18   17   19   21                                                  
CONECT   19   18    2   20                                                  
CONECT   20   19                                                            
CONECT   21   18    4    7                                                  
MASTER        0    0    0    0    0    0    0    0   21    0   50    0
END

COMPND    HMDB0254256
HETATM    1  O1  UNL     1      -2.782  -3.233   0.601  1.00  0.00           O  
HETATM    2  C1  UNL     1      -2.300  -2.220  -0.227  1.00  0.00           C  
HETATM    3  C2  UNL     1      -3.164  -1.049  -0.028  1.00  0.00           C  
HETATM    4  C3  UNL     1      -2.757   0.169   0.226  1.00  0.00           C  
HETATM    5  C4  UNL     1      -3.370   1.501   0.465  1.00  0.00           C  
HETATM    6  C5  UNL     1      -2.221   2.470   0.150  1.00  0.00           C  
HETATM    7  N1  UNL     1      -1.215   1.660  -0.482  1.00  0.00           N  
HETATM    8  C6  UNL     1       0.109   2.171  -0.406  1.00  0.00           C  
HETATM    9  C7  UNL     1       1.161   1.155  -0.222  1.00  0.00           C  
HETATM   10  C8  UNL     1       2.454   1.653  -0.029  1.00  0.00           C  
HETATM   11  C9  UNL     1       3.502   0.806   0.153  1.00  0.00           C  
HETATM   12  C10 UNL     1       3.256  -0.543   0.143  1.00  0.00           C  
HETATM   13  C11 UNL     1       1.967  -1.052  -0.049  1.00  0.00           C  
HETATM   14  C12 UNL     1       0.920  -0.208  -0.231  1.00  0.00           C  
HETATM   15  C13 UNL     1      -0.494  -0.599  -0.444  1.00  0.00           C  
HETATM   16  C14 UNL     1      -0.830  -1.978  -0.038  1.00  0.00           C  
HETATM   17  O2  UNL     1      -0.187  -2.874  -0.926  1.00  0.00           O  
HETATM   18  C15 UNL     1      -1.290   0.433   0.328  1.00  0.00           C  
HETATM   19  O3  UNL     1       4.476  -1.162   0.348  1.00  0.00           O  
HETATM   20  C16 UNL     1       5.518  -0.200   0.178  1.00  0.00           C  
HETATM   21  O4  UNL     1       4.852   1.048   0.360  1.00  0.00           O  
HETATM   22  H1  UNL     1      -3.643  -3.532   0.203  1.00  0.00           H  
HETATM   23  H2  UNL     1      -2.488  -2.582  -1.277  1.00  0.00           H  
HETATM   24  H3  UNL     1      -4.234  -1.216  -0.098  1.00  0.00           H  
HETATM   25  H4  UNL     1      -3.577   1.610   1.549  1.00  0.00           H  
HETATM   26  H5  UNL     1      -4.244   1.682  -0.168  1.00  0.00           H  
HETATM   27  H6  UNL     1      -2.528   3.253  -0.547  1.00  0.00           H  
HETATM   28  H7  UNL     1      -1.798   2.911   1.056  1.00  0.00           H  
HETATM   29  H8  UNL     1       0.167   2.972   0.369  1.00  0.00           H  
HETATM   30  H9  UNL     1       0.329   2.675  -1.393  1.00  0.00           H  
HETATM   31  H10 UNL     1       2.645   2.721  -0.021  1.00  0.00           H  
HETATM   32  H11 UNL     1       1.805  -2.100  -0.051  1.00  0.00           H  
HETATM   33  H12 UNL     1      -0.721  -0.480  -1.521  1.00  0.00           H  
HETATM   34  H13 UNL     1      -0.552  -2.234   1.005  1.00  0.00           H  
HETATM   35  H14 UNL     1      -0.031  -3.735  -0.423  1.00  0.00           H  
HETATM   36  H15 UNL     1      -0.942   0.588   1.348  1.00  0.00           H  
HETATM   37  H16 UNL     1       5.921  -0.210  -0.836  1.00  0.00           H  
HETATM   38  H17 UNL     1       6.283  -0.273   0.951  1.00  0.00           H  
CONECT    1    2   22
CONECT    2    3   16   23
CONECT    3    4    4   24
CONECT    4    5   18
CONECT    5    6   25   26
CONECT    6    7   27   28
CONECT    7    8   18
CONECT    8    9   29   30
CONECT    9   10   10   14
CONECT   10   11   31
CONECT   11   12   12   21
CONECT   12   13   19
CONECT   13   14   14   32
CONECT   14   15
CONECT   15   16   18   33
CONECT   16   17   34
CONECT   17   35
CONECT   18   36
CONECT   19   20
CONECT   20   21   37   38
END

HMDB0254256
     RDKit          3D
lycorine
 38 42  0  0  0  0  0  0  0  0999 V2000
   -2.7818   -3.2334    0.6012 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2997   -2.2195   -0.2274 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1640   -1.0490   -0.0279 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7565    0.1690    0.2256 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3701    1.5008    0.4648 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2209    2.4697    0.1498 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2148    1.6595   -0.4816 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.1090    2.1715   -0.4059 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1608    1.1551   -0.2216 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4542    1.6532   -0.0289 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5021    0.8057    0.1534 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2557   -0.5431    0.1430 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9669   -1.0518   -0.0487 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9204   -0.2082   -0.2308 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4939   -0.5995   -0.4444 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8299   -1.9780   -0.0377 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1869   -2.8743   -0.9260 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2902    0.4332    0.3276 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.4760   -1.1619    0.3476 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.5180   -0.2000    0.1776 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.8522    1.0478    0.3603 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6433   -3.5316    0.2030 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4877   -2.5820   -1.2768 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2336   -1.2156   -0.0982 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5765    1.6100    1.5490 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2438    1.6821   -0.1680 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5278    3.2532   -0.5471 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7978    2.9112    1.0564 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1673    2.9724    0.3692 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3288    2.6751   -1.3931 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.6448    2.7214   -0.0213 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8055   -2.0996   -0.0508 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7210   -0.4799   -1.5212 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5525   -2.2336    1.0048 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0309   -3.7346   -0.4232 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9418    0.5883    1.3483 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.9207   -0.2102   -0.8365 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.2831   -0.2732    0.9510 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  2  0
  4  5  1  0
  5  6  1  0
  6  7  1  0
  7  8  1  0
  8  9  1  0
  9 10  2  0
 10 11  1  0
 11 12  2  0
 12 13  1  0
 13 14  2  0
 14 15  1  0
 15 16  1  0
 16 17  1  0
 15 18  1  0
 12 19  1  0
 19 20  1  0
 20 21  1  0
 16  2  1  0
 18  4  1  0
 18  7  1  0
 14  9  1  0
 21 11  1  0
  1 22  1  0
  2 23  1  0
  3 24  1  0
  5 25  1  0
  5 26  1  0
  6 27  1  0
  6 28  1  0
  8 29  1  0
  8 30  1  0
 10 31  1  0
 13 32  1  0
 15 33  1  0
 16 34  1  0
 17 35  1  0
 18 36  1  0
 20 37  1  0
 20 38  1  0
M  END

View in JSmol View NMR Assignments View Stereo Labels

Synonyms

Not Available

Chemical Formula

C₁₆H₁₇NO₄

Average Molecular Weight

287.315

Monoisotopic Molecular Weight

287.115758031

IUPAC Name

5,7-dioxa-12-azapentacyclo[10.6.1.0²,¹⁰.0⁴,⁸.0¹⁵,¹⁹]nonadeca-2,4(8),9,15-tetraene-17,18-diol

Traditional Name

lycorine

CAS Registry Number

Not Available

SMILES

OC1C=C2CCN3CC4=CC5=C(OCO5)C=C4C(C23)C1O

InChI Identifier

InChI=1S/C16H17NO4/c18-11-3-8-1-2-17-6-9-4-12-13(21-7-20-12)5-10(9)14(15(8)17)16(11)19/h3-5,11,14-16,18-19H,1-2,6-7H2

InChI Key

XGVJWXAYKUHDOO-UHFFFAOYSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as lycorine-type amaryllidaceae alkaloids. These are amaryllidaceae alkaloids compounds containing the lycorine skeleton, made up of a pyrrolo[d,e]phenanthridine ring system.

Kingdom

Organic compounds

Super Class

Alkaloids and derivatives

Class

Amaryllidaceae alkaloids

Sub Class

Lycorine-type amaryllidaceae alkaloids

Direct Parent

Lycorine-type amaryllidaceae alkaloids

Alternative Parents

Substituents

Lycorine skeleton
Benzoquinoline
Phenanthridine
Quinoline
Tetrahydroisoquinoline
Benzodioxole
Indole or derivatives
Aralkylamine
Benzenoid
N-alkylpyrrolidine
Pyrrolidine
Tertiary aliphatic amine
Tertiary amine
Secondary alcohol
1,2-diol
Organoheterocyclic compound
Azacycle
Oxacycle
Acetal
Hydrocarbon derivative
Organonitrogen compound
Organooxygen compound
Organic nitrogen compound
Organic oxygen compound
Amine
Alcohol
Organopnictogen compound
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic heteropolycyclic compounds

External Descriptors

Not Available

Ontology

Physiological effect

Not Available

Disposition

Biological location

Non-excretory biofluid

Biofluid or Excreta

Blood (PMID: 31557052)

Cellular substructure

Cytoplasm (HMDB: HMDB0254256)
Extracellular (HMDB: HMDB0254256)
Endoplasmic reticulum membrane (HMDB: HMDB0254256)

Organelle

Ribosome (HMDB: HMDB0254256)
Mitochondrion (HMDB: HMDB0254256)

Source

Exogenous

Exogenous (PMID: 31557052)

Process

Naturally occurring process

Biological process

Cellular process

Apoptosis (HMDB: HMDB0254256)

Biochemical process

Cell cycle (HMDB: HMDB0254256)

Role

Biological role

Metabolite (HMDB: HMDB0254256)

Modulator

Inhibitor

Enzyme inhibitor

Protein synthesis inhibitor (HMDB: HMDB0254256)

Physical Properties

State

Not Available

Experimental Molecular 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

Experimental Chromatographic Properties

Not Available

Predicted Molecular Properties

Property	Value	Source
logP	0.01	ALOGPS
logP	0.16	ChemAxon
logS	-1.6	ALOGPS
pKa (Strongest Acidic)	13.46	ChemAxon
pKa (Strongest Basic)	7.62	ChemAxon
Physiological Charge	1	ChemAxon
Hydrogen Acceptor Count	5	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	62.16 Å²	ChemAxon
Rotatable Bond Count	0	ChemAxon
Refractivity	76.18 m³·mol⁻¹	ChemAxon
Polarizability	30.25 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

Predicted Chromatographic Properties

Predicted Collision Cross Sections

Predictor	Adduct Type	CCS Value (Å²)	Reference
DeepCCS	[M-2H]-	204.367	30932474
DeepCCS	[M+Na]+	179.594	30932474
AllCCS	[M+H]+	167.3	32859911
AllCCS	[M+H-H2O]+	163.9	32859911
AllCCS	[M+NH4]+	170.5	32859911
AllCCS	[M+Na]+	171.4	32859911
AllCCS	[M-H]-	169.7	32859911
AllCCS	[M+Na-2H]-	168.9	32859911
AllCCS	[M+HCOO]-	168.2	32859911

Predicted Retention Times

Underivatized

Chromatographic Method	Retention Time	Reference
Predicted by Siyang on May 30, 2022	9.5905 minutes	33406817
Predicted by Siyang using ReTip algorithm on June 8, 2022	4.65 minutes	32390414
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid	691.4 seconds	40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid	235.5 seconds	40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid	109.0 seconds	40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid	173.0 seconds	40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	50.1 seconds	40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid	268.2 seconds	40023050
BfG_NTS_RP1 =Agilent Zorbax Eclipse Plus C18 (2.1 mm x 150 mm, 3.5 um) with Water:ACN and 0.1% Formic Acid	301.2 seconds	40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)	559.5 seconds	40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid	633.3 seconds	40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid	141.7 seconds	40023050
UFZ_Phenomenex = Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex with Water:MeOH and 0.1% Formic Acid	736.2 seconds	40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	178.4 seconds	40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	197.3 seconds	40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate	621.7 seconds	40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA	447.1 seconds	40023050
Meister zic-pHILIC pH9.3 = Merck SeQuant ZIC-pHILIC column with ACN:Water 5mM NH4Ac pH9.3 and 5mM ammonium acetate in water	257.7 seconds	40023050

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
lycorine	OC1C=C2CCN3CC4=CC5=C(OCO5)C=C4C(C23)C1O	3749.1	Standard polar	33892256
lycorine	OC1C=C2CCN3CC4=CC5=C(OCO5)C=C4C(C23)C1O	2496.7	Standard non polar	33892256
lycorine	OC1C=C2CCN3CC4=CC5=C(OCO5)C=C4C(C23)C1O	2722.9	Semi standard non polar	33892256

Spectra

GC-MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Predicted GC-MS	Predicted GC-MS Spectrum - lycorine GC-MS (Non-derivatized) - 70eV, Positive	splash10-0bvi-0090000000-0f4b3ba14b5702aef058	2021-09-24	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - lycorine GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - lycorine GC-MS (TMS_1_1) - 70eV, Positive	Not Available	2021-11-04	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - lycorine GC-MS (TMS_1_2) - 70eV, Positive	Not Available	2021-11-04	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - lycorine GC-MS (TMS_2_1) - 70eV, Positive	Not Available	2021-11-04	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - lycorine GC-MS (TBDMS_1_1) - 70eV, Positive	Not Available	2021-11-04	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - lycorine GC-MS (TBDMS_1_2) - 70eV, Positive	Not Available	2021-11-04	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - lycorine GC-MS (TBDMS_2_1) - 70eV, Positive	Not Available	2021-11-04	Wishart Lab	View Spectrum

MS/MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - lycorine 10V, Positive-QTOF	splash10-000i-0090000000-7df6ac01694af44ff067	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - lycorine 20V, Positive-QTOF	splash10-000i-0090000000-b5f7ce270eff52233e05	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - lycorine 40V, Positive-QTOF	splash10-06tu-1490000000-d1f9cbda5352ceb8b5c8	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - lycorine 10V, Negative-QTOF	splash10-000i-0090000000-391b5b08416ef05aabb7	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - lycorine 20V, Negative-QTOF	splash10-000i-0090000000-a52e183081d22076ac0d	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - lycorine 40V, Negative-QTOF	splash10-05i0-0090000000-a74fdbc1eaf441855432	2021-10-12	Wishart Lab	View Spectrum

NMR Spectra

Spectrum Type	Description	Deposition Date	Source	View
Predicted 1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)	2021-10-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 100 MHz, D₂O, predicted)	2021-10-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	2021-10-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	2021-10-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)	2021-10-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 200 MHz, D₂O, predicted)	2021-10-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 300 MHz, D₂O, predicted)	2021-10-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)	2021-10-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 400 MHz, D₂O, predicted)	2021-10-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)	2021-10-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 500 MHz, D₂O, predicted)	2021-10-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)	2021-10-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)	2021-10-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 600 MHz, D₂O, predicted)	2021-10-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)	2021-10-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 700 MHz, D₂O, predicted)	2021-10-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 800 MHz, D₂O, predicted)	2021-10-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)	2021-10-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, predicted)	2021-10-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 900 MHz, D₂O, predicted)	2021-10-25	Wishart Lab	View Spectrum

Biological Properties

Cellular Locations

Not Available

Biospecimen Locations

Blood

Tissue Locations

Not Available

Pathways

Not Available

Name	SMPDB/PathBank	KEGG

Normal Concentrations

Biospecimen	Status	Value	Age	Sex	Condition	Reference	Details
Blood	Detected but not Quantified	Not Quantified	Not Specified	Not Specified	Normal	31557052	details

Abnormal Concentrations

Not Available

Associated Disorders and Diseases

Disease References

None

Associated OMIM IDs

None

External Links

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

Not Available

KNApSAcK ID

Not Available

Chemspider ID

3840

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

3978

PDB ID

Not Available

ChEBI ID

Not Available

Food Biomarker Ontology

Not Available

VMH ID

Not Available

MarkerDB ID

Not Available

Good Scents ID

Not Available

References

Synthesis Reference

Not Available

Material Safety Data Sheet (MSDS)

Not Available

General References

Barupal DK, Fiehn O: Generating the Blood Exposome Database Using a Comprehensive Text Mining and Database Fusion Approach. Environ Health Perspect. 2019 Sep;127(9):97008. doi: 10.1289/EHP4713. Epub 2019 Sep 26. [PubMed:31557052 ]

Showing metabocard for lycorine (HMDB0254256)

MOL for HMDB0254256 (lycorine)

3D MOL for HMDB0254256 (lycorine)

3D SDF for HMDB0254256 (lycorine)

3D-SDF for HMDB0254256 (lycorine)

PDB for HMDB0254256 (lycorine)

3D PDB for HMDB0254256 (lycorine)

SMILES for HMDB0254256 (lycorine)

INCHI for HMDB0254256 (lycorine)

Structure for HMDB0254256 (lycorine)

3D Structure for HMDB0254256 (lycorine)

Predicted Collision Cross Sections

Predicted Retention Times

Underivatized

Predicted Kovats Retention Indices

Underivatized

GC-MS Spectra

MS/MS Spectra

NMR Spectra