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Record Information

Version

5.0

Status

Expected but not Quantified

Creation Date

2021-09-23 02:59:56 UTC

Update Date

2021-09-23 02:59:56 UTC

HMDB ID

HMDB0301845

Secondary Accession Numbers

None

Metabolite Identification

Common Name

Xylopine

Description

Xylopine, also known as (-)-xylopine, is a member of the class of compounds known as aporphines. Aporphines are quinoline alkaloids containing the dibenzo[de,g]quinoline ring system or a dehydrogenated derivative thereof. Xylopine is practically insoluble (in water) and a very strong basic compound (based on its pKa). Xylopine can be found in cherimoya and custard apple, which makes xylopine a potential biomarker for the consumption of these food products. Xylopine is an antimicrobial benzylisoquinoline alkaloid .

Structure

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

HMDB0301845
     RDKit          3D
Xylopine
 39 43  0  0  0  0  0  0  0  0999 V2000
    5.8228    1.1255   -0.1779 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.5985    1.7576   -0.3891 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.3586    1.1308   -0.3151 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2651   -0.2043   -0.0169 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0207   -0.8430    0.0616 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9083   -0.0631   -0.1751 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9898    1.2709   -0.4778 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2504    1.8793   -0.5464 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1990    2.0544   -0.8388 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4435    1.5870   -0.2065 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.6044    2.0661   -1.0049 N   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7616    1.8684   -0.1384 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0322    0.3840   -0.0706 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7950   -0.4138    0.0297 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9397   -1.7749    0.2428 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8374   -2.5850    0.3520 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5452   -2.0592    0.2500 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3992   -0.7097    0.0374 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5094    0.1252   -0.0729 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3132   -3.1225    0.4019 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3975   -4.3306    0.2671 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7345   -3.9487    0.5630 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.5684    1.9246    0.1067 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.7610    0.3800    0.6242 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.2382    0.6218   -1.0756 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.1467   -0.7777    0.1605 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9875   -1.8792    0.2971 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2471    2.9286   -0.7847 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3838    1.9877   -1.9705 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0189    3.1588   -0.6850 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5633    2.0577    0.8142 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6420    1.3818   -1.8166 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4913    2.2669    0.8555 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5913    2.4385   -0.5580 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5800    0.1058   -0.9964 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7067    0.2065    0.8138 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9462   -2.2077    0.3247 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3503   -4.7319   -0.7739 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0038   -5.0564    1.0048 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  2  0
  6  7  1  0
  7  8  2  0
  7  9  1  0
  9 10  1  0
 10 11  1  0
 11 12  1  0
 12 13  1  0
 13 14  1  0
 14 15  1  0
 15 16  2  0
 16 17  1  0
 17 18  2  0
 18 19  1  0
 17 20  1  0
 20 21  1  0
 21 22  1  0
  8  3  1  0
 19 10  1  0
 18  6  1  0
 19 14  2  0
 22 16  1  0
  1 23  1  0
  1 24  1  0
  1 25  1  0
  4 26  1  0
  5 27  1  0
  8 28  1  0
  9 29  1  0
  9 30  1  0
 10 31  1  1
 11 32  1  0
 12 33  1  0
 12 34  1  0
 13 35  1  0
 13 36  1  0
 15 37  1  0
 21 38  1  0
 21 39  1  0
M  END


  Mrv0541 02241221322D          

 22 26  0  0  1  0            999 V2000
    1.6005   -2.4570    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7565   -1.7895    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.4209   -2.5432    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    1.2375    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.8250    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.1434    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2868    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0013    1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.7158    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2868    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579    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  2  0  0  0  0
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  1  5  1  0  0  0  0
  3  6  1  0  0  0  0
  6  7  2  0  0  0  0
  7  8  1  0  0  0  0
  8  9  2  0  0  0  0
  2  9  1  0  0  0  0
  8 10  1  0  0  0  0
 10 11  1  0  0  0  0
 11 12  1  0  0  0  0
 13 12  1  6  0  0  0
  7 13  1  0  0  0  0
 13 14  1  0  0  0  0
 14 15  1  0  0  0  0
 15 16  2  0  0  0  0
 16 17  1  0  0  0  0
 17 18  1  0  0  0  0
 18 19  1  0  0  0  0
 17 20  2  0  0  0  0
 20 21  1  0  0  0  0
 21 22  2  0  0  0  0
  6 22  1  0  0  0  0
 15 22  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0301845

> <DATABASE_NAME>
hmdb

> <SMILES>
COC1=CC=C2C(C[C@H]3NCCC4=CC5=C(OCO5)C2=C34)=C1

> <INCHI_IDENTIFIER>
InChI=1S/C18H17NO3/c1-20-12-2-3-13-11(6-12)7-14-16-10(4-5-19-14)8-15-18(17(13)16)22-9-21-15/h2-3,6,8,14,19H,4-5,7,9H2,1H3/t14-/m1/s1

> <INCHI_KEY>
RFWCCZDSXIZJMF-CQSZACIVSA-N

> <FORMULA>
C18H17NO3

> <MOLECULAR_WEIGHT>
295.3325

> <EXACT_MASS>
295.120843415

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_AVERAGE_POLARIZABILITY>
32.34063990657006

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
(12R)-16-methoxy-3,5-dioxa-11-azapentacyclo[10.7.1.0²,⁶.0⁸,²⁰.0¹⁴,¹⁹]icosa-1(20),2(6),7,14,16,18-hexaene

> <ALOGPS_LOGP>
2.11

> <JCHEM_LOGP>
2.7839262923333328

> <ALOGPS_LOGS>
-3.98

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
5

> <JCHEM_PHYSIOLOGICAL_CHARGE>
1

> <JCHEM_PKA_STRONGEST_BASIC>
9.434138836280734

> <JCHEM_POLAR_SURFACE_AREA>
39.72

> <JCHEM_REFRACTIVITY>
82.9617

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
3.09e-02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
xylopine

> <JCHEM_VEBER_RULE>
1

$$$$

HMDB0301845
     RDKit          3D
Xylopine
 39 43  0  0  0  0  0  0  0  0999 V2000
    5.8228    1.1255   -0.1779 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.5985    1.7576   -0.3891 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.3586    1.1308   -0.3151 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2651   -0.2043   -0.0169 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0207   -0.8430    0.0616 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9083   -0.0631   -0.1751 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9898    1.2709   -0.4778 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2504    1.8793   -0.5464 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1990    2.0544   -0.8388 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4435    1.5870   -0.2065 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.6044    2.0661   -1.0049 N   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7616    1.8684   -0.1384 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0322    0.3840   -0.0706 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7950   -0.4138    0.0297 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9397   -1.7749    0.2428 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8374   -2.5850    0.3520 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5452   -2.0592    0.2500 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3992   -0.7097    0.0374 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5094    0.1252   -0.0729 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3132   -3.1225    0.4019 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3975   -4.3306    0.2671 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7345   -3.9487    0.5630 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.5684    1.9246    0.1067 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.7610    0.3800    0.6242 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.2382    0.6218   -1.0756 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.1467   -0.7777    0.1605 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9875   -1.8792    0.2971 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2471    2.9286   -0.7847 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3838    1.9877   -1.9705 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0189    3.1588   -0.6850 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5633    2.0577    0.8142 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6420    1.3818   -1.8166 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4913    2.2669    0.8555 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5913    2.4385   -0.5580 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5800    0.1058   -0.9964 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7067    0.2065    0.8138 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9462   -2.2077    0.3247 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3503   -4.7319   -0.7739 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0038   -5.0564    1.0048 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  2  0
  6  7  1  0
  7  8  2  0
  7  9  1  0
  9 10  1  0
 10 11  1  0
 11 12  1  0
 12 13  1  0
 13 14  1  0
 14 15  1  0
 15 16  2  0
 16 17  1  0
 17 18  2  0
 18 19  1  0
 17 20  1  0
 20 21  1  0
 21 22  1  0
  8  3  1  0
 19 10  1  0
 18  6  1  0
 19 14  2  0
 22 16  1  0
  1 23  1  0
  1 24  1  0
  1 25  1  0
  4 26  1  0
  5 27  1  0
  8 28  1  0
  9 29  1  0
  9 30  1  0
 10 31  1  1
 11 32  1  0
 12 33  1  0
 12 34  1  0
 13 35  1  0
 13 36  1  0
 15 37  1  0
 21 38  1  0
 21 39  1  0
M  END

HEADER    PROTEIN                                 24-FEB-12   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   24-FEB-12         0                                  
HETATM    1  O   UNK     0       2.988  -4.586   0.000  0.00  0.00           O+0
HETATM    2  C   UNK     0       2.667  -3.080   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       4.001  -2.310   0.000  0.00  0.00           C+0
HETATM    4  O   UNK     0       5.145  -3.340   0.000  0.00  0.00           O+0
HETATM    5  C   UNK     0       4.519  -4.747   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       4.001  -0.770   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       2.667   0.000   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       1.334  -2.310   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       0.000   1.540   0.000  0.00  0.00           C+0
HETATM   12  N   UNK     0       1.334   2.310   0.000  0.00  0.00           N+0
HETATM   13  C   UNK     0       2.667   1.540   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       4.001   2.310   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       5.335   1.540   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       6.668   2.310   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       8.002   1.540   0.000  0.00  0.00           C+0
HETATM   18  O   UNK     0       9.336   2.310   0.000  0.00  0.00           O+0
HETATM   19  C   UNK     0      10.669   1.540   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       8.002   0.000   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0       6.668  -0.770   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0       5.335   0.000   0.000  0.00  0.00           C+0
CONECT    1    2    5                                                       
CONECT    2    1    3    9                                                  
CONECT    3    2    4    6                                                  
CONECT    4    3    5                                                       
CONECT    5    4    1                                                       
CONECT    6    3    7   22                                                  
CONECT    7    6    8   13                                                  
CONECT    8    7    9   10                                                  
CONECT    9    8    2                                                       
CONECT   10    8   11                                                       
CONECT   11   10   12                                                       
CONECT   12   11   13                                                       
CONECT   13   12    7   14                                                  
CONECT   14   13   15                                                       
CONECT   15   14   16   22                                                  
CONECT   16   15   17                                                       
CONECT   17   16   18   20                                                  
CONECT   18   17   19                                                       
CONECT   19   18                                                            
CONECT   20   17   21                                                       
CONECT   21   20   22                                                       
CONECT   22   21    6   15                                                  
MASTER        0    0    0    0    0    0    0    0   22    0   52    0
END

COMPND    HMDB0301845
HETATM    1  C1  UNL     1       5.823   1.126  -0.178  1.00  0.00           C  
HETATM    2  O1  UNL     1       4.598   1.758  -0.389  1.00  0.00           O  
HETATM    3  C2  UNL     1       3.359   1.131  -0.315  1.00  0.00           C  
HETATM    4  C3  UNL     1       3.265  -0.204  -0.017  1.00  0.00           C  
HETATM    5  C4  UNL     1       2.021  -0.843   0.062  1.00  0.00           C  
HETATM    6  C5  UNL     1       0.908  -0.063  -0.175  1.00  0.00           C  
HETATM    7  C6  UNL     1       0.990   1.271  -0.478  1.00  0.00           C  
HETATM    8  C7  UNL     1       2.250   1.879  -0.546  1.00  0.00           C  
HETATM    9  C8  UNL     1      -0.199   2.054  -0.839  1.00  0.00           C  
HETATM   10  C9  UNL     1      -1.444   1.587  -0.207  1.00  0.00           C  
HETATM   11  N1  UNL     1      -2.604   2.066  -1.005  1.00  0.00           N  
HETATM   12  C10 UNL     1      -3.762   1.868  -0.138  1.00  0.00           C  
HETATM   13  C11 UNL     1      -4.032   0.384  -0.071  1.00  0.00           C  
HETATM   14  C12 UNL     1      -2.795  -0.414   0.030  1.00  0.00           C  
HETATM   15  C13 UNL     1      -2.940  -1.775   0.243  1.00  0.00           C  
HETATM   16  C14 UNL     1      -1.837  -2.585   0.352  1.00  0.00           C  
HETATM   17  C15 UNL     1      -0.545  -2.059   0.250  1.00  0.00           C  
HETATM   18  C16 UNL     1      -0.399  -0.710   0.037  1.00  0.00           C  
HETATM   19  C17 UNL     1      -1.509   0.125  -0.073  1.00  0.00           C  
HETATM   20  O2  UNL     1       0.313  -3.123   0.402  1.00  0.00           O  
HETATM   21  C18 UNL     1      -0.397  -4.331   0.267  1.00  0.00           C  
HETATM   22  O3  UNL     1      -1.735  -3.949   0.563  1.00  0.00           O  
HETATM   23  H1  UNL     1       6.568   1.925   0.107  1.00  0.00           H  
HETATM   24  H2  UNL     1       5.761   0.380   0.624  1.00  0.00           H  
HETATM   25  H3  UNL     1       6.238   0.622  -1.076  1.00  0.00           H  
HETATM   26  H4  UNL     1       4.147  -0.778   0.160  1.00  0.00           H  
HETATM   27  H5  UNL     1       1.987  -1.879   0.297  1.00  0.00           H  
HETATM   28  H6  UNL     1       2.247   2.929  -0.785  1.00  0.00           H  
HETATM   29  H7  UNL     1      -0.384   1.988  -1.970  1.00  0.00           H  
HETATM   30  H8  UNL     1      -0.019   3.159  -0.685  1.00  0.00           H  
HETATM   31  H9  UNL     1      -1.563   2.058   0.814  1.00  0.00           H  
HETATM   32  H10 UNL     1      -2.642   1.382  -1.817  1.00  0.00           H  
HETATM   33  H11 UNL     1      -3.491   2.267   0.856  1.00  0.00           H  
HETATM   34  H12 UNL     1      -4.591   2.438  -0.558  1.00  0.00           H  
HETATM   35  H13 UNL     1      -4.580   0.106  -0.996  1.00  0.00           H  
HETATM   36  H14 UNL     1      -4.707   0.206   0.814  1.00  0.00           H  
HETATM   37  H15 UNL     1      -3.946  -2.208   0.325  1.00  0.00           H  
HETATM   38  H16 UNL     1      -0.350  -4.732  -0.774  1.00  0.00           H  
HETATM   39  H17 UNL     1      -0.004  -5.056   1.005  1.00  0.00           H  
CONECT    1    2   23   24   25
CONECT    2    3
CONECT    3    4    4    8
CONECT    4    5   26
CONECT    5    6    6   27
CONECT    6    7   18
CONECT    7    8    8    9
CONECT    8   28
CONECT    9   10   29   30
CONECT   10   11   19   31
CONECT   11   12   32
CONECT   12   13   33   34
CONECT   13   14   35   36
CONECT   14   15   19   19
CONECT   15   16   16   37
CONECT   16   17   22
CONECT   17   18   18   20
CONECT   18   19
CONECT   20   21
CONECT   21   22   38   39
END

HMDB0301845
     RDKit          3D
Xylopine
 39 43  0  0  0  0  0  0  0  0999 V2000
    5.8228    1.1255   -0.1779 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.5985    1.7576   -0.3891 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.3586    1.1308   -0.3151 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2651   -0.2043   -0.0169 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0207   -0.8430    0.0616 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9083   -0.0631   -0.1751 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9898    1.2709   -0.4778 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2504    1.8793   -0.5464 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1990    2.0544   -0.8388 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4435    1.5870   -0.2065 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.6044    2.0661   -1.0049 N   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7616    1.8684   -0.1384 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0322    0.3840   -0.0706 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7950   -0.4138    0.0297 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9397   -1.7749    0.2428 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8374   -2.5850    0.3520 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5452   -2.0592    0.2500 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3992   -0.7097    0.0374 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5094    0.1252   -0.0729 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3132   -3.1225    0.4019 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3975   -4.3306    0.2671 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7345   -3.9487    0.5630 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.5684    1.9246    0.1067 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.7610    0.3800    0.6242 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.2382    0.6218   -1.0756 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.1467   -0.7777    0.1605 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9875   -1.8792    0.2971 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2471    2.9286   -0.7847 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3838    1.9877   -1.9705 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0189    3.1588   -0.6850 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5633    2.0577    0.8142 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6420    1.3818   -1.8166 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4913    2.2669    0.8555 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5913    2.4385   -0.5580 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5800    0.1058   -0.9964 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7067    0.2065    0.8138 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9462   -2.2077    0.3247 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3503   -4.7319   -0.7739 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0038   -5.0564    1.0048 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  2  0
  6  7  1  0
  7  8  2  0
  7  9  1  0
  9 10  1  0
 10 11  1  0
 11 12  1  0
 12 13  1  0
 13 14  1  0
 14 15  1  0
 15 16  2  0
 16 17  1  0
 17 18  2  0
 18 19  1  0
 17 20  1  0
 20 21  1  0
 21 22  1  0
  8  3  1  0
 19 10  1  0
 18  6  1  0
 19 14  2  0
 22 16  1  0
  1 23  1  0
  1 24  1  0
  1 25  1  0
  4 26  1  0
  5 27  1  0
  8 28  1  0
  9 29  1  0
  9 30  1  0
 10 31  1  1
 11 32  1  0
 12 33  1  0
 12 34  1  0
 13 35  1  0
 13 36  1  0
 15 37  1  0
 21 38  1  0
 21 39  1  0
M  END

View in JSmol View Stereo Labels

Synonyms

Value	Source
(-)-Xylopine	ChEMBL

Chemical Formula

C₁₈H₁₇NO₃

Average Molecular Weight

295.3325

Monoisotopic Molecular Weight

295.120843415

IUPAC Name

(12R)-16-methoxy-3,5-dioxa-11-azapentacyclo[10.7.1.0²,⁶.0⁸,²⁰.0¹⁴,¹⁹]icosa-1(20),2(6),7,14,16,18-hexaene

Traditional Name

xylopine

CAS Registry Number

Not Available

SMILES

COC1=CC=C2C(C[C@H]3NCCC4=CC5=C(OCO5)C2=C34)=C1

InChI Identifier

InChI=1S/C18H17NO3/c1-20-12-2-3-13-11(6-12)7-14-16-10(4-5-19-14)8-15-18(17(13)16)22-9-21-15/h2-3,6,8,14,19H,4-5,7,9H2,1H3/t14-/m1/s1

InChI Key

RFWCCZDSXIZJMF-CQSZACIVSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as aporphines. These are quinoline alkaloids containing the dibenzo[de,g]quinoline ring system or a dehydrogenated derivative thereof.

Kingdom

Organic compounds

Super Class

Alkaloids and derivatives

Class

Aporphines

Sub Class

Not Available

Direct Parent

Aporphines

Alternative Parents

Substituents

Aporphine
Benzoquinoline
Phenanthrene
Naphthalene
Quinoline
Tetrahydroisoquinoline
Benzodioxole
Anisole
Aralkylamine
Alkyl aryl ether
Benzenoid
Organoheterocyclic compound
Azacycle
Secondary amine
Oxacycle
Acetal
Ether
Secondary aliphatic amine
Hydrocarbon derivative
Organic oxygen compound
Organopnictogen compound
Organic nitrogen compound
Organonitrogen compound
Amine
Organooxygen compound
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic heteropolycyclic compounds

External Descriptors

isoquinoline alkaloid (CHEBI:10083 )
Isoquinoline alkaloids (C09670 )

Ontology

Not Available

Exogenous (HMDB: HMDB0301845)

Food

Fruit

Tropical fruit

Cherimoya (FooDB: FOOD00326)
Custard apple (FooDB: FOOD00014)

Process

Not Available

Role

Not Available

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	2.11	ALOGPS
logP	2.78	ChemAxon
logS	-4	ALOGPS
pKa (Strongest Basic)	9.43	ChemAxon
Physiological Charge	1	ChemAxon
Hydrogen Acceptor Count	4	ChemAxon
Hydrogen Donor Count	1	ChemAxon
Polar Surface Area	39.72 Å²	ChemAxon
Rotatable Bond Count	1	ChemAxon
Refractivity	82.96 m³·mol⁻¹	ChemAxon
Polarizability	32.34 Å³	ChemAxon
Number of Rings	5	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	ChemAxon
Veber's Rule	Yes	ChemAxon
MDDR-like Rule	No	ChemAxon

Predicted Chromatographic Properties

Predicted Collision Cross Sections

Predictor	Adduct Type	CCS Value (Å²)	Reference
AllCCS	[M+H]+	169.915	32859911
AllCCS	[M+H-H2O]+	166.382	32859911
AllCCS	[M+Na]+	174.134	32859911
AllCCS	[M+NH4]+	173.192	32859911
AllCCS	[M-H]-	176.925	32859911
AllCCS	[M+Na-2H]-	176.061	32859911
AllCCS	[M+HCOO]-	175.248	32859911
DeepCCS	[M-2H]-	216.922	30932474
DeepCCS	[M+Na]+	192.247	30932474

Predicted Retention Times

Underivatized

Chromatographic Method	Retention Time	Reference
Predicted by Siyang on May 30, 2022	11.0903 minutes	33406817
Predicted by Siyang using ReTip algorithm on June 8, 2022	3.68 minutes	32390414
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid	1468.8 seconds	40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid	258.0 seconds	40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid	165.1 seconds	40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid	182.9 seconds	40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	100.0 seconds	40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid	347.3 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	396.9 seconds	40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)	347.8 seconds	40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid	896.8 seconds	40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid	387.0 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	1121.0 seconds	40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	283.5 seconds	40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	279.6 seconds	40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate	438.0 seconds	40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA	287.1 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	36.0 seconds	40023050

Predicted Kovats Retention Indices

Derivatized

Derivative Name / Structure	SMILES	Kovats RI Value	Column Type	Reference
Xylopine,1TMS,isomer #1	COC1=CC=C2C(=C1)C[C@@H]1C3=C(C=C4OCOC4=C23)CCN1[Si](C)(C)C	2798.0	Semi standard non polar	33892256
Xylopine,1TMS,isomer #1	COC1=CC=C2C(=C1)C[C@@H]1C3=C(C=C4OCOC4=C23)CCN1[Si](C)(C)C	2791.4	Standard non polar	33892256
Xylopine,1TMS,isomer #1	COC1=CC=C2C(=C1)C[C@@H]1C3=C(C=C4OCOC4=C23)CCN1[Si](C)(C)C	3654.6	Standard polar	33892256
Xylopine,1TBDMS,isomer #1	COC1=CC=C2C(=C1)C[C@@H]1C3=C(C=C4OCOC4=C23)CCN1[Si](C)(C)C(C)(C)C	2999.2	Semi standard non polar	33892256
Xylopine,1TBDMS,isomer #1	COC1=CC=C2C(=C1)C[C@@H]1C3=C(C=C4OCOC4=C23)CCN1[Si](C)(C)C(C)(C)C	3020.5	Standard non polar	33892256
Xylopine,1TBDMS,isomer #1	COC1=CC=C2C(=C1)C[C@@H]1C3=C(C=C4OCOC4=C23)CCN1[Si](C)(C)C(C)(C)C	3815.4	Standard polar	33892256

Spectra

MS/MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Xylopine 10V, Positive-QTOF	splash10-0002-0090000000-2f05a9287c8f61681e5b	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Xylopine 20V, Positive-QTOF	splash10-0002-0090000000-047b0b05686c6f93889e	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Xylopine 40V, Positive-QTOF	splash10-00lu-0390000000-193a1e3b8c54d1c49587	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Xylopine 10V, Negative-QTOF	splash10-0006-0090000000-b637672f1416623d1d58	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Xylopine 20V, Negative-QTOF	splash10-0006-0090000000-96200255e20b71b78965	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Xylopine 40V, Negative-QTOF	splash10-004i-1190000000-231196c8222c33bb2efe	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Xylopine 10V, Positive-QTOF	splash10-0002-0090000000-807fb2619769e9d71665	2021-10-21	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Xylopine 20V, Positive-QTOF	splash10-0002-0090000000-807fb2619769e9d71665	2021-10-21	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Xylopine 40V, Positive-QTOF	splash10-0006-0390000000-83cc85f11a4db6331f53	2021-10-21	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Xylopine 10V, Negative-QTOF	splash10-0006-0090000000-617cac9c409742842799	2021-10-21	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Xylopine 20V, Negative-QTOF	splash10-0006-0090000000-2b719eb619faa1b40824	2021-10-21	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Xylopine 40V, Negative-QTOF	splash10-01r6-0090000000-4a358b74722d9c82121b	2021-10-21	Wishart Lab	View Spectrum

Biological Properties

Cellular Locations

Not Available

Biospecimen Locations

Not Available

Tissue Locations

Not Available

Pathways

Not Available

Name	SMPDB/PathBank	KEGG

Normal Concentrations

Not Available

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

KNApSAcK ID

Chemspider ID

KEGG Compound ID

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

Not Available

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

Not Available

Showing metabocard for Xylopine (HMDB0301845)

MOL for HMDB0301845 (Xylopine)

3D MOL for HMDB0301845 (Xylopine)

3D SDF for HMDB0301845 (Xylopine)

3D-SDF for HMDB0301845 (Xylopine)

PDB for HMDB0301845 (Xylopine)

3D PDB for HMDB0301845 (Xylopine)

SMILES for HMDB0301845 (Xylopine)

INCHI for HMDB0301845 (Xylopine)

Structure for HMDB0301845 (Xylopine)

3D Structure for HMDB0301845 (Xylopine)

Predicted Collision Cross Sections

Predicted Retention Times

Underivatized

Predicted Kovats Retention Indices

Derivatized

MS/MS Spectra