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Showing metabocard for norajmaline (HMDB0304439)

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Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2021-09-24 09:47:17 UTC
Update Date2021-09-24 09:47:17 UTC
HMDB IDHMDB0304439
Secondary Accession NumbersNone
Metabolite Identification
Common Namenorajmaline
DescriptionNorajmaline is a member of the class of compounds known as ajmaline-sarpagine alkaloids. Ajmaline-sarpagine alkaloids are organic compounds containing either of the ajmalan, sarpagan skeleton, or derivative thereof. The Sarpagine (Akuammidine) group, based on the sarpagan nucleus, arises from bond formation between C-16 and C-5 of the corynantheine precursor. Ajmaline alkaloids are based on a 17,19-secoyohimban skeleton (oxayohimban) which is invariably present as an ether. Norajmaline is slightly soluble (in water) and a very weakly acidic compound (based on its pKa). Norajmaline can be found in a number of food items such as roselle, chayote, savoy cabbage, and onion-family vegetables, which makes norajmaline a potential biomarker for the consumption of these food products.
Structure
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MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0304439 (norajmaline)


  Mrv1533004251508342D          

 23 28  0  0  0  0            999 V2000
   -1.2724    0.6461    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4772    0.8658    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1106    0.2870    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9791    0.1877    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9515    1.0223    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5871    0.4291    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4498    0.5739    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0204    1.2285    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.6572    0.6743    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.4211    0.9859    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0729    0.4801    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.9608   -0.3372    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.1969   -0.6488    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5451   -0.1430    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6786   -0.2627    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1182   -1.0762    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3140   -1.1684    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7535   -0.4514    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6022   -0.9752    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9651   -1.7161    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.0676   -0.3823    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.2173   -0.5325    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2709   -1.1975    0.0000 O   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  1  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  2  0  0  0  0
 12 13  1  0  0  0  0
 13 14  2  0  0  0  0
  9 14  1  0  0  0  0
 14 15  1  0  0  0  0
  7 15  1  0  0  0  0
 15 16  1  0  0  0  0
 16 17  1  0  0  0  0
 17 18  1  0  0  0  0
  4 18  1  0  0  0  0
 18 19  1  0  0  0  0
 15 19  1  0  0  0  0
 19 20  1  0  0  0  0
 17 21  1  0  0  0  0
  6 21  1  0  0  0  0
 21 22  1  0  0  0  0
  3 22  1  0  0  0  0
 22 23  1  0  0  0  0
M  END
Download

3D MOL for HMDB0304439 (norajmaline)

HMDB0304439
     RDKit          3D
norajmaline
 47 52  0  0  0  0  0  0  0  0999 V2000
   -4.6736    0.6436   -0.8101 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0806   -0.6898   -0.3757 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8175   -0.3782    0.3932 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8124    0.3745   -0.4552 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0880   -0.6752   -1.2917 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1629   -1.4210   -0.4066 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2180   -0.9619   -0.3161 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9867   -0.7709   -1.4894 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.1381   -0.0346   -1.0366 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.4460    0.0868   -1.5145 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.3825    0.8733   -0.8739 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.9912    1.5461    0.2653 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7089    1.4622    0.7829 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7969    0.6626    0.1115 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4095    0.3707    0.3742 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9908    0.1800    1.7988 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5089   -0.0698    1.5578 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8346    1.0032    0.5201 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4440    1.4243   -0.1004 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4304    1.6230   -1.4494 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7261   -1.3798    0.9558 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1407   -1.6148    0.9283 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4882   -2.7533    0.2091 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2187    1.0159   -1.7507 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4313    1.3771   -0.0143 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.7795    0.5509   -0.8888 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8137   -1.1501    0.2982 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9025   -1.3680   -1.2210 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0530    0.2615    1.2684 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2870    1.1343   -1.1070 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6720   -0.2846   -2.2156 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9008   -1.3968   -1.6039 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1577   -2.5196   -0.6589 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7800   -1.7004    0.3238 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8311   -1.0567   -2.4649 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.7425   -0.4560   -2.4245 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.3964    0.9502   -1.2685 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.7438    2.1660    0.7634 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.4456    2.0110    1.6845 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4664   -0.6800    2.2765 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.0544    1.1172    2.3649 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0969    0.0127    2.4633 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3337    1.8273    1.0537 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7622    2.3785    0.3801 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3912    1.6335   -1.7586 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4646   -1.8023    1.9806 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1117   -3.5225    0.6858 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  1  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
 17 18  1  0
 18 19  1  0
 19 20  1  0
 17 21  1  0
 21 22  1  0
 22 23  1  0
 22  3  1  0
 18  4  1  0
 21  6  1  0
 15  7  1  0
 14  9  1  0
 19 15  1  0
  1 24  1  0
  1 25  1  0
  1 26  1  0
  2 27  1  0
  2 28  1  0
  3 29  1  0
  4 30  1  0
  5 31  1  0
  5 32  1  0
  6 33  1  0
  7 34  1  0
  8 35  1  0
 10 36  1  0
 11 37  1  0
 12 38  1  0
 13 39  1  0
 16 40  1  0
 16 41  1  0
 17 42  1  0
 18 43  1  0
 19 44  1  0
 20 45  1  0
 22 46  1  0
 23 47  1  0
M  END
Download

3D SDF for HMDB0304439 (norajmaline)


  Mrv1533004251508342D          

 23 28  0  0  0  0            999 V2000
   -1.2724    0.6461    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4772    0.8658    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1106    0.2870    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9791    0.1877    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9515    1.0223    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5871    0.4291    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4498    0.5739    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0204    1.2285    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.6572    0.6743    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.4211    0.9859    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0729    0.4801    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.9608   -0.3372    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.1969   -0.6488    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5451   -0.1430    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6786   -0.2627    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1182   -1.0762    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3140   -1.1684    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7535   -0.4514    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6022   -0.9752    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9651   -1.7161    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.0676   -0.3823    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.2173   -0.5325    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2709   -1.1975    0.0000 O   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  1  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  2  0  0  0  0
 12 13  1  0  0  0  0
 13 14  2  0  0  0  0
  9 14  1  0  0  0  0
 14 15  1  0  0  0  0
  7 15  1  0  0  0  0
 15 16  1  0  0  0  0
 16 17  1  0  0  0  0
 17 18  1  0  0  0  0
  4 18  1  0  0  0  0
 18 19  1  0  0  0  0
 15 19  1  0  0  0  0
 19 20  1  0  0  0  0
 17 21  1  0  0  0  0
  6 21  1  0  0  0  0
 21 22  1  0  0  0  0
  3 22  1  0  0  0  0
 22 23  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0304439

> <DATABASE_NAME>
hmdb

> <SMILES>
CCC1C(O)N2C3CC45C(O)C3C1CC2C4NC1=CC=CC=C51

> <INCHI_IDENTIFIER>
InChI=1S/C19H24N2O2/c1-2-9-10-7-13-16-19(11-5-3-4-6-12(11)20-16)8-14(15(10)17(19)22)21(13)18(9)23/h3-6,9-10,13-18,20,22-23H,2,7-8H2,1H3

> <INCHI_KEY>
HIOAYNMZFIHQNS-UHFFFAOYSA-N

> <FORMULA>
C19H24N2O2

> <MOLECULAR_WEIGHT>
312.413

> <EXACT_MASS>
312.183778021

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_ATOM_COUNT>
47

> <JCHEM_AVERAGE_POLARIZABILITY>
34.67343565325607

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
13-ethyl-8,15-diazahexacyclo[14.2.1.0¹,⁹.0²,⁷.0¹⁰,¹⁵.0¹²,¹⁷]nonadeca-2,4,6-triene-14,18-diol

> <ALOGPS_LOGP>
1.40

> <JCHEM_LOGP>
1.2155420556666663

> <ALOGPS_LOGS>
-2.21

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
6

> <JCHEM_PHYSIOLOGICAL_CHARGE>
1

> <JCHEM_PKA>
14.33118206530321

> <JCHEM_PKA_STRONGEST_ACIDIC>
13.280390285454537

> <JCHEM_PKA_STRONGEST_BASIC>
7.019399405233089

> <JCHEM_POLAR_SURFACE_AREA>
55.730000000000004

> <JCHEM_REFRACTIVITY>
88.331

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.94e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
13-ethyl-8,15-diazahexacyclo[14.2.1.0¹,⁹.0²,⁷.0¹⁰,¹⁵.0¹²,¹⁷]nonadeca-2,4,6-triene-14,18-diol

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for HMDB0304439 (norajmaline)

HMDB0304439
     RDKit          3D
norajmaline
 47 52  0  0  0  0  0  0  0  0999 V2000
   -4.6736    0.6436   -0.8101 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0806   -0.6898   -0.3757 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8175   -0.3782    0.3932 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8124    0.3745   -0.4552 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0880   -0.6752   -1.2917 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1629   -1.4210   -0.4066 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2180   -0.9619   -0.3161 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9867   -0.7709   -1.4894 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.1381   -0.0346   -1.0366 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.4460    0.0868   -1.5145 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.3825    0.8733   -0.8739 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.9912    1.5461    0.2653 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7089    1.4622    0.7829 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7969    0.6626    0.1115 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4095    0.3707    0.3742 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9908    0.1800    1.7988 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5089   -0.0698    1.5578 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8346    1.0032    0.5201 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4440    1.4243   -0.1004 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4304    1.6230   -1.4494 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7261   -1.3798    0.9558 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1407   -1.6148    0.9283 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4882   -2.7533    0.2091 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2187    1.0159   -1.7507 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4313    1.3771   -0.0143 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.7795    0.5509   -0.8888 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8137   -1.1501    0.2982 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9025   -1.3680   -1.2210 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0530    0.2615    1.2684 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2870    1.1343   -1.1070 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6720   -0.2846   -2.2156 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9008   -1.3968   -1.6039 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1577   -2.5196   -0.6589 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7800   -1.7004    0.3238 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8311   -1.0567   -2.4649 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.7425   -0.4560   -2.4245 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.3964    0.9502   -1.2685 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.7438    2.1660    0.7634 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.4456    2.0110    1.6845 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4664   -0.6800    2.2765 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.0544    1.1172    2.3649 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0969    0.0127    2.4633 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3337    1.8273    1.0537 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7622    2.3785    0.3801 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3912    1.6335   -1.7586 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4646   -1.8023    1.9806 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1117   -3.5225    0.6858 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  1  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
 17 18  1  0
 18 19  1  0
 19 20  1  0
 17 21  1  0
 21 22  1  0
 22 23  1  0
 22  3  1  0
 18  4  1  0
 21  6  1  0
 15  7  1  0
 14  9  1  0
 19 15  1  0
  1 24  1  0
  1 25  1  0
  1 26  1  0
  2 27  1  0
  2 28  1  0
  3 29  1  0
  4 30  1  0
  5 31  1  0
  5 32  1  0
  6 33  1  0
  7 34  1  0
  8 35  1  0
 10 36  1  0
 11 37  1  0
 12 38  1  0
 13 39  1  0
 16 40  1  0
 16 41  1  0
 17 42  1  0
 18 43  1  0
 19 44  1  0
 20 45  1  0
 22 46  1  0
 23 47  1  0
M  END
Download

PDB for HMDB0304439 (norajmaline)

HEADER    PROTEIN                                 25-APR-15   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   25-APR-15         0                                  
HETATM    1  C   UNK     0      -2.375   1.206   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -0.891   1.616   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       0.207   0.536   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       1.828   0.350   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       1.776   1.908   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       2.963   0.801   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       4.573   1.071   0.000  0.00  0.00           C+0
HETATM    8  N   UNK     0       5.638   2.293   0.000  0.00  0.00           N+0
HETATM    9  C   UNK     0       6.827   1.259   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       8.253   1.840   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       9.469   0.896   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       9.260  -0.629   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       7.834  -1.211   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       6.618  -0.267   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       5.000  -0.490   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       3.954  -2.009   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       2.453  -2.181   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       3.273  -0.843   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       4.857  -1.820   0.000  0.00  0.00           C+0
HETATM   20  O   UNK     0       5.535  -3.203   0.000  0.00  0.00           O+0
HETATM   21  N   UNK     0       1.993  -0.714   0.000  0.00  0.00           N+0
HETATM   22  C   UNK     0       0.406  -0.994   0.000  0.00  0.00           C+0
HETATM   23  O   UNK     0      -0.506  -2.235   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4   22                                                  
CONECT    4    3    5   18                                                  
CONECT    5    4    6                                                       
CONECT    6    5    7   21                                                  
CONECT    7    6    8   15                                                  
CONECT    8    7    9                                                       
CONECT    9    8   10   14                                                  
CONECT   10    9   11                                                       
CONECT   11   10   12                                                       
CONECT   12   11   13                                                       
CONECT   13   12   14                                                       
CONECT   14   13    9   15                                                  
CONECT   15   14    7   16   19                                             
CONECT   16   15   17                                                       
CONECT   17   16   18   21                                                  
CONECT   18   17    4   19                                                  
CONECT   19   18   15   20                                                  
CONECT   20   19                                                            
CONECT   21   17    6   22                                                  
CONECT   22   21    3   23                                                  
CONECT   23   22                                                            
MASTER        0    0    0    0    0    0    0    0   23    0   56    0
END
Download

3D PDB for HMDB0304439 (norajmaline)

COMPND    HMDB0304439
HETATM    1  C1  UNL     1      -4.674   0.644  -0.810  1.00  0.00           C  
HETATM    2  C2  UNL     1      -4.081  -0.690  -0.376  1.00  0.00           C  
HETATM    3  C3  UNL     1      -2.818  -0.378   0.393  1.00  0.00           C  
HETATM    4  C4  UNL     1      -1.812   0.374  -0.455  1.00  0.00           C  
HETATM    5  C5  UNL     1      -1.088  -0.675  -1.292  1.00  0.00           C  
HETATM    6  C6  UNL     1      -0.163  -1.421  -0.407  1.00  0.00           C  
HETATM    7  C7  UNL     1       1.218  -0.962  -0.316  1.00  0.00           C  
HETATM    8  N1  UNL     1       1.987  -0.771  -1.489  1.00  0.00           N  
HETATM    9  C8  UNL     1       3.138  -0.035  -1.037  1.00  0.00           C  
HETATM   10  C9  UNL     1       4.446   0.087  -1.515  1.00  0.00           C  
HETATM   11  C10 UNL     1       5.382   0.873  -0.874  1.00  0.00           C  
HETATM   12  C11 UNL     1       4.991   1.546   0.265  1.00  0.00           C  
HETATM   13  C12 UNL     1       3.709   1.462   0.783  1.00  0.00           C  
HETATM   14  C13 UNL     1       2.797   0.663   0.111  1.00  0.00           C  
HETATM   15  C14 UNL     1       1.410   0.371   0.374  1.00  0.00           C  
HETATM   16  C15 UNL     1       0.991   0.180   1.799  1.00  0.00           C  
HETATM   17  C16 UNL     1      -0.509  -0.070   1.558  1.00  0.00           C  
HETATM   18  C17 UNL     1      -0.835   1.003   0.520  1.00  0.00           C  
HETATM   19  C18 UNL     1       0.444   1.424  -0.100  1.00  0.00           C  
HETATM   20  O1  UNL     1       0.430   1.623  -1.449  1.00  0.00           O  
HETATM   21  N2  UNL     1      -0.726  -1.380   0.956  1.00  0.00           N  
HETATM   22  C19 UNL     1      -2.141  -1.615   0.928  1.00  0.00           C  
HETATM   23  O2  UNL     1      -2.488  -2.753   0.209  1.00  0.00           O  
HETATM   24  H1  UNL     1      -4.219   1.016  -1.751  1.00  0.00           H  
HETATM   25  H2  UNL     1      -4.431   1.377  -0.014  1.00  0.00           H  
HETATM   26  H3  UNL     1      -5.780   0.551  -0.889  1.00  0.00           H  
HETATM   27  H4  UNL     1      -4.814  -1.150   0.298  1.00  0.00           H  
HETATM   28  H5  UNL     1      -3.902  -1.368  -1.221  1.00  0.00           H  
HETATM   29  H6  UNL     1      -3.053   0.261   1.268  1.00  0.00           H  
HETATM   30  H7  UNL     1      -2.287   1.134  -1.107  1.00  0.00           H  
HETATM   31  H8  UNL     1      -0.672  -0.285  -2.216  1.00  0.00           H  
HETATM   32  H9  UNL     1      -1.901  -1.397  -1.604  1.00  0.00           H  
HETATM   33  H10 UNL     1      -0.158  -2.520  -0.659  1.00  0.00           H  
HETATM   34  H11 UNL     1       1.780  -1.700   0.324  1.00  0.00           H  
HETATM   35  H12 UNL     1       1.831  -1.057  -2.465  1.00  0.00           H  
HETATM   36  H13 UNL     1       4.743  -0.456  -2.425  1.00  0.00           H  
HETATM   37  H14 UNL     1       6.396   0.950  -1.269  1.00  0.00           H  
HETATM   38  H15 UNL     1       5.744   2.166   0.763  1.00  0.00           H  
HETATM   39  H16 UNL     1       3.446   2.011   1.685  1.00  0.00           H  
HETATM   40  H17 UNL     1       1.466  -0.680   2.277  1.00  0.00           H  
HETATM   41  H18 UNL     1       1.054   1.117   2.365  1.00  0.00           H  
HETATM   42  H19 UNL     1      -1.097   0.013   2.463  1.00  0.00           H  
HETATM   43  H20 UNL     1      -1.334   1.827   1.054  1.00  0.00           H  
HETATM   44  H21 UNL     1       0.762   2.379   0.380  1.00  0.00           H  
HETATM   45  H22 UNL     1       1.391   1.633  -1.759  1.00  0.00           H  
HETATM   46  H23 UNL     1      -2.465  -1.802   1.981  1.00  0.00           H  
HETATM   47  H24 UNL     1      -2.112  -3.523   0.686  1.00  0.00           H  
CONECT    1    2   24   25   26
CONECT    2    3   27   28
CONECT    3    4   22   29
CONECT    4    5   18   30
CONECT    5    6   31   32
CONECT    6    7   21   33
CONECT    7    8   15   34
CONECT    8    9   35
CONECT    9   10   10   14
CONECT   10   11   36
CONECT   11   12   12   37
CONECT   12   13   38
CONECT   13   14   14   39
CONECT   14   15
CONECT   15   16   19
CONECT   16   17   40   41
CONECT   17   18   21   42
CONECT   18   19   43
CONECT   19   20   44
CONECT   20   45
CONECT   21   22
CONECT   22   23   46
CONECT   23   47
END
Download

SMILES for HMDB0304439 (norajmaline)

CCC1C(O)N2C3CC45C(O)C3C1CC2C4NC1=CC=CC=C51
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INCHI for HMDB0304439 (norajmaline)

InChI=1S/C19H24N2O2/c1-2-9-10-7-13-16-19(11-5-3-4-6-12(11)20-16)8-14(15(10)17(19)22)21(13)18(9)23/h3-6,9-10,13-18,20,22-23H,2,7-8H2,1H3
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View in JSmolView Stereo Labels
SynonymsNot Available
Chemical FormulaC19H24N2O2
Average Molecular Weight312.413
Monoisotopic Molecular Weight312.183778021
IUPAC Name13-ethyl-8,15-diazahexacyclo[14.2.1.0¹,⁹.0²,⁷.0¹⁰,¹⁵.0¹²,¹⁷]nonadeca-2,4,6-triene-14,18-diol
Traditional Name13-ethyl-8,15-diazahexacyclo[14.2.1.0¹,⁹.0²,⁷.0¹⁰,¹⁵.0¹²,¹⁷]nonadeca-2,4,6-triene-14,18-diol
CAS Registry NumberNot Available
SMILES
CCC1C(O)N2C3CC45C(O)C3C1CC2C4NC1=CC=CC=C51
InChI Identifier
InChI=1S/C19H24N2O2/c1-2-9-10-7-13-16-19(11-5-3-4-6-12(11)20-16)8-14(15(10)17(19)22)21(13)18(9)23/h3-6,9-10,13-18,20,22-23H,2,7-8H2,1H3
InChI KeyHIOAYNMZFIHQNS-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as ajmaline-sarpagine alkaloids. These are organic compounds containing either of the ajmalan, sarpagan skeleton, or derivative thereof. The Sarpagine (Akuammidine) group, based on the sarpagan nucleus, arises from bond formation between C-16 and C-5 of the corynantheine precursor. Ajmaline alkaloids are based on a 17,19-secoyohimban skeleton (oxayohimban) which is invariably present as an ether.
KingdomOrganic compounds
Super ClassAlkaloids and derivatives
ClassAjmaline-sarpagine alkaloids
Sub ClassNot Available
Direct ParentAjmaline-sarpagine alkaloids
Alternative Parents
Substituents
  • Sarpagine-skeleton
  • Beta-carboline
  • Pyridoindole
  • Quinolizidine
  • Indole or derivatives
  • Dihydroindole
  • Quinuclidine
  • Azepane
  • Aralkylamine
  • Secondary aliphatic/aromatic amine
  • Piperidine
  • Benzenoid
  • Cyclic alcohol
  • Hemiaminal
  • Secondary alcohol
  • Secondary amine
  • Organoheterocyclic compound
  • Azacycle
  • Alkanolamine
  • Organooxygen compound
  • Organonitrogen compound
  • Hydrocarbon derivative
  • Organic nitrogen compound
  • Organopnictogen compound
  • Organic oxygen compound
  • Amine
  • Alcohol
  • Aromatic heteropolycyclic compound
Molecular FrameworkAromatic heteropolycyclic compounds
External Descriptors
Ontology
Physiological effectNot Available
Disposition
Source
Process
Naturally occurring process
RoleNot Available
Physical Properties
StateNot Available
Experimental Molecular Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
PropertyValueSource
logP1.4ALOGPS
logP1.22ChemAxon
logS-2.2ALOGPS
pKa (Strongest Acidic)13.28ChemAxon
pKa (Strongest Basic)7.02ChemAxon
Physiological Charge1ChemAxon
Hydrogen Acceptor Count4ChemAxon
Hydrogen Donor Count3ChemAxon
Polar Surface Area55.73 ŲChemAxon
Rotatable Bond Count1ChemAxon
Refractivity88.33 m³·mol⁻¹ChemAxon
Polarizability34.67 ųChemAxon
Number of Rings6ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
Predicted Chromatographic Properties

Predicted Collision Cross Sections

PredictorAdduct TypeCCS Value (Å2)Reference
AllCCS[M+H]+178.8832859911
AllCCS[M+H-H2O]+175.76732859911
AllCCS[M+Na]+182.58832859911
AllCCS[M+NH4]+181.76132859911
AllCCS[M-H]-185.10932859911
AllCCS[M+Na-2H]-184.66732859911
AllCCS[M+HCOO]-184.32732859911
DeepCCS[M-2H]-207.11230932474
DeepCCS[M+Na]+182.57630932474

Predicted Kovats Retention Indices

Derivatized

Derivative Name / StructureSMILESKovats RI ValueColumn TypeReference
norajmaline,3TMS,isomer #1CCC1C2CC3C4N([Si](C)(C)C)C5=CC=CC=C5C45CC(C2C5O[Si](C)(C)C)N3C1O[Si](C)(C)C2713.2Semi standard non polar33892256
norajmaline,3TMS,isomer #1CCC1C2CC3C4N([Si](C)(C)C)C5=CC=CC=C5C45CC(C2C5O[Si](C)(C)C)N3C1O[Si](C)(C)C2785.8Standard non polar33892256
norajmaline,3TMS,isomer #1CCC1C2CC3C4N([Si](C)(C)C)C5=CC=CC=C5C45CC(C2C5O[Si](C)(C)C)N3C1O[Si](C)(C)C3024.5Standard polar33892256
norajmaline,3TBDMS,isomer #1CCC1C2CC3C4N([Si](C)(C)C(C)(C)C)C5=CC=CC=C5C45CC(C2C5O[Si](C)(C)C(C)(C)C)N3C1O[Si](C)(C)C(C)(C)C3303.8Semi standard non polar33892256
norajmaline,3TBDMS,isomer #1CCC1C2CC3C4N([Si](C)(C)C(C)(C)C)C5=CC=CC=C5C45CC(C2C5O[Si](C)(C)C(C)(C)C)N3C1O[Si](C)(C)C(C)(C)C3527.7Standard non polar33892256
norajmaline,3TBDMS,isomer #1CCC1C2CC3C4N([Si](C)(C)C(C)(C)C)C5=CC=CC=C5C45CC(C2C5O[Si](C)(C)C(C)(C)C)N3C1O[Si](C)(C)C(C)(C)C3302.6Standard polar33892256
Spectra

MS/MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - norajmaline 10V, Negative-QTOFsplash10-03di-0029000000-027ecd5807c87855bfcb2015-05-27Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - norajmaline 20V, Negative-QTOFsplash10-03di-0079000000-2de1832867f0fe55aaef2015-05-27Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - norajmaline 40V, Negative-QTOFsplash10-001i-0091000000-43c2c30cd6a46db24db42015-05-27Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - norajmaline 10V, Negative-QTOFsplash10-03di-0009000000-0e6a8c1ea40029b59edb2021-10-21Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - norajmaline 20V, Negative-QTOFsplash10-03di-0009000000-0e6a8c1ea40029b59edb2021-10-21Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - norajmaline 40V, Negative-QTOFsplash10-001i-0091000000-73f589f80a65e7c4a8bb2021-10-21Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - norajmaline 10V, Positive-QTOFsplash10-01ot-0097000000-2a44b03174eeaffdca272015-05-27Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - norajmaline 20V, Positive-QTOFsplash10-01ot-0093000000-f6d33c953c62038372042015-05-27Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - norajmaline 40V, Positive-QTOFsplash10-0f92-2190000000-18ffdb217d2b60d75a002015-05-27Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - norajmaline 10V, Positive-QTOFsplash10-03di-0009000000-9a73b7f64213b1f23bdb2021-10-21Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - norajmaline 20V, Positive-QTOFsplash10-03di-0039000000-aeff63defab2754395782021-10-21Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - norajmaline 40V, Positive-QTOFsplash10-03yi-0093000000-f18dea87cc02a59517ac2021-10-21Wishart LabView Spectrum
Biological Properties
Cellular LocationsNot Available
Biospecimen LocationsNot Available
Tissue LocationsNot Available
Pathways
Normal Concentrations
Not Available
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDFDB031061
KNApSAcK IDNot Available
Chemspider IDNot Available
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound4491371
PDB IDNot Available
ChEBI IDNot Available
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDNot Available
Good Scents IDNot Available
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Not Available
General ReferencesNot Available