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Showing metabocard for Grandilodine C (HMDB0341163)

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Record Information
Version5.0
StatusDetected but not Quantified
Creation Date2022-09-09 19:26:28 UTC
Update Date2022-09-22 18:35:04 UTC
HMDB IDHMDB0341163
Secondary Accession NumbersNone
Metabolite Identification
Common NameGrandilodine C
DescriptionGrandilodine C belongs to the class of organic compounds known as indolecarboxylic acids. Indolecarboxylic acids are compounds containing a carboxylic acid group linked to an indole. Based on a literature review a small amount of articles have been published on Grandilodine C.
Structure
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MOLSDFPDBSMILESInChI

MOL for HMDB0341163 (Grandilodine C)


  Mrv1652309092222042D          

 29 34  0  0  1  0            999 V2000
    5.8482   -0.0513    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.7058    0.7613    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    6.6486    0.4741    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.9569   -0.0551    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    6.8244    0.9653    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.8699    1.2161    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.1710    0.3609    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    4.1407    0.6379    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.9146    1.4313    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.4886    2.0238    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.1144    1.6321    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.8883    2.4255    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5911    0.0512    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7723   -0.0504    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4509   -0.8102    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9482   -1.4684    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7669   -1.3669    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0884   -0.6071    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.8346   -0.2122    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    5.1529   -1.0103    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.9380   -1.2991    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.6863   -0.9035    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    7.3127   -1.4279    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.2594   -2.2512    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    8.0111   -0.9827    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.8081   -0.1739    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.5980    0.7307    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.1144    1.3630    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0765    2.1871    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  1  0  0  0
  2  3  1  0  0  0  0
  4  3  1  6  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  1  0  0  0  0
  2  7  1  0  0  0  0
  7  8  1  6  0  0  0
  8  9  1  0  0  0  0
  9 10  2  0  0  0  0
  9 11  1  0  0  0  0
 11 12  1  0  0  0  0
  8 13  1  0  0  0  0
 13 14  2  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  2  0  0  0  0
 13 18  1  0  0  0  0
 18 19  1  0  0  0  0
  7 19  1  0  0  0  0
 19 20  1  0  0  0  0
 20 21  1  0  0  0  0
 21 22  1  0  0  0  0
  4 22  1  0  0  0  0
 22 23  1  0  0  0  0
 23 24  2  0  0  0  0
 23 25  1  0  0  0  0
 25 26  2  0  0  0  0
  4 26  1  0  0  0  0
 19 27  1  6  0  0  0
 27 28  1  0  0  0  0
  2 28  1  0  0  0  0
 28 29  2  0  0  0  0
M  END
Download

3D MOL for HMDB0341163 (Grandilodine C)

Download
3D SDF for HMDB0341163 (Grandilodine C)

  Mrv1652309092222042D          

 29 34  0  0  1  0            999 V2000
    5.8482   -0.0513    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.7058    0.7613    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    6.6486    0.4741    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.9569   -0.0551    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    6.8244    0.9653    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.8699    1.2161    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.1710    0.3609    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    4.1407    0.6379    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.9146    1.4313    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.4886    2.0238    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.1144    1.6321    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.8883    2.4255    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5911    0.0512    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7723   -0.0504    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4509   -0.8102    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9482   -1.4684    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7669   -1.3669    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0884   -0.6071    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.8346   -0.2122    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    5.1529   -1.0103    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.9380   -1.2991    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.6863   -0.9035    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    7.3127   -1.4279    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.2594   -2.2512    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    8.0111   -0.9827    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.8081   -0.1739    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.5980    0.7307    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.1144    1.3630    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0765    2.1871    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  1  0  0  0
  2  3  1  0  0  0  0
  4  3  1  6  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  1  0  0  0  0
  2  7  1  0  0  0  0
  7  8  1  6  0  0  0
  8  9  1  0  0  0  0
  9 10  2  0  0  0  0
  9 11  1  0  0  0  0
 11 12  1  0  0  0  0
  8 13  1  0  0  0  0
 13 14  2  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  2  0  0  0  0
 13 18  1  0  0  0  0
 18 19  1  0  0  0  0
  7 19  1  0  0  0  0
 19 20  1  0  0  0  0
 20 21  1  0  0  0  0
 21 22  1  0  0  0  0
  4 22  1  0  0  0  0
 22 23  1  0  0  0  0
 23 24  2  0  0  0  0
 23 25  1  0  0  0  0
 25 26  2  0  0  0  0
  4 26  1  0  0  0  0
 19 27  1  6  0  0  0
 27 28  1  0  0  0  0
  2 28  1  0  0  0  0
 28 29  2  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0341163

> <DATABASE_NAME>
hmdb

> <SMILES>
[H][C@@]12C[C@@]34CC[C@@]11N(C(=O)OC)C5=CC=CC=C5[C@@]1(CCN3C(=O)C=C4)OC2=O

> <INCHI_IDENTIFIER>
InChI=1S/C21H20N2O5/c1-27-18(26)23-15-5-3-2-4-13(15)21-10-11-22-16(24)6-7-19(22)8-9-20(21,23)14(12-19)17(25)28-21/h2-7,14H,8-12H2,1H3/t14-,19+,20+,21+/m0/s1

> <INCHI_KEY>
STACHDUHGOCYFP-RKTMXUFFSA-N

> <FORMULA>
C21H20N2O5

> <MOLECULAR_WEIGHT>
380.4

> <EXACT_MASS>
380.137221752

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_ATOM_COUNT>
48

> <JCHEM_AVERAGE_POLARIZABILITY>
38.48043270239228

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
methyl (1R,9R,10R,12R)-15,20-dioxo-19-oxa-8,16-diazahexacyclo[8.8.2.2^{9,12}.0^{1,9}.0^{2,7}.0^{12,16}]docosa-2,4,6,13-tetraene-8-carboxylate

> <JCHEM_LOGP>
1.2469965723333334

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
6

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_BASIC>
-0.10784315996760163

> <JCHEM_POLAR_SURFACE_AREA>
76.15

> <JCHEM_REFRACTIVITY>
97.85279999999999

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
methyl (1R,9R,10R,12R)-15,20-dioxo-19-oxa-8,16-diazahexacyclo[8.8.2.2^{9,12}.0^{1,9}.0^{2,7}.0^{12,16}]docosa-2,4,6,13-tetraene-8-carboxylate

> <JCHEM_VEBER_RULE>
0

$$$$

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3D-SDF for HMDB0341163 (Grandilodine C)
Download
PDB for HMDB0341163 (Grandilodine C)
HEADER    PROTEIN                                 09-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   09-SEP-22         0                                  
HETATM    1  H   UNK     0      10.917  -0.096   0.000  0.00  0.00           H+0
HETATM    2  C   UNK     0      10.651   1.421   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      12.411   0.885   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      12.986  -0.103   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      12.739   1.802   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      10.957   2.270   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       9.652   0.674   0.000  0.00  0.00           C+0
HETATM    8  N   UNK     0       7.729   1.191   0.000  0.00  0.00           N+0
HETATM    9  C   UNK     0       7.307   2.672   0.000  0.00  0.00           C+0
HETATM   10  O   UNK     0       8.379   3.778   0.000  0.00  0.00           O+0
HETATM   11  O   UNK     0       5.814   3.047   0.000  0.00  0.00           O+0
HETATM   12  C   UNK     0       5.391   4.528   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       6.703   0.096   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       5.175  -0.094   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       4.575  -1.512   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       5.503  -2.741   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       7.032  -2.552   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       7.632  -1.133   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       9.025  -0.396   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       9.619  -1.886   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0      11.084  -2.425   0.000  0.00  0.00           C+0
HETATM   22  N   UNK     0      12.481  -1.687   0.000  0.00  0.00           N+0
HETATM   23  C   UNK     0      13.650  -2.665   0.000  0.00  0.00           C+0
HETATM   24  O   UNK     0      13.551  -4.202   0.000  0.00  0.00           O+0
HETATM   25  C   UNK     0      14.954  -1.834   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0      14.575  -0.325   0.000  0.00  0.00           C+0
HETATM   27  O   UNK     0       8.583   1.364   0.000  0.00  0.00           O+0
HETATM   28  C   UNK     0       9.547   2.544   0.000  0.00  0.00           C+0
HETATM   29  O   UNK     0       9.476   4.083   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3    7   28                                             
CONECT    3    2    4                                                       
CONECT    4    3    5   22   26                                             
CONECT    5    4    6                                                       
CONECT    6    5    7                                                       
CONECT    7    6    2    8   19                                             
CONECT    8    7    9   13                                                  
CONECT    9    8   10   11                                                  
CONECT   10    9                                                            
CONECT   11    9   12                                                       
CONECT   12   11                                                            
CONECT   13    8   14   18                                                  
CONECT   14   13   15                                                       
CONECT   15   14   16                                                       
CONECT   16   15   17                                                       
CONECT   17   16   18                                                       
CONECT   18   17   13   19                                                  
CONECT   19   18    7   20   27                                             
CONECT   20   19   21                                                       
CONECT   21   20   22                                                       
CONECT   22   21    4   23                                                  
CONECT   23   22   24   25                                                  
CONECT   24   23                                                            
CONECT   25   23   26                                                       
CONECT   26   25    4                                                       
CONECT   27   19   28                                                       
CONECT   28   27    2   29                                                  
CONECT   29   28                                                            
MASTER        0    0    0    0    0    0    0    0   29    0   68    0
END

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3D PDB for HMDB0341163 (Grandilodine C)
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SMILES for HMDB0341163 (Grandilodine C)
[H][C@@]12C[C@@]34CC[C@@]11N(C(=O)OC)C5=CC=CC=C5[C@@]1(CCN3C(=O)C=C4)OC2=O
Download
INCHI for HMDB0341163 (Grandilodine C)
InChI=1S/C21H20N2O5/c1-27-18(26)23-15-5-3-2-4-13(15)21-10-11-22-16(24)6-7-19(22)8-9-20(21,23)14(12-19)17(25)28-21/h2-7,14H,8-12H2,1H3/t14-,19+,20+,21+/m0/s1
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View in JSmolView Stereo Labels
SynonymsNot Available
Chemical FormulaC21H20N2O5
Average Molecular Weight380.4
Monoisotopic Molecular Weight380.137221752
IUPAC Namemethyl (1R,9R,10R,12R)-15,20-dioxo-19-oxa-8,16-diazahexacyclo[8.8.2.2^{9,12}.0^{1,9}.0^{2,7}.0^{12,16}]docosa-2,4,6,13-tetraene-8-carboxylate
Traditional Namemethyl (1R,9R,10R,12R)-15,20-dioxo-19-oxa-8,16-diazahexacyclo[8.8.2.2^{9,12}.0^{1,9}.0^{2,7}.0^{12,16}]docosa-2,4,6,13-tetraene-8-carboxylate
CAS Registry NumberNot Available
SMILES
[H][C@@]12C[C@@]34CC[C@@]11N(C(=O)OC)C5=CC=CC=C5[C@@]1(CCN3C(=O)C=C4)OC2=O
InChI Identifier
InChI=1S/C21H20N2O5/c1-27-18(26)23-15-5-3-2-4-13(15)21-10-11-22-16(24)6-7-19(22)8-9-20(21,23)14(12-19)17(25)28-21/h2-7,14H,8-12H2,1H3/t14-,19+,20+,21+/m0/s1
InChI KeySTACHDUHGOCYFP-RKTMXUFFSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as indolecarboxylic acids. Indolecarboxylic acids are compounds containing a carboxylic acid group linked to an indole.
KingdomOrganic compounds  
Super ClassOrganoheterocyclic compounds  
ClassIndoles and derivatives  
Sub ClassIndolecarboxylic acids and derivatives  
Direct ParentIndolecarboxylic acids  
Alternative Parents
Substituents
  • Indolecarboxylic acid
    • 

  • Gamma butyrolactone
    • 

  • Benzenoid
    • 

  • Carbamic acid ester
    • 

  • Tetrahydrofuran
    • 

  • Tertiary carboxylic acid amide
    • 

  • Pyrroline
    • 

  • Carboxamide group
    • 

  • Carboxylic acid ester
    • 

  • Lactam
    • 

  • Lactone
    • 

  • Carbonic acid derivative
    • 

  • Carboxylic acid derivative
    • 

  • Oxacycle
    • 

  • Monocarboxylic acid or derivatives
    • 

  • Azacycle
    • 

  • Carbonyl group
    • 

  • Hydrocarbon derivative
    • 

  • Organic oxide
    • 

  • Organopnictogen compound
    • 

  • Organic oxygen compound
    • 

  • Organic nitrogen compound
    • 

  • Organonitrogen compound
    • 

  • Organooxygen compound
    • 

  • Aromatic heteropolycyclic compound
Molecular FrameworkAromatic heteropolycyclic compounds
External Descriptors
Ontology
Not AvailableNot 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
logP1.25ChemAxon
pKa (Strongest Basic)-0.11ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count4ChemAxon
Hydrogen Donor Count0ChemAxon
Polar Surface Area76.15 ŲChemAxon
Rotatable Bond Count1ChemAxon
Refractivity97.85 m³·mol⁻¹ChemAxon
Polarizability38.48 ųChemAxon
Number of Rings6ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
Predicted Chromatographic Properties
Predicted Kovats Retention Indices
Not Available
Spectra
Biological Properties
Cellular LocationsNot Available
Biospecimen Locations
  • Blood
    • 

  • Urine
Tissue LocationsNot Available
Pathways
Normal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
BloodExpected but not QuantifiedNot QuantifiedNot SpecifiedNot SpecifiedNormal  details
UrineDetected but not QuantifiedNot QuantifiedNot SpecifiedNot SpecifiedNormal  details
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDNot Available
KNApSAcK IDNot Available
Chemspider ID26630846  
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound56662978  
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 References
  1. Neto FC, Raftery D: Expanding Urinary Metabolite Annotation through Integrated Mass Spectral Similarity Networking. Anal Chem. 2021 Sep 7;93(35):12001-12010. doi: 10.1021/acs.analchem.1c02041. Epub 2021 Aug 26. [PubMed:34436864  ]