NP-MRD: Showing NP-Card for Gardenine (NP0138778)

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Record Information

Version

1.0

Created at

2022-06-29 19:16:37 UTC

Updated at

2022-06-29 19:16:37 UTC

NP-MRD ID

NP0138778

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Gardenine

Description

Gardenine belongs to the class of organic compounds known as tetrahydropyridines. These are derivatives of pyridine in which two double bonds in the pyridine moiety are reduced by adding four hydrogen atoms. Based on a literature review very few articles have been published on Gardenine.

Structure

MOL 3D MOL SDF PDB SMILES InChI

     RDKit          3D

 29 31  0  0  0  0  0  0  0  0999 V2000
    4.8928    0.2125   -0.2935 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6147   -0.1701    0.2006 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.4416    0.3593   -0.3255 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5635    1.1902   -1.2563 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.1179    0.0077    0.1366 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0325   -0.8794    1.1279 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2526   -1.2676    1.6282 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3610   -0.9582    0.8248 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.6075   -0.9240    1.3569 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3847   -0.2809    0.3693 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4360    0.5791   -0.4467 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.8988    1.8332   -0.7038 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9185   -0.1477   -1.6381 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5909   -0.1264   -1.6672 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0558    0.6262   -0.4854 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.2122    0.5306    0.4420 C   0  0  2  0  0  0  0  0  0  0  0  0
    5.3732    0.9687    0.3733 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.8284    0.6881   -1.2953 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.5797   -0.6522   -0.3704 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9542   -1.2775    1.5218 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3062   -1.7474    2.5377 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3948   -1.4800   -0.1573 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9122   -0.9824   -0.2757 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1030    0.4363    0.8519 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4173    1.8129   -1.5541 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5206   -0.6349   -2.3913 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0792   -0.5713   -2.4132 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1239    1.6681   -0.8275 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2294    1.1872    1.2883 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
  3  5  1  0
  5  6  2  0
  6  7  1  0
  7  8  1  0
  8  9  1  0
  9 10  1  0
 10 11  1  0
 11 12  1  6
 11 13  1  0
 13 14  2  0
 14 15  1  0
 15 16  1  0
 15  5  1  0
 16  8  1  0
 16 11  1  0
  1 17  1  0
  1 18  1  0
  1 19  1  0
  6 20  1  0
  7 21  1  0
  8 22  1  6
 10 23  1  0
 10 24  1  0
 12 25  1  0
 13 26  1  0
 14 27  1  0
 15 28  1  6
 16 29  1  1
M  END


  Mrv1652306292221162D          

 16 18  0  0  0  0            999 V2000
    5.4359   -1.6247    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.8106   -1.0866    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.0319   -1.3591    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.8785   -2.1697    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.4065   -0.8210    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5599   -0.0103    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9345    0.5278    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.1559    0.2553    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0025   -0.5554    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6278   -1.0935    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3093   -1.8545    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4871   -1.7867    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2975   -0.9838    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6721   -0.4457    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9907    0.3153    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.5925   -1.4123    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  2  0  0  0  0
  3  5  1  0  0  0  0
  5  6  2  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  1  0  0  0  0
  5 10  1  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
  9 13  1  0  0  0  0
 13 14  1  0  0  0  0
 14 15  1  0  0  0  0
  8 15  1  0  0  0  0
 13 16  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0138778

> <DATABASE_NAME>
NP-MRD

> <SMILES>
COC(=O)C1=CNC2OCC3(O)C=CC1C23

> <INCHI_IDENTIFIER>
InChI=1S/C11H13NO4/c1-15-10(13)7-4-12-9-8-6(7)2-3-11(8,14)5-16-9/h2-4,6,8-9,12,14H,5H2,1H3

> <INCHI_KEY>
QIGMCZARMNNIKC-UHFFFAOYSA-N

> <FORMULA>
C11H13NO4

> <MOLECULAR_WEIGHT>
223.228

> <EXACT_MASS>
223.084457903

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_ATOM_COUNT>
29

> <JCHEM_AVERAGE_POLARIZABILITY>
21.736897801718648

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
methyl 4-hydroxy-2-oxa-10-azatricyclo[5.3.1.0^{4,11}]undeca-5,8-diene-8-carboxylate

> <ALOGPS_LOGP>
-1.00

> <JCHEM_LOGP>
-0.29827532333333273

> <ALOGPS_LOGS>
-0.74

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
19.27110208706071

> <JCHEM_PKA_STRONGEST_ACIDIC>
13.258599699526556

> <JCHEM_PKA_STRONGEST_BASIC>
-3.560488275989976

> <JCHEM_POLAR_SURFACE_AREA>
67.79

> <JCHEM_REFRACTIVITY>
55.544000000000004

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
4.05e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
methyl 4-hydroxy-2-oxa-10-azatricyclo[5.3.1.0^{4,11}]undeca-5,8-diene-8-carboxylate

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 29-JUN-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   29-JUN-22         0                                  
HETATM    1  C   UNK     0      10.147  -3.033   0.000  0.00  0.00           C+0
HETATM    2  O   UNK     0       8.980  -2.028   0.000  0.00  0.00           O+0
HETATM    3  C   UNK     0       7.526  -2.537   0.000  0.00  0.00           C+0
HETATM    4  O   UNK     0       7.240  -4.050   0.000  0.00  0.00           O+0
HETATM    5  C   UNK     0       6.359  -1.532   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       6.645  -0.019   0.000  0.00  0.00           C+0
HETATM    7  N   UNK     0       5.478   0.985   0.000  0.00  0.00           N+0
HETATM    8  C   UNK     0       4.024   0.477   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       3.738  -1.037   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       4.905  -2.041   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       4.311  -3.462   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       2.776  -3.335   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       2.422  -1.836   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       1.255  -0.832   0.000  0.00  0.00           C+0
HETATM   15  O   UNK     0       1.849   0.589   0.000  0.00  0.00           O+0
HETATM   16  O   UNK     0       1.106  -2.636   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4    5                                                  
CONECT    4    3                                                            
CONECT    5    3    6   10                                                  
CONECT    6    5    7                                                       
CONECT    7    6    8                                                       
CONECT    8    7    9   15                                                  
CONECT    9    8   10   13                                                  
CONECT   10    9    5   11                                                  
CONECT   11   10   12                                                       
CONECT   12   11   13                                                       
CONECT   13   12    9   14   16                                             
CONECT   14   13   15                                                       
CONECT   15   14    8                                                       
CONECT   16   13                                                            
MASTER        0    0    0    0    0    0    0    0   16    0   36    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₁₁H₁₃NO₄

Average Mass

223.2280 Da

Monoisotopic Mass

223.08446 Da

IUPAC Name

Not Available

Traditional Name

Not Available

CAS Registry Number

139682-36-3

SMILES

COC(=O)C1=CNC2OCC3(O)C=CC1C23

InChI Identifier

InChI=1S/C11H13NO4/c1-15-10(13)7-4-12-9-8-6(7)2-3-11(8,14)5-16-9/h2-4,6,8-9,12,14H,5H2,1H3

InChI Key

QIGMCZARMNNIKC-UHFFFAOYSA-N

Experimental Spectra

Not Available

Predicted Spectra

Spectrum Type	Description	Depositor ID	Depositor Organization	Depositor	Deposition Date	View
1D NMR	¹³C NMR Spectrum (1D, 25 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 252 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 50 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 75 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 101 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 126 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 151 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 176 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 201 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 226 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum

Chemical Shift Submissions

Not Available

Species

Species of Origin

Not Available

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as tetrahydropyridines. These are derivatives of pyridine in which two double bonds in the pyridine moiety are reduced by adding four hydrogen atoms.

Kingdom

Organic compounds

Super Class

Organoheterocyclic compounds

Class

Pyridines and derivatives

Sub Class

Hydropyridines

Direct Parent

Tetrahydropyridines

Alternative Parents

Substituents

Tetrahydropyridine
Tertiary alcohol
Tetrahydrofuran
Methyl ester
Enoate ester
Alpha,beta-unsaturated carboxylic ester
Vinylogous amide
Amino acid or derivatives
Carboxylic acid ester
Carboxylic acid derivative
Oxacycle
Azacycle
Secondary aliphatic amine
Enamine
Secondary amine
Monocarboxylic acid or derivatives
Organic oxygen compound
Organonitrogen compound
Organooxygen compound
Alcohol
Organic nitrogen compound
Amine
Carbonyl group
Hydrocarbon derivative
Organic oxide
Organopnictogen compound
Aliphatic heteropolycyclic compound

Molecular Framework

Aliphatic heteropolycyclic compounds

External Descriptors

Not Available

Physical Properties

State

Not Available

Experimental Properties

Property	Value	Reference
Melting Point	Not Available	Not Available
Boiling Point	Not Available	Not Available
Water Solubility	Not Available	Not Available
LogP	Not Available	Not Available

Predicted Properties

Property	Value	Source

External Links

HMDB ID

Not Available

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

Not Available

KNApSAcK ID

Not Available

Chemspider ID

170936

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

197414

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Not Available

Showing NP-Card for Gardenine (NP0138778)

MOL for NP0138778 (Gardenine)

3D MOL for NP0138778 (Gardenine)

3D SDF for NP0138778 (Gardenine)

3D-SDF for NP0138778 (Gardenine)

PDB for NP0138778 (Gardenine)

3D PDB for NP0138778 (Gardenine)

SMILES for NP0138778 (Gardenine)

INCHI for NP0138778 (Gardenine)

Structure for NP0138778 (Gardenine)

3D Structure for NP0138778 (Gardenine)