NP-MRD: Showing NP-Card for ( )-intermedine (NP0214016)

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Record Information

Version

2.0

Created at

2022-09-05 13:11:46 UTC

Updated at

2022-09-05 13:11:46 UTC

NP-MRD ID

NP0214016

Secondary Accession Numbers

None

Natural Product Identification

Common Name

( )-intermedine

Description

CHEMBL450265 belongs to the class of organic compounds known as alkaloids and derivatives. These are naturally occurring chemical compounds that contain mostly basic nitrogen atoms. This group also includes some related compounds with neutral and even weakly acidic properties. Also some synthetic compounds of similar structure are attributed to alkaloids. In addition to carbon, hydrogen and nitrogen, alkaloids may also contain oxygen, sulfur and more rarely other elements such as chlorine, bromine, and phosphorus. ( )-intermedine is found in Critonia morifolia and Heliotropium megalanthum. Based on a literature review very few articles have been published on CHEMBL450265.

Structure

MOL 3D MOL SDF PDB SMILES InChI

     RDKit          3D

 46 47  0  0  0  0  0  0  0  0999 V2000
   -4.7642    1.2820    0.4549 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2734    1.4034    0.3774 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8143    2.1413   -0.8571 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5381    0.0956    0.5775 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.8752   -0.3760    1.8349 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0885    0.4260    0.5240 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5360    0.8604   -0.5145 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3116    0.2545    1.6472 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.0656    0.5155    1.7551 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9283   -0.2987    0.8940 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5746   -1.2326    0.0498 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7523   -1.8314   -0.6434 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.8739   -1.3582    0.1077 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.9573   -0.9072   -0.7570 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.4625    0.4420   -1.1989 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.8796    1.0136    0.0713 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.8260    1.8868   -0.1924 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.4356   -0.1881    0.8372 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.9647   -0.8790   -0.4546 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.3307   -2.2242   -0.3576 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3469   -1.0418   -0.3571 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0218    0.5366    1.2176 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.1497    2.2618    0.8685 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.2264    1.1012   -0.5379 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9597    2.0382    1.2600 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9207    2.7363   -0.5920 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6324    1.5047   -1.7221 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6127    2.8856   -1.0903 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1118   -0.9402    2.1495 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3312    0.2757    2.8280 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2837    1.6115    1.6744 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5663   -1.5710   -0.1511 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.7024   -2.9352   -0.6099 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8290   -1.4828   -1.6937 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.8846   -0.7808   -0.1659 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.0858   -1.6123   -1.6033 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.3037    1.0851   -1.5855 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.6596    0.3621   -1.9546 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.6696    1.5347    0.6645 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.6511    1.9322   -1.1645 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.7927   -0.1822    1.8775 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7959   -0.5138   -1.5034 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0850   -2.9891   -0.6348 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0287   -2.4889    0.6971 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4928   -2.3754   -1.0684 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6344   -1.9777   -0.4598 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  2  4  1  0
  4  5  1  1
  4 19  1  0
 19 20  1  0
 19 21  1  0
  4  6  1  0
  6  7  2  0
  6  8  1  0
  8  9  1  0
  9 10  1  0
 10 11  2  0
 11 12  1  0
 12 13  1  0
 13 14  1  0
 14 15  1  0
 15 16  1  0
 16 17  1  0
 16 18  1  0
 18 10  1  0
 18 13  1  0
  1 22  1  0
  1 23  1  0
  1 24  1  0
  2 25  1  0
  3 26  1  0
  3 27  1  0
  3 28  1  0
  5 29  1  0
 19 42  1  6
 20 43  1  0
 20 44  1  0
 20 45  1  0
 21 46  1  0
  9 30  1  0
  9 31  1  0
 11 32  1  0
 12 33  1  0
 12 34  1  0
 14 35  1  0
 14 36  1  0
 15 37  1  0
 15 38  1  0
 16 39  1  1
 17 40  1  0
 18 41  1  1
M  END


  Mrv1652309052215112D          

 21 22  0  0  1  0            999 V2000
   -1.9162   -3.7908    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6612   -3.0062    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2133   -2.3931    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8543   -2.8347    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.6827   -3.6416    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0473   -2.6631    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5047   -3.2762    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.2076   -1.8785    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.0146   -1.7070    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2695   -0.9224    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7846   -0.2549    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2695    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0542    0.1576    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.8388    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3237   -0.2549    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8388   -0.9224    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    3.0937   -1.7070    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.0542   -0.6674    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.0258   -2.0277    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.4127   -1.4757    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8104   -1.7728    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
  2  4  1  0  0  0  0
  4  5  1  6  0  0  0
  4  6  1  1  0  0  0
  6  7  2  0  0  0  0
  6  8  1  0  0  0  0
  8  9  1  0  0  0  0
  9 10  1  0  0  0  0
 10 11  2  0  0  0  0
 11 12  1  0  0  0  0
 12 13  1  0  0  0  0
 13 14  1  0  0  0  0
 14 15  1  0  0  0  0
 15 16  1  0  0  0  0
 16 17  1  1  0  0  0
 16 18  1  0  0  0  0
 10 18  1  0  0  0  0
 18 13  1  1  0  0  0
  4 19  1  0  0  0  0
 19 20  1  0  0  0  0
 19 21  1  6  0  0  0
M  END
> <DATABASE_ID>
NP0214016

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CC(C)[C@@](O)([C@@H](C)O)C(=O)OCC1=CCN2CC[C@@H](O)[C@@H]12

> <INCHI_IDENTIFIER>
InChI=1S/C15H25NO5/c1-9(2)15(20,10(3)17)14(19)21-8-11-4-6-16-7-5-12(18)13(11)16/h4,9-10,12-13,17-18,20H,5-8H2,1-3H3/t10-,12-,13-,15-/m1/s1

> <INCHI_KEY>
SFVVQRJOGUKCEG-BPGGGUHBSA-N

> <FORMULA>
C15H25NO5

> <MOLECULAR_WEIGHT>
299.367

> <EXACT_MASS>
299.173272909

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_ATOM_COUNT>
46

> <JCHEM_AVERAGE_POLARIZABILITY>
31.490389312799394

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
[(1R,7aR)-1-hydroxy-2,3,5,7a-tetrahydro-1H-pyrrolizin-7-yl]methyl (2R)-2-hydroxy-2-[(1R)-1-hydroxyethyl]-3-methylbutanoate

> <JCHEM_LOGP>
-0.291114993666667

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
1

> <JCHEM_PKA>
14.312685181459287

> <JCHEM_PKA_STRONGEST_ACIDIC>
11.342357304233317

> <JCHEM_PKA_STRONGEST_BASIC>
7.816512056494238

> <JCHEM_POLAR_SURFACE_AREA>
90.23

> <JCHEM_REFRACTIVITY>
77.94250000000001

> <JCHEM_ROTATABLE_BOND_COUNT>
6

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
[(7R,7aR)-7-hydroxy-5,6,7,7a-tetrahydro-3H-pyrrolizin-1-yl]methyl (2R)-2-hydroxy-2-[(1R)-1-hydroxyethyl]-3-methylbutanoate

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 05-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   05-SEP-22         0                                  
HETATM    1  C   UNK     0      -3.577  -7.076   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -3.101  -5.612   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -4.131  -4.467   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -1.595  -5.291   0.000  0.00  0.00           C+0
HETATM    5  O   UNK     0      -1.274  -6.798   0.000  0.00  0.00           O+0
HETATM    6  C   UNK     0      -0.088  -4.971   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0       0.942  -6.116   0.000  0.00  0.00           O+0
HETATM    8  O   UNK     0       0.388  -3.507   0.000  0.00  0.00           O+0
HETATM    9  C   UNK     0       1.894  -3.186   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       2.370  -1.722   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       1.465  -0.476   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       2.370   0.770   0.000  0.00  0.00           C+0
HETATM   13  N   UNK     0       3.834   0.294   0.000  0.00  0.00           N+0
HETATM   14  C   UNK     0       5.299   0.770   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       6.204  -0.476   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       5.299  -1.722   0.000  0.00  0.00           C+0
HETATM   17  O   UNK     0       5.775  -3.186   0.000  0.00  0.00           O+0
HETATM   18  C   UNK     0       3.834  -1.246   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0      -1.915  -3.785   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0      -0.770  -2.755   0.000  0.00  0.00           C+0
HETATM   21  O   UNK     0      -3.379  -3.309   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3    4                                                  
CONECT    3    2                                                            
CONECT    4    2    5    6   19                                             
CONECT    5    4                                                            
CONECT    6    4    7    8                                                  
CONECT    7    6                                                            
CONECT    8    6    9                                                       
CONECT    9    8   10                                                       
CONECT   10    9   11   18                                                  
CONECT   11   10   12                                                       
CONECT   12   11   13                                                       
CONECT   13   12   14   18                                                  
CONECT   14   13   15                                                       
CONECT   15   14   16                                                       
CONECT   16   15   17   18                                                  
CONECT   17   16                                                            
CONECT   18   16   10   13                                                  
CONECT   19    4   20   21                                                  
CONECT   20   19                                                            
CONECT   21   19                                                            
MASTER        0    0    0    0    0    0    0    0   21    0   44    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₁₅H₂₅NO₅

Average Mass

299.3670 Da

Monoisotopic Mass

299.17327 Da

IUPAC Name

[(1R,7aR)-1-hydroxy-2,3,5,7a-tetrahydro-1H-pyrrolizin-7-yl]methyl (2R)-2-hydroxy-2-[(1R)-1-hydroxyethyl]-3-methylbutanoate

Traditional Name

[(7R,7aR)-7-hydroxy-5,6,7,7a-tetrahydro-3H-pyrrolizin-1-yl]methyl (2R)-2-hydroxy-2-[(1R)-1-hydroxyethyl]-3-methylbutanoate

CAS Registry Number

Not Available

SMILES

CC(C)[C@@](O)([C@@H](C)O)C(=O)OCC1=CCN2CC[C@@H](O)[C@@H]12

InChI Identifier

InChI=1S/C15H25NO5/c1-9(2)15(20,10(3)17)14(19)21-8-11-4-6-16-7-5-12(18)13(11)16/h4,9-10,12-13,17-18,20H,5-8H2,1-3H3/t10-,12-,13-,15-/m1/s1

InChI Key

SFVVQRJOGUKCEG-BPGGGUHBSA-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

Species Name	Source	Reference
Critonia morifolia	LOTUS Database	35616633
Heliotropium megalanthum	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as alkaloids and derivatives. These are naturally occurring chemical compounds that contain mostly basic nitrogen atoms. This group also includes some related compounds with neutral and even weakly acidic properties. Also some synthetic compounds of similar structure are attributed to alkaloids. In addition to carbon, hydrogen and nitrogen, alkaloids may also contain oxygen, sulfur and more rarely other elements such as chlorine, bromine, and phosphorus.

Kingdom

Organic compounds

Super Class

Alkaloids and derivatives

Class

Not Available

Sub Class

Not Available

Direct Parent

Alkaloids and derivatives

Alternative Parents

Substituents

Alkaloid or derivatives
Pyrrolizine
Beta-hydroxy acid
Fatty acid ester
Hydroxy acid
Fatty acyl
N-alkylpyrrolidine
Pyrrolidine
Pyrroline
Tertiary alcohol
Amino acid or derivatives
Carboxylic acid ester
Secondary alcohol
Tertiary aliphatic amine
Tertiary amine
Monocarboxylic acid or derivatives
Carboxylic acid derivative
Azacycle
Organoheterocyclic compound
Hydrocarbon derivative
Organooxygen compound
Organonitrogen compound
Organic oxide
Organic oxygen compound
Carbonyl group
Amine
Alcohol
Organic nitrogen 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
logP	-0.29	ChemAxon
pKa (Strongest Acidic)	11.34	ChemAxon
pKa (Strongest Basic)	7.82	ChemAxon
Physiological Charge	1	ChemAxon
Hydrogen Acceptor Count	5	ChemAxon
Hydrogen Donor Count	3	ChemAxon
Polar Surface Area	90.23 Å²	ChemAxon
Rotatable Bond Count	6	ChemAxon
Refractivity	77.94 m³·mol⁻¹	ChemAxon
Polarizability	31.49 Å³	ChemAxon
Number of Rings	2	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

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

24688350

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

44584035

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

LOTUS database [Link]

Showing NP-Card for ( )-intermedine (NP0214016)

MOL for NP0214016 (( )-intermedine)

3D MOL for NP0214016 (( )-intermedine)

3D SDF for NP0214016 (( )-intermedine)

3D-SDF for NP0214016 (( )-intermedine)

PDB for NP0214016 (( )-intermedine)

3D PDB for NP0214016 (( )-intermedine)

SMILES for NP0214016 (( )-intermedine)

INCHI for NP0214016 (( )-intermedine)

Structure for NP0214016 (( )-intermedine)

3D Structure for NP0214016 (( )-intermedine)