NP-MRD: Showing NP-Card for Pseudoecgonine (NP0334756)

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Record Information

Version

2.0

Created at

2024-09-10 19:49:35 UTC

Updated at

2024-09-10 19:49:35 UTC

NP-MRD ID

NP0334756

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Pseudoecgonine

Description

Pseudoecgonine, also known as D-psi-ecgonine, belongs to the class of organic compounds known as tropane alkaloids. These are organic compounds containing the nitrogenous bicyclic alkaloid parent N-Methyl-8-azabicyclo[3.2.1]Octane. Pseudoecgonine is a very strong basic compound (based on its pKa). Pseudoecgonine was first documented in 1996 (PMID: 8572717). Pseudoecgonine exists in all living organisms, ranging from bacteria to humans.

Structure

MOL SDF PDB SMILES InChI


  Mrv0541 02231220382D          

 13 14  0  0  1  0            999 V2000
   15.2778   -6.7990    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   17.7019   -7.7839    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   16.3043   -8.0809    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   17.6181   -4.0892    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   18.0122   -5.6965    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   18.2257   -4.8997    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   16.7458   -6.7221    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   19.5235   -6.3225    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   19.7370   -5.5257    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   16.0785   -5.5661    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   15.9922   -6.3865    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   17.2056   -3.3747    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   16.9173   -7.5290    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 11  1  1  1  0  0  0
  2 13  1  0  0  0  0
  3 13  2  0  0  0  0
  4  5  1  0  0  0  0
  4  6  1  0  0  0  0
  4 12  1  0  0  0  0
  5  7  1  0  0  0  0
  5  8  1  0  0  0  0
  6  9  1  0  0  0  0
  6 10  1  0  0  0  0
  7 11  1  0  0  0  0
  7 13  1  6  0  0  0
  8  9  1  0  0  0  0
 10 11  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0334756

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CN1C2CCC1[C@@H]([C@@H](O)C2)C(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C9H15NO3/c1-10-5-2-3-6(10)8(9(12)13)7(11)4-5/h5-8,11H,2-4H2,1H3,(H,12,13)/t5?,6?,7-,8-/m0/s1

> <INCHI_KEY>
PHMBVCPLDPDESM-GHNGIAPOSA-N

> <FORMULA>
C9H15NO3

> <MOLECULAR_WEIGHT>
185.2203

> <EXACT_MASS>
185.105193351

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_AVERAGE_POLARIZABILITY>
18.958509301748336

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2S,3S)-3-hydroxy-8-methyl-8-azabicyclo[3.2.1]octane-2-carboxylic acid

> <ALOGPS_LOGP>
-0.69

> <JCHEM_LOGP>
-3.0901585696393723

> <ALOGPS_LOGS>
0.75

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
14.871788470590886

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.4801822466094126

> <JCHEM_PKA_STRONGEST_BASIC>
9.69054450259908

> <JCHEM_POLAR_SURFACE_AREA>
60.77

> <JCHEM_REFRACTIVITY>
46.5693

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.05e+03 g/l

> <JCHEM_TRADITIONAL_IUPAC>
pseudoecgonine

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 23-FEB-12   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   23-FEB-12         0                                  
HETATM    1  O   UNK     0      28.519 -12.691   0.000  0.00  0.00           O+0
HETATM    2  O   UNK     0      33.044 -14.530   0.000  0.00  0.00           O+0
HETATM    3  O   UNK     0      30.435 -15.084   0.000  0.00  0.00           O+0
HETATM    4  N   UNK     0      32.887  -7.633   0.000  0.00  0.00           N+0
HETATM    5  C   UNK     0      33.623 -10.633   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      34.021  -9.146   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      31.259 -12.548   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      36.444 -11.802   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      36.842 -10.315   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      30.013 -10.390   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      29.852 -11.921   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      32.117  -6.299   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      31.579 -14.054   0.000  0.00  0.00           C+0
CONECT    1   11                                                            
CONECT    2   13                                                            
CONECT    3   13                                                            
CONECT    4    5    6   12                                                  
CONECT    5    4    7    8                                                  
CONECT    6    4    9   10                                                  
CONECT    7    5   11   13                                                  
CONECT    8    5    9                                                       
CONECT    9    6    8                                                       
CONECT   10    6   11                                                       
CONECT   11    1    7   10                                                  
CONECT   12    4                                                            
CONECT   13    2    3    7                                                  
MASTER        0    0    0    0    0    0    0    0   13    0   28    0
END

View in JSmol

Synonyms

Value	Source
(+)-Pseudoecgonine	HMDB
(2S,3S)-3-Hydroxy-8-methyl-8-azabicyclo[3.2.1]octane-2-carboxylate	HMDB
(2S,3S)-3-Hydroxy-8-methyl-8-azabicyclo[3.2.1]octane-2-carboxylic acid	HMDB
D-Pseudoecgonine	HMDB
D-Psi-ecgonine	HMDB
delta-Pseudoecgonine	HMDB
delta-Psi-ecgonine	HMDB
Pseudo-ecgonine	HMDB

Chemical Formula

C₉H₁₅NO₃

Average Mass

185.2203 Da

Monoisotopic Mass

185.10519 Da

IUPAC Name

(2S,3S)-3-hydroxy-8-methyl-8-azabicyclo[3.2.1]octane-2-carboxylic acid

Traditional Name

pseudoecgonine

CAS Registry Number

Not Available

SMILES

CN1C2CCC1[C@@H]([C@@H](O)C2)C(O)=O

InChI Identifier

InChI=1S/C9H15NO3/c1-10-5-2-3-6(10)8(9(12)13)7(11)4-5/h5-8,11H,2-4H2,1H3,(H,12,13)/t5?,6?,7-,8-/m0/s1

InChI Key

PHMBVCPLDPDESM-GHNGIAPOSA-N

Experimental Spectra

Not Available

Predicted Spectra

Not Available

Chemical Shift Submissions

Not Available

Species

Species of Origin

Not Available

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as tropane alkaloids. These are organic compounds containing the nitrogenous bicyclic alkaloid parent N-Methyl-8-azabicyclo[3.2.1]Octane.

Kingdom

Organic compounds

Super Class

Alkaloids and derivatives

Class

Tropane alkaloids

Sub Class

Not Available

Direct Parent

Tropane alkaloids

Alternative Parents

Substituents

Piperidinecarboxylic acid
Tropane alkaloid
Beta-hydroxy acid
Hydroxy acid
Piperidine
N-alkylpyrrolidine
Cyclic alcohol
Pyrrolidine
Amino acid or derivatives
Amino acid
Tertiary aliphatic amine
Tertiary amine
Secondary alcohol
Carboxylic acid derivative
Carboxylic acid
Monocarboxylic acid or derivatives
Azacycle
Organoheterocyclic compound
Amine
Organic oxide
Organopnictogen compound
Alcohol
Carbonyl group
Organonitrogen compound
Organooxygen compound
Hydrocarbon derivative
Organic nitrogen compound
Organic oxygen compound
Aliphatic heteropolycyclic compound

Molecular Framework

Aliphatic heteropolycyclic compounds

External Descriptors

tropane alkaloid (CHEBI:32072 )
Tropane alkaloids (C12449 )

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	-0.69	ALOGPS
logP	-3.1	ChemAxon
logS	0.75	ALOGPS
pKa (Strongest Acidic)	3.48	ChemAxon
pKa (Strongest Basic)	9.69	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	4	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	60.77 Å²	ChemAxon
Rotatable Bond Count	1	ChemAxon
Refractivity	46.57 m³·mol⁻¹	ChemAxon
Polarizability	18.96 Å³	ChemAxon
Number of Rings	2	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

External Links

HMDB ID

HMDB0006348

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

FDB023899

KNApSAcK ID

Not Available

Chemspider ID

391940

KEGG Compound ID

C12449

BioCyc ID

Not Available

BiGG ID

2282520

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

443845

PDB ID

Not Available

ChEBI ID

32072

Good Scents ID

Not Available

References

General References

Lister DL, Sproule RF, Britt AJ, Lowe CR, Bruce NC: Degradation of cocaine by a mixed culture of Pseudomonas fluorescens MBER and Comamonas acidovorans MBLF. Appl Environ Microbiol. 1996 Jan;62(1):94-9. doi: 10.1128/aem.62.1.94-99.1996. [PubMed:8572717 ]

Showing NP-Card for Pseudoecgonine (NP0334756)

MOL for NP0334756 (Pseudoecgonine)

3D MOL for NP0334756 (Pseudoecgonine)

3D SDF for NP0334756 (Pseudoecgonine)

3D-SDF for NP0334756 (Pseudoecgonine)

PDB for NP0334756 (Pseudoecgonine)

3D PDB for NP0334756 (Pseudoecgonine)

SMILES for NP0334756 (Pseudoecgonine)

INCHI for NP0334756 (Pseudoecgonine)

Structure for NP0334756 (Pseudoecgonine)

3D Structure for NP0334756 (Pseudoecgonine)