NP-MRD: Showing NP-Card for [(5r)-5-carboxy-5-hydroxypentyl]trimethylazanium (NP0152492)

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Record Information

Version

2.0

Created at

2022-09-02 08:59:05 UTC

Updated at

2022-09-02 08:59:05 UTC

NP-MRD ID

NP0152492

Secondary Accession Numbers

None

Natural Product Identification

Common Name

[(5r)-5-carboxy-5-hydroxypentyl]trimethylazanium

Description

Halocynine belongs to the class of organic compounds known as medium-chain fatty acids. These are fatty acids with an aliphatic tail that contains between 4 and 12 carbon atoms. [(5r)-5-carboxy-5-hydroxypentyl]trimethylazanium is found in Halocynthia roretzi. Based on a literature review very few articles have been published on Halocynine.

Structure

MOL 3D MOL SDF PDB SMILES InChI

     RDKit          3D

 33 32  0  0  0  0  0  0  0  0999 V2000
   -3.2720   -1.5253   -0.1325 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4578   -0.3381    0.1395 N   0  0  0  0  0  4  0  0  0  0  0  0
   -2.5307   -0.0761    1.5638 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0029    0.7697   -0.5863 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1320   -0.6216   -0.3114 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1336    0.3974    0.1870 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2492   -0.0162   -0.3635 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1915    1.0310    0.1651 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6113    0.8659   -0.2520 C   0  0  1  0  0  0  0  0  0  0  0  0
    4.3586    1.9160    0.3143 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.1257   -0.4378    0.2232 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0455   -0.4136    1.0982 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.6655   -1.6493   -0.2303 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2420   -1.2549   -0.5656 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4457   -2.0790    0.7970 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7610   -2.1901   -0.8746 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9182    0.7812    1.8655 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5811    0.1711    1.8215 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2180   -0.9849    2.1425 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9167    1.6749    0.0481 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1034    0.5687   -0.7222 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5326    0.8918   -1.5671 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1260   -0.5949   -1.4169 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7619   -1.6239    0.0380 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3526    1.4002   -0.1895 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0109    0.3416    1.2912 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2379   -0.1096   -1.4519 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5293   -0.9897    0.1141 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.1023    0.9904    1.2781 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8147    2.0583   -0.1120 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.7301    0.9037   -1.3415 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.0586    1.9846    1.2608 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.7790   -1.8414   -1.2354 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
  2  5  1  0
  5  6  1  0
  6  7  1  0
  7  8  1  0
  8  9  1  0
  9 10  1  0
  9 11  1  0
 11 13  1  0
 11 12  2  0
  1 14  1  0
  1 15  1  0
  1 16  1  0
  3 17  1  0
  3 18  1  0
  3 19  1  0
  4 20  1  0
  4 21  1  0
  4 22  1  0
  5 23  1  0
  5 24  1  0
  6 25  1  0
  6 26  1  0
  7 27  1  0
  7 28  1  0
  8 29  1  0
  8 30  1  0
  9 31  1  6
 10 32  1  0
 13 33  1  0
M  CHG  1   2   1
M  END


  Mrv1652309022210592D          

 13 12  0  0  1  0            999 V2000
   -2.3349    0.3020    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6204    0.7145    0.0000 N   0  3  0  0  0  0  0  0  0  0  0  0
   -1.2079    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0329    1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9059    1.1270    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1914    0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5230    1.1270    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2375    0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9520    1.1270    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.9520    1.9520    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.6664    0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3809    1.1270    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.6664   -0.1105    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
  2  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  1  1  0  0  0
  9 11  1  0  0  0  0
 11 12  2  0  0  0  0
 11 13  1  0  0  0  0
M  CHG  1   2   1
M  END
> <DATABASE_ID>
NP0152492

> <DATABASE_NAME>
NP-MRD

> <SMILES>
C[N+](C)(C)CCCC[C@@H](O)C(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C9H19NO3/c1-10(2,3)7-5-4-6-8(11)9(12)13/h8,11H,4-7H2,1-3H3/p+1/t8-/m1/s1

> <INCHI_KEY>
RGNCPYJIFMKRFI-MRVPVSSYSA-O

> <FORMULA>
C9H20NO3

> <MOLECULAR_WEIGHT>
190.262

> <EXACT_MASS>
190.143769928

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_ATOM_COUNT>
33

> <JCHEM_AVERAGE_POLARIZABILITY>
21.549456686120667

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
1

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
[(5R)-5-carboxy-5-hydroxypentyl]trimethylazanium

> <ALOGPS_LOGP>
-3.19

> <JCHEM_LOGP>
-3.9504384918050786

> <ALOGPS_LOGS>
-2.66

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
14.28378670667335

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.99103151459705

> <JCHEM_PKA_STRONGEST_BASIC>
-3.7976872948815776

> <JCHEM_POLAR_SURFACE_AREA>
57.53

> <JCHEM_REFRACTIVITY>
62.13490000000001

> <JCHEM_ROTATABLE_BOND_COUNT>
6

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
4.91e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
[(5R)-5-carboxy-5-hydroxypentyl]trimethylazanium

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 02-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   02-SEP-22         0                                  
HETATM    1  C   UNK     0      -4.358   0.564   0.000  0.00  0.00           C+0
HETATM    2  N   UNK     0      -3.025   1.334   0.000  0.00  0.00           N+1
HETATM    3  C   UNK     0      -2.255   0.000   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -3.795   2.667   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      -1.691   2.104   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      -0.357   1.334   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       0.976   2.104   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       2.310   1.334   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       3.644   2.104   0.000  0.00  0.00           C+0
HETATM   10  O   UNK     0       3.644   3.644   0.000  0.00  0.00           O+0
HETATM   11  C   UNK     0       4.977   1.334   0.000  0.00  0.00           C+0
HETATM   12  O   UNK     0       6.311   2.104   0.000  0.00  0.00           O+0
HETATM   13  O   UNK     0       4.977  -0.206   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3    4    5                                             
CONECT    3    2                                                            
CONECT    4    2                                                            
CONECT    5    2    6                                                       
CONECT    6    5    7                                                       
CONECT    7    6    8                                                       
CONECT    8    7    9                                                       
CONECT    9    8   10   11                                                  
CONECT   10    9                                                            
CONECT   11    9   12   13                                                  
CONECT   12   11                                                            
CONECT   13   11                                                            
MASTER        0    0    0    0    0    0    0    0   13    0   24    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₉H₂₀NO₃

Average Mass

190.2620 Da

Monoisotopic Mass

190.14377 Da

IUPAC Name

[(5R)-5-carboxy-5-hydroxypentyl]trimethylazanium

Traditional Name

[(5R)-5-carboxy-5-hydroxypentyl]trimethylazanium

CAS Registry Number

Not Available

SMILES

C[N+](C)(C)CCCC[C@@H](O)C(O)=O

InChI Identifier

InChI=1S/C9H19NO3/c1-10(2,3)7-5-4-6-8(11)9(12)13/h8,11H,4-7H2,1-3H3/p+1/t8-/m1/s1

InChI Key

RGNCPYJIFMKRFI-MRVPVSSYSA-O

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
Halocynthia roretzi	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as medium-chain fatty acids. These are fatty acids with an aliphatic tail that contains between 4 and 12 carbon atoms.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Fatty Acyls

Sub Class

Fatty acids and conjugates

Direct Parent

Medium-chain fatty acids

Alternative Parents

Substituents

Medium-chain fatty acid
Amino fatty acid
Hydroxy fatty acid
Alpha-hydroxy acid
Hydroxy acid
Monosaccharide
Tetraalkylammonium salt
Quaternary ammonium salt
Secondary alcohol
Carboxylic acid derivative
Carboxylic acid
Monocarboxylic acid or derivatives
Organic oxide
Hydrocarbon derivative
Alcohol
Organic oxygen compound
Organonitrogen compound
Organooxygen compound
Carbonyl group
Organic nitrogen compound
Amine
Organic cation
Aliphatic acyclic compound

Molecular Framework

Aliphatic acyclic 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	-3.2	ALOGPS
logP	-4	ChemAxon
logS	-2.7	ALOGPS
pKa (Strongest Acidic)	3.99	ChemAxon
pKa (Strongest Basic)	-3.8	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	3	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	57.53 Å²	ChemAxon
Rotatable Bond Count	6	ChemAxon
Refractivity	62.13 m³·mol⁻¹	ChemAxon
Polarizability	21.55 Å³	ChemAxon
Number of Rings	0	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

Not Available

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

Not Available

KNApSAcK ID

Not Available

Chemspider ID

Not Available

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

101287062

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

LOTUS database [Link]

Showing NP-Card for [(5r)-5-carboxy-5-hydroxypentyl]trimethylazanium (NP0152492)

MOL for NP0152492 ([(5r)-5-carboxy-5-hydroxypentyl]trimethylazanium)

3D MOL for NP0152492 ([(5r)-5-carboxy-5-hydroxypentyl]trimethylazanium)

3D SDF for NP0152492 ([(5r)-5-carboxy-5-hydroxypentyl]trimethylazanium)

3D-SDF for NP0152492 ([(5r)-5-carboxy-5-hydroxypentyl]trimethylazanium)

PDB for NP0152492 ([(5r)-5-carboxy-5-hydroxypentyl]trimethylazanium)

3D PDB for NP0152492 ([(5r)-5-carboxy-5-hydroxypentyl]trimethylazanium)

SMILES for NP0152492 ([(5r)-5-carboxy-5-hydroxypentyl]trimethylazanium)

INCHI for NP0152492 ([(5r)-5-carboxy-5-hydroxypentyl]trimethylazanium)

Structure for NP0152492 ([(5r)-5-carboxy-5-hydroxypentyl]trimethylazanium)

3D Structure for NP0152492 ([(5r)-5-carboxy-5-hydroxypentyl]trimethylazanium)