NP-MRD: Showing NP-Card for (2s,5s)-5-(aminomethyl)-5,6-dihydroxy-3,4-dihydro-2h-pyridine-2-carboxylic acid (NP0144486)

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Record Information

Version

2.0

Created at

2022-09-01 23:28:20 UTC

Updated at

2022-09-01 23:28:20 UTC

NP-MRD ID

NP0144486

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(2s,5s)-5-(aminomethyl)-5,6-dihydroxy-3,4-dihydro-2h-pyridine-2-carboxylic acid

Description

Tabtoxinine-delta-lactam belongs to the class of organic compounds known as hybrid peptides. Hybrid peptides are compounds containing at least two different types of amino acids (alpha, beta, gamma, delta) linked to each other through a peptide bond. Tabtoxinine-delta-lactam is a secondary metabolite. Secondary metabolites are metabolically or physiologically non-essential metabolites that may serve a role as defense or signalling molecules. In some cases they are simply molecules that arise from the incomplete metabolism of other secondary metabolites. (2s,5s)-5-(aminomethyl)-5,6-dihydroxy-3,4-dihydro-2h-pyridine-2-carboxylic acid is found in Apis cerana. (2s,5s)-5-(aminomethyl)-5,6-dihydroxy-3,4-dihydro-2h-pyridine-2-carboxylic acid was first documented in 1975 (PMID: 1185324). Based on a literature review very few articles have been published on tabtoxinine-delta-lactam.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652309022201282D          

 13 13  0  0  1  0            999 V2000
    2.0572    1.7262    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.2448    1.8695    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    1.2375    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.1842    1.8695    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -0.4125    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.7145   -1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -1.6500    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0000   -1.6500    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145    1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  3  2  1  1  0  0  0
  3  4  1  6  0  0  0
  3  5  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  1  0  0  0  0
  7  8  1  1  0  0  0
  8  9  2  0  0  0  0
  8 10  1  0  0  0  0
  7 11  1  0  0  0  0
 11 12  2  0  0  0  0
  3 12  1  0  0  0  0
 12 13  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0144486

> <DATABASE_NAME>
NP-MRD

> <SMILES>
NC[C@@]1(O)CC[C@H](N=C1O)C(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C7H12N2O4/c8-3-7(13)2-1-4(5(10)11)9-6(7)12/h4,13H,1-3,8H2,(H,9,12)(H,10,11)/t4-,7-/m0/s1

> <INCHI_KEY>
ROTDGSCRRKYCRZ-FFWSUHOLSA-N

> <FORMULA>
C7H12N2O4

> <MOLECULAR_WEIGHT>
188.183

> <EXACT_MASS>
188.079706874

> <JCHEM_ACCEPTOR_COUNT>
6

> <JCHEM_ATOM_COUNT>
25

> <JCHEM_AVERAGE_POLARIZABILITY>
17.568548187539932

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2S,5S)-5-(aminomethyl)-5,6-dihydroxy-2,3,4,5-tetrahydropyridine-2-carboxylic acid

> <ALOGPS_LOGP>
-3.07

> <JCHEM_LOGP>
-3.7153148062094075

> <ALOGPS_LOGS>
-1.10

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
3.9441698392427003

> <JCHEM_PKA_STRONGEST_ACIDIC>
2.9166419296247335

> <JCHEM_PKA_STRONGEST_BASIC>
9.724518486531238

> <JCHEM_POLAR_SURFACE_AREA>
116.14

> <JCHEM_REFRACTIVITY>
42.61720000000001

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.49e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(2S,5S)-5-(aminomethyl)-5,6-dihydroxy-3,4-dihydro-2H-pyridine-2-carboxylic acid

> <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  N   UNK     0       3.840   3.222   0.000  0.00  0.00           N+0
HETATM    2  C   UNK     0       2.324   3.490   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       1.334   2.310   0.000  0.00  0.00           C+0
HETATM    4  O   UNK     0       0.344   3.490   0.000  0.00  0.00           O+0
HETATM    5  C   UNK     0       2.667   1.540   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       2.667  -0.000   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       1.334  -2.310   0.000  0.00  0.00           C+0
HETATM    9  O   UNK     0       2.667  -3.080   0.000  0.00  0.00           O+0
HETATM   10  O   UNK     0      -0.000  -3.080   0.000  0.00  0.00           O+0
HETATM   11  N   UNK     0       0.000   0.000   0.000  0.00  0.00           N+0
HETATM   12  C   UNK     0       0.000   1.540   0.000  0.00  0.00           C+0
HETATM   13  O   UNK     0      -1.334   2.310   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4    5   12                                             
CONECT    4    3                                                            
CONECT    5    3    6                                                       
CONECT    6    5    7                                                       
CONECT    7    6    8   11                                                  
CONECT    8    7    9   10                                                  
CONECT    9    8                                                            
CONECT   10    8                                                            
CONECT   11    7   12                                                       
CONECT   12   11    3   13                                                  
CONECT   13   12                                                            
MASTER        0    0    0    0    0    0    0    0   13    0   26    0
END

View in JSmol

Synonyms

Value	Source
Tabtoxinine-δ-lactam	Generator

Chemical Formula

C₇H₁₂N₂O₄

Average Mass

188.1830 Da

Monoisotopic Mass

188.07971 Da

IUPAC Name

(2S,5S)-5-(aminomethyl)-5,6-dihydroxy-2,3,4,5-tetrahydropyridine-2-carboxylic acid

Traditional Name

(2S,5S)-5-(aminomethyl)-5,6-dihydroxy-3,4-dihydro-2H-pyridine-2-carboxylic acid

CAS Registry Number

Not Available

SMILES

NC[C@@]1(O)CC[C@H](N=C1O)C(O)=O

InChI Identifier

InChI=1S/C7H12N2O4/c8-3-7(13)2-1-4(5(10)11)9-6(7)12/h4,13H,1-3,8H2,(H,9,12)(H,10,11)/t4-,7-/m0/s1

InChI Key

ROTDGSCRRKYCRZ-FFWSUHOLSA-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
Apis cerana	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as hybrid peptides. Hybrid peptides are compounds containing at least two different types of amino acids (alpha, beta, gamma, delta) linked to each other through a peptide bond.

Kingdom

Organic compounds

Super Class

Organic acids and derivatives

Class

Peptidomimetics

Sub Class

Hybrid peptides

Direct Parent

Hybrid peptides

Alternative Parents

Substituents

Hybrid peptide
Beta amino acid or derivatives
Alpha-amino acid or derivatives
Piperidinecarboxylic acid
Piperidinone
Delta-lactam
Piperidine
Tertiary alcohol
Amino acid
Secondary carboxylic acid amide
Lactam
Carboxamide group
Amino acid or derivatives
Azacycle
Organoheterocyclic compound
Monocarboxylic acid or derivatives
Carboxylic acid
Carboxylic acid derivative
Organic nitrogen compound
Organic oxygen compound
Organopnictogen compound
Organic oxide
Hydrocarbon derivative
Primary amine
Organooxygen compound
Organonitrogen compound
Primary aliphatic amine
Carbonyl group
Amine
Alcohol
Aliphatic heteromonocyclic compound

Molecular Framework

Aliphatic heteromonocyclic 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	-3.1	ALOGPS
logP	-3.7	ChemAxon
logS	-1.1	ALOGPS
pKa (Strongest Acidic)	2.92	ChemAxon
pKa (Strongest Basic)	9.72	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	6	ChemAxon
Hydrogen Donor Count	4	ChemAxon
Polar Surface Area	116.14 Å²	ChemAxon
Rotatable Bond Count	2	ChemAxon
Refractivity	42.62 m³·mol⁻¹	ChemAxon
Polarizability	17.57 Å³	ChemAxon
Number of Rings	1	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

58827520

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

92042783

PDB ID

Not Available

ChEBI ID

133888

Good Scents ID

Not Available

References

General References

Lee DL, Rapoport H: Synthesis of tabtoxinine-delta-lactam. J Org Chem. 1975 Nov 28;40(24):3491-5. doi: 10.1021/jo00912a005. [PubMed:1185324 ]
LOTUS database [Link]

Showing NP-Card for (2s,5s)-5-(aminomethyl)-5,6-dihydroxy-3,4-dihydro-2h-pyridine-2-carboxylic acid (NP0144486)

MOL for NP0144486 ((2s,5s)-5-(aminomethyl)-5,6-dihydroxy-3,4-dihydro-2h-pyridine-2-carboxylic acid)

3D MOL for NP0144486 ((2s,5s)-5-(aminomethyl)-5,6-dihydroxy-3,4-dihydro-2h-pyridine-2-carboxylic acid)

3D SDF for NP0144486 ((2s,5s)-5-(aminomethyl)-5,6-dihydroxy-3,4-dihydro-2h-pyridine-2-carboxylic acid)

3D-SDF for NP0144486 ((2s,5s)-5-(aminomethyl)-5,6-dihydroxy-3,4-dihydro-2h-pyridine-2-carboxylic acid)

PDB for NP0144486 ((2s,5s)-5-(aminomethyl)-5,6-dihydroxy-3,4-dihydro-2h-pyridine-2-carboxylic acid)

3D PDB for NP0144486 ((2s,5s)-5-(aminomethyl)-5,6-dihydroxy-3,4-dihydro-2h-pyridine-2-carboxylic acid)

SMILES for NP0144486 ((2s,5s)-5-(aminomethyl)-5,6-dihydroxy-3,4-dihydro-2h-pyridine-2-carboxylic acid)

INCHI for NP0144486 ((2s,5s)-5-(aminomethyl)-5,6-dihydroxy-3,4-dihydro-2h-pyridine-2-carboxylic acid)

Structure for NP0144486 ((2s,5s)-5-(aminomethyl)-5,6-dihydroxy-3,4-dihydro-2h-pyridine-2-carboxylic acid)

3D Structure for NP0144486 ((2s,5s)-5-(aminomethyl)-5,6-dihydroxy-3,4-dihydro-2h-pyridine-2-carboxylic acid)