NP-MRD: Showing NP-Card for Histamine-betaxanthin (NP0050121)

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Record Information

Version

2.0

Created at

2022-03-17 21:23:37 UTC

Updated at

2022-03-17 21:23:37 UTC

NP-MRD ID

NP0050121

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Histamine-betaxanthin

Description

(2S,4E)-4-[(2Z)-2-{[2-(1H-imidazol-5-yl)ethyl]imino}ethylidene]-1,2,3,4-tetrahydropyridine-2,6-dicarboxylic acid belongs to the class of organic compounds known as l-alpha-amino acids. Histamine-betaxanthin is found in Beta vulgaris. These are alpha amino acids which have the L-configuration of the alpha-carbon atom (2S,4E)-4-[(2Z)-2-{[2-(1H-imidazol-5-yl)ethyl]imino}ethylidene]-1,2,3,4-tetrahydropyridine-2,6-dicarboxylic acid is a very strong basic compound (based on its pKa).

Structure

MOL SDF PDB SMILES InChI

Histamine-betaxanthin
  Mrv1652304022019462D          

 23 24  0  0  1  0            999 V2000
   13.7357  -11.5849    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   13.7357  -12.4099    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   13.0212  -11.1724    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   13.0212  -12.8224    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   12.3067  -11.5849    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.3067  -12.4099    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   11.5922  -12.8224    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.5922  -13.6474    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   10.8777  -12.4098    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   14.4502  -12.8224    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   15.1646  -12.4100    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   14.4501  -13.6475    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   13.0311  -10.3772    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.4447   -9.8007    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.4447   -8.9061    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   11.6600   -7.8262    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.4446   -7.5712    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.9295   -8.2387    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.9073   -7.4884    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.3535   -8.1000    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   11.5714   -8.6464    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   10.7640   -8.8157    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.6595  -11.8284    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  2  0  0  0  0
  3  1  1  0  0  0  0
  4  2  1  0  0  0  0
  5  3  1  0  0  0  0
  6  4  1  0  0  0  0
  6  5  1  0  0  0  0
  8  7  2  0  0  0  0
  9  7  1  0  0  0  0
  6  7  1  6  0  0  0
 11 10  2  0  0  0  0
 12 10  1  0  0  0  0
  2 10  1  0  0  0  0
  3 13  2  0  0  0  0
 13 14  1  0  0  0  0
 14 15  2  0  0  0  0
 17 16  1  0  0  0  0
 18 17  1  0  0  0  0
 15 18  1  0  0  0  0
 16 19  2  0  0  0  0
 20 19  1  0  0  0  0
 21 16  1  0  0  0  0
 22 20  2  0  0  0  0
 22 21  1  0  0  0  0
  6 23  1  1  0  0  0
M  END
> <DATABASE_ID>
NP0050121

> <DATABASE_NAME>
NP-MRD

> <SMILES>
[H][C@]1(C\C(=C/C=N\CCC2=CN=CN2)C=C(N1)C(O)=O)C(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C14H16N4O4/c19-13(20)11-5-9(6-12(18-11)14(21)22)1-3-15-4-2-10-7-16-8-17-10/h1,3,5,7-8,12,18H,2,4,6H2,(H,16,17)(H,19,20)(H,21,22)/b9-1-,15-3-/t12-/m0/s1

> <INCHI_KEY>
NKVDSHYVFXEPFV-MSLONMJQSA-N

> <FORMULA>
C14H16N4O4

> <MOLECULAR_WEIGHT>
304.306

> <EXACT_MASS>
304.117155011

> <JCHEM_ACCEPTOR_COUNT>
7

> <JCHEM_ATOM_COUNT>
38

> <JCHEM_AVERAGE_POLARIZABILITY>
30.43190786315457

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2S,4E)-4-[(2Z)-2-{[2-(1H-imidazol-5-yl)ethyl]imino}ethylidene]-1,2,3,4-tetrahydropyridine-2,6-dicarboxylic acid

> <ALOGPS_LOGP>
0.74

> <JCHEM_LOGP>
-6.04321548264313

> <ALOGPS_LOGS>
-3.18

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
1

> <JCHEM_PKA>
4.301930927171696

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.5974654794176404

> <JCHEM_PKA_STRONGEST_BASIC>
10.086568752422476

> <JCHEM_POLAR_SURFACE_AREA>
127.67000000000002

> <JCHEM_REFRACTIVITY>
80.0441

> <JCHEM_ROTATABLE_BOND_COUNT>
6

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
2.00e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(2S,4E)-4-[(2Z)-2-{[2-(3H-imidazol-4-yl)ethyl]imino}ethylidene]-2,3-dihydro-1H-pyridine-2,6-dicarboxylic acid

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 02-APR-20   NONE
TITLE     NULL                                                        
COMPND    MOLECULE: Histamine-betaxanthin                             
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   02-APR-20         0                                  
HETATM    1  C   UNK     0      25.640 -21.625   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      25.640 -23.165   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      24.306 -20.855   0.000  0.00  0.00           C+0
HETATM    4  N   UNK     0      24.306 -23.935   0.000  0.00  0.00           N+0
HETATM    5  C   UNK     0      22.973 -21.625   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      22.973 -23.165   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      21.639 -23.935   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0      21.639 -25.475   0.000  0.00  0.00           O+0
HETATM    9  O   UNK     0      20.305 -23.165   0.000  0.00  0.00           O+0
HETATM   10  C   UNK     0      26.974 -23.935   0.000  0.00  0.00           C+0
HETATM   11  O   UNK     0      28.307 -23.165   0.000  0.00  0.00           O+0
HETATM   12  O   UNK     0      26.974 -25.475   0.000  0.00  0.00           O+0
HETATM   13  C   UNK     0      24.325 -19.371   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      23.230 -18.295   0.000  0.00  0.00           C+0
HETATM   15  N   UNK     0      23.230 -16.625   0.000  0.00  0.00           N+0
HETATM   16  C   UNK     0      21.765 -14.609   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0      23.230 -14.133   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0      24.135 -15.379   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0      20.360 -13.978   0.000  0.00  0.00           C+0
HETATM   20  N   UNK     0      19.327 -15.120   0.000  0.00  0.00           N+0
HETATM   21  N   UNK     0      21.600 -16.140   0.000  0.00  0.00           N+0
HETATM   22  C   UNK     0      20.093 -16.456   0.000  0.00  0.00           C+0
HETATM   23  H   UNK     0      21.764 -22.080   0.000  0.00  0.00           H+0
CONECT    1    2    3                                                       
CONECT    2    1    4   10                                                  
CONECT    3    1    5   13                                                  
CONECT    4    2    6                                                       
CONECT    5    3    6                                                       
CONECT    6    4    5    7   23                                             
CONECT    7    8    9    6                                                  
CONECT    8    7                                                            
CONECT    9    7                                                            
CONECT   10   11   12    2                                                  
CONECT   11   10                                                            
CONECT   12   10                                                            
CONECT   13    3   14                                                       
CONECT   14   13   15                                                       
CONECT   15   14   18                                                       
CONECT   16   17   19   21                                                  
CONECT   17   16   18                                                       
CONECT   18   17   15                                                       
CONECT   19   16   20                                                       
CONECT   20   19   22                                                       
CONECT   21   16   22                                                       
CONECT   22   20   21                                                       
CONECT   23    6                                                            
MASTER        0    0    0    0    0    0    0    0   23    0   48    0
END

View in JSmol

Synonyms

Value	Source
(2S,4E)-4-[(2Z)-2-{[2-(1H-imidazol-5-yl)ethyl]imino}ethylidene]-1,2,3,4-tetrahydropyridine-2,6-dicarboxylate	Generator

Chemical Formula

C₁₄H₁₆N₄O₄

Average Mass

304.3060 Da

Monoisotopic Mass

304.11716 Da

IUPAC Name

(2S,4E)-4-[(2Z)-2-{[2-(1H-imidazol-5-yl)ethyl]imino}ethylidene]-1,2,3,4-tetrahydropyridine-2,6-dicarboxylic acid

Traditional Name

(2S,4E)-4-[(2Z)-2-{[2-(3H-imidazol-4-yl)ethyl]imino}ethylidene]-2,3-dihydro-1H-pyridine-2,6-dicarboxylic acid

CAS Registry Number

Not Available

SMILES

[H][C@]1(C\C(=C/C=N\CCC2=CN=CN2)C=C(N1)C(O)=O)C(O)=O

InChI Identifier

InChI=1S/C14H16N4O4/c19-13(20)11-5-9(6-12(18-11)14(21)22)1-3-15-4-2-10-7-16-8-17-10/h1,3,5,7-8,12,18H,2,4,6H2,(H,16,17)(H,19,20)(H,21,22)/b9-1-,15-3-/t12-/m0/s1

InChI Key

NKVDSHYVFXEPFV-MSLONMJQSA-N

Experimental Spectra

Not Available

Predicted Spectra

Not Available

Chemical Shift Submissions

Not Available

Species

Species of Origin

Species Name	Source	Reference
Beta vulgaris	LOTUS Database	35616633
Beta vulgaris ssp. cicla	FooDB	PHYTOHUB

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as l-alpha-amino acids. These are alpha amino acids which have the L-configuration of the alpha-carbon atom.

Kingdom

Organic compounds

Super Class

Organic acids and derivatives

Class

Carboxylic acids and derivatives

Sub Class

Amino acids, peptides, and analogues

Direct Parent

L-alpha-amino acids

Alternative Parents

Substituents

L-alpha-amino acid
Imidazolyl carboxylic acid derivative
Tetrahydropyridine
Dicarboxylic acid or derivatives
Hydropyridine
Azole
Imidazole
Heteroaromatic compound
Amino acid
Shiff base
Azacycle
Aldimine
Carboxylic acid
Secondary aliphatic amine
Enamine
Secondary amine
Organoheterocyclic compound
Propargyl-type 1,3-dipolar organic compound
Organic 1,3-dipolar compound
Amine
Organic oxygen compound
Organopnictogen compound
Imine
Organonitrogen compound
Organooxygen compound
Hydrocarbon derivative
Organic oxide
Organic nitrogen compound
Carbonyl group
Aromatic heteromonocyclic compound

Molecular Framework

Aromatic 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	0.74	ALOGPS
logP	-6	ChemAxon
logS	-3.2	ALOGPS
pKa (Strongest Acidic)	3.6	ChemAxon
pKa (Strongest Basic)	10.09	ChemAxon
Physiological Charge	1	ChemAxon
Hydrogen Acceptor Count	7	ChemAxon
Hydrogen Donor Count	4	ChemAxon
Polar Surface Area	127.67 Å²	ChemAxon
Rotatable Bond Count	6	ChemAxon
Refractivity	80.04 m³·mol⁻¹	ChemAxon
Polarizability	30.43 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

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

Not Available

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Not Available

Showing NP-Card for Histamine-betaxanthin (NP0050121)

MOL for NP0050121 (Histamine-betaxanthin)

3D MOL for NP0050121 (Histamine-betaxanthin)

3D SDF for NP0050121 (Histamine-betaxanthin)

3D-SDF for NP0050121 (Histamine-betaxanthin)

PDB for NP0050121 (Histamine-betaxanthin)

3D PDB for NP0050121 (Histamine-betaxanthin)

SMILES for NP0050121 (Histamine-betaxanthin)

INCHI for NP0050121 (Histamine-betaxanthin)

Structure for NP0050121 (Histamine-betaxanthin)

3D Structure for NP0050121 (Histamine-betaxanthin)