NP-MRD: Showing NP-Card for 4,5-seco-dopa (NP0334331)

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Record Information

Version

2.0

Created at

2024-09-09 23:11:58 UTC

Updated at

2024-09-09 23:11:58 UTC

NP-MRD ID

NP0334331

Secondary Accession Numbers

None

Natural Product Identification

Common Name

4,5-seco-dopa

Description

4,5-Seco-dopa is a member of the class of compounds known as L-alpha-amino acids. L-alpha-amino acids are alpha amino acids which have the L-configuration of the alpha-carbon atom. 4,5-Seco-dopa is practically insoluble (in water) and a moderately acidic compound (based on its pKa). 4,5-Seco-dopa can be found in a number of food items such as safflower, yautia, pitanga, and anise, which makes 4,5-seco-dopa a potential biomarker for the consumption of these food products.

Structure

MOL SDF PDB SMILES InChI


  Mrv1533007131514092D          

 20 19  0  0  1  0            999 V2000
   -0.4125    0.7145    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
   -0.4125   -0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8250    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2375   -0.7145    0.0000 C   0  0  1  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
   -1.6500   -1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0625    0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6500   -0.0000    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6500    1.4289    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.8250    1.4289    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4750   -1.4289    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2375   -2.1434    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.4750    1.4289    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.4750    0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    1.4289    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0625    0.7145    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2375   -0.7145    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8250   -1.4289    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  2  0  0  0  0
  5  1  1  0  0  0  0
  5  3  1  0  0  0  0
  5  4  2  0  0  0  0
  6  3  1  0  0  0  0
  7  4  1  0  0  0  0
  8  6  1  0  0  0  0
  9  7  1  0  0  0  0
  6 10  1  6  0  0  0
 11  2  1  0  0  0  0
 12  7  2  0  0  0  0
 13  8  2  0  0  0  0
 14  8  1  0  0  0  0
 15  9  1  0  0  0  0
 16  9  2  0  0  0  0
 17  1  1  0  0  0  0
 18  2  1  0  0  0  0
 19  4  1  0  0  0  0
  6 20  1  6  0  0  0
M  END
> <DATABASE_ID>
NP0334331

> <DATABASE_NAME>
NP-MRD

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

> <INCHI_IDENTIFIER>
InChI=1S/C9H11NO6/c10-6(8(13)14)3-5(1-2-11)4-7(12)9(15)16/h1-2,4,6,11H,3,10H2,(H,13,14)(H,15,16)/b2-1+,5-4+/t6-/m0/s1

> <INCHI_KEY>
PIYTUGMLAKPQKI-OMQYJPGKSA-N

> <FORMULA>
C9H11NO6

> <MOLECULAR_WEIGHT>
229.188

> <EXACT_MASS>
229.058637078

> <JCHEM_ACCEPTOR_COUNT>
7

> <JCHEM_ATOM_COUNT>
27

> <JCHEM_AVERAGE_POLARIZABILITY>
20.832729726177092

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(3Z,6S)-6-amino-4-[(E)-2-hydroxyethenyl]-2-oxohept-3-enedioic acid

> <ALOGPS_LOGP>
-2.74

> <JCHEM_LOGP>
-2.8389844711497423

> <ALOGPS_LOGS>
-2.62

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
3.125062510572014

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.7315234853730246

> <JCHEM_PKA_STRONGEST_BASIC>
9.594461409368186

> <JCHEM_POLAR_SURFACE_AREA>
137.92000000000002

> <JCHEM_REFRACTIVITY>
53.232800000000005

> <JCHEM_ROTATABLE_BOND_COUNT>
6

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
5.45e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(3Z,6S)-6-amino-4-[(E)-2-hydroxyethenyl]-2-oxohept-3-enedioic acid

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 13-JUL-15   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   13-JUL-15         0                                  
HETATM    1  C   UNK     0      -0.770   1.334   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -2.310   1.334   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -0.770  -1.334   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       1.540   0.000   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      -2.310  -1.334   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       2.310   1.334   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      -3.080  -2.667   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       3.850   1.334   0.000  0.00  0.00           C+0
HETATM   10  N   UNK     0      -3.080  -0.000   0.000  0.00  0.00           N+0
HETATM   11  O   UNK     0      -3.080   2.667   0.000  0.00  0.00           O+0
HETATM   12  O   UNK     0       1.540   2.667   0.000  0.00  0.00           O+0
HETATM   13  O   UNK     0      -4.620  -2.667   0.000  0.00  0.00           O+0
HETATM   14  O   UNK     0      -2.310  -4.001   0.000  0.00  0.00           O+0
HETATM   15  O   UNK     0       4.620   2.667   0.000  0.00  0.00           O+0
HETATM   16  O   UNK     0       4.620   0.000   0.000  0.00  0.00           O+0
HETATM   17  H   UNK     0       0.000   2.667   0.000  0.00  0.00           H+0
HETATM   18  H   UNK     0      -3.850   1.334   0.000  0.00  0.00           H+0
HETATM   19  H   UNK     0       2.310  -1.334   0.000  0.00  0.00           H+0
HETATM   20  H   UNK     0      -1.540  -2.667   0.000  0.00  0.00           H+0
CONECT    1    2    5   17                                                  
CONECT    2    1   11   18                                                  
CONECT    3    5    6                                                       
CONECT    4    5    7   19                                                  
CONECT    5    1    3    4                                                  
CONECT    6    3    8   10   20                                             
CONECT    7    4    9   12                                                  
CONECT    8    6   13   14                                                  
CONECT    9    7   15   16                                                  
CONECT   10    6                                                            
CONECT   11    2                                                            
CONECT   12    7                                                            
CONECT   13    8                                                            
CONECT   14    8                                                            
CONECT   15    9                                                            
CONECT   16    9                                                            
CONECT   17    1                                                            
CONECT   18    2                                                            
CONECT   19    4                                                            
CONECT   20    6                                                            
MASTER        0    0    0    0    0    0    0    0   20    0   38    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₉H₁₁NO₆

Average Mass

229.1880 Da

Monoisotopic Mass

229.05864 Da

IUPAC Name

(3Z,6S)-6-amino-4-[(E)-2-hydroxyethenyl]-2-oxohept-3-enedioic acid

Traditional Name

(3Z,6S)-6-amino-4-[(E)-2-hydroxyethenyl]-2-oxohept-3-enedioic acid

CAS Registry Number

Not Available

SMILES

[H]C(O)=C([H])C(\C[C@]([H])(N)C(O)=O)=C(\[H])C(=O)C(O)=O

InChI Identifier

InChI=1S/C9H11NO6/c10-6(8(13)14)3-5(1-2-11)4-7(12)9(15)16/h1-2,4,6,11H,3,10H2,(H,13,14)(H,15,16)/b2-1+,5-4+/t6-/m0/s1

InChI Key

PIYTUGMLAKPQKI-OMQYJPGKSA-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 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
Medium-chain keto acid
Amino fatty acid
Branched fatty acid
Hydroxy fatty acid
Alpha-keto acid
Fatty acyl
Unsaturated fatty acid
Dicarboxylic acid or derivatives
Keto acid
Acryloyl-group
Alpha-hydroxy ketone
Alpha,beta-unsaturated ketone
Enone
Amino acid
Ketone
Enol
Carboxylic acid
Organonitrogen compound
Organooxygen compound
Primary amine
Carbonyl group
Hydrocarbon derivative
Organic nitrogen compound
Amine
Organic oxide
Organic oxygen compound
Primary aliphatic amine
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	-2.7	ALOGPS
logP	-2.8	ChemAxon
logS	-2.6	ALOGPS
pKa (Strongest Acidic)	1.73	ChemAxon
pKa (Strongest Basic)	9.59	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	7	ChemAxon
Hydrogen Donor Count	4	ChemAxon
Polar Surface Area	137.92 Å²	ChemAxon
Rotatable Bond Count	6	ChemAxon
Refractivity	53.23 m³·mol⁻¹	ChemAxon
Polarizability	20.83 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

FDB030477

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

14803858

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Not Available

Showing NP-Card for 4,5-seco-dopa (NP0334331)

MOL for NP0334331 (4,5-seco-dopa)

3D MOL for NP0334331 (4,5-seco-dopa)

3D SDF for NP0334331 (4,5-seco-dopa)

3D-SDF for NP0334331 (4,5-seco-dopa)

PDB for NP0334331 (4,5-seco-dopa)

3D PDB for NP0334331 (4,5-seco-dopa)

SMILES for NP0334331 (4,5-seco-dopa)

INCHI for NP0334331 (4,5-seco-dopa)

Structure for NP0334331 (4,5-seco-dopa)

3D Structure for NP0334331 (4,5-seco-dopa)