NP-MRD: Showing NP-Card for selenocystathionine (NP0250074)

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Record Information

Version

2.0

Created at

2022-09-07 12:48:55 UTC

Updated at

2022-09-07 12:48:55 UTC

NP-MRD ID

NP0250074

Secondary Accession Numbers

None

Natural Product Identification

Common Name

selenocystathionine

Description

Selenocystathionine, also known as secysta, belongs to the class of organic compounds known as alpha amino acids. These are amino acids in which the amino group is attached to the carbon atom immediately adjacent to the carboxylate group (alpha carbon). Selenocystathionine is a very strong basic compound (based on its pKa). Selenocystathionine exists in all living species, ranging from bacteria to humans. Within humans, selenocystathionine participates in a number of enzymatic reactions. In particular, selenocystathionine can be converted into selenocysteine and 2-ketobutyric acid through its interaction with the enzyme cystathionine gamma-lyase. In addition, selenocystathionine can be biosynthesized from L-serine and selenohomocysteine through the action of the enzyme cystathionine beta-synthase. selenocystathionine is found in Astragalus pectinatus. selenocystathionine was first documented in 1981 (PMID: 6456763). In humans, selenocystathionine is involved in selenoamino acid metabolism (PMID: 16920881).

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv0541 02231220382D          

 14 13  0  0  0  0            999 V2000
   17.3500   -6.2242    0.0000 Se  0  0  0  0  0  0  0  0  0  0  0  0
   19.4934   -4.1619    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   18.7789   -2.9244    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   15.9211   -8.6992    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   15.2066   -7.4618    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   17.3500   -3.7494    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   17.3500   -7.8743    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   18.0645   -4.9868    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   18.0645   -4.1619    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   17.3500   -5.3993    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   16.6357   -6.6367    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   16.6357   -7.4618    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   18.7789   -3.7494    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   15.9211   -7.8743    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1 10  1  0  0  0  0
  1 11  1  0  0  0  0
  2 13  1  0  0  0  0
  3 13  2  0  0  0  0
  4 14  1  0  0  0  0
  5 14  2  0  0  0  0
  6  9  1  0  0  0  0
  7 12  1  0  0  0  0
  8  9  1  0  0  0  0
  8 10  1  0  0  0  0
  9 13  1  0  0  0  0
 11 12  1  0  0  0  0
 12 14  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0250074

> <DATABASE_NAME>
NP-MRD

> <SMILES>
NC(CC[Se]CC(N)C(O)=O)C(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C7H14N2O4Se/c8-4(6(10)11)1-2-14-3-5(9)7(12)13/h4-5H,1-3,8-9H2,(H,10,11)(H,12,13)

> <INCHI_KEY>
ZNWYDQPOUQRDLY-UHFFFAOYSA-N

> <FORMULA>
C7H14N2O4Se

> <MOLECULAR_WEIGHT>
269.16

> <EXACT_MASS>
270.011878774

> <JCHEM_ACCEPTOR_COUNT>
6

> <JCHEM_AVERAGE_POLARIZABILITY>
21.049926594881462

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
2-amino-4-[(2-amino-2-carboxyethyl)selanyl]butanoic acid

> <ALOGPS_LOGP>
-3.99

> <JCHEM_LOGP>
-7.430536159693446

> <ALOGPS_LOGS>
-0.49

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
1.9009368083323284

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.1989938422458568

> <JCHEM_PKA_STRONGEST_BASIC>
9.535051728649085

> <JCHEM_POLAR_SURFACE_AREA>
126.63999999999999

> <JCHEM_REFRACTIVITY>
56.89030000000001

> <JCHEM_ROTATABLE_BOND_COUNT>
7

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
8.68e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
selenocystathionine

> <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 Se   UNK     0      32.387 -11.619   0.000  0.00  0.00          Se+0
HETATM    2  O   UNK     0      36.388  -7.769   0.000  0.00  0.00           O+0
HETATM    3  O   UNK     0      35.054  -5.459   0.000  0.00  0.00           O+0
HETATM    4  O   UNK     0      29.719 -16.239   0.000  0.00  0.00           O+0
HETATM    5  O   UNK     0      28.386 -13.929   0.000  0.00  0.00           O+0
HETATM    6  N   UNK     0      32.387  -6.999   0.000  0.00  0.00           N+0
HETATM    7  N   UNK     0      32.387 -14.699   0.000  0.00  0.00           N+0
HETATM    8  C   UNK     0      33.720  -9.309   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      33.720  -7.769   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      32.387 -10.079   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      31.053 -12.389   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      31.053 -13.929   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      35.054  -6.999   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      29.719 -14.699   0.000  0.00  0.00           C+0
CONECT    1   10   11                                                       
CONECT    2   13                                                            
CONECT    3   13                                                            
CONECT    4   14                                                            
CONECT    5   14                                                            
CONECT    6    9                                                            
CONECT    7   12                                                            
CONECT    8    9   10                                                       
CONECT    9    6    8   13                                                  
CONECT   10    1    8                                                       
CONECT   11    1   12                                                       
CONECT   12    7   11   14                                                  
CONECT   13    2    3    9                                                  
CONECT   14    4    5   12                                                  
MASTER        0    0    0    0    0    0    0    0   14    0   26    0
END

View in JSmol

Synonyms

Value	Source
2-Amino-4-[(2-amino-2-carboxyethyl)selanyl]butyric acid	ChEBI
Selenocystathionines	ChEBI
2-Amino-4-[(2-amino-2-carboxyethyl)selanyl]butyrate	Generator
2-Amino-4-((2-amino-2-carboxyethyl)seleno)-butanoate	HMDB
2-Amino-4-((2-amino-2-carboxyethyl)seleno)-butanoic acid	HMDB
2-Amino-4-((2-amino-2-carboxyethyl)seleno)butanoate	HMDB
2-Amino-4-((2-amino-2-carboxyethyl)seleno)butanoic acid	HMDB
SeCysta	HMDB

Chemical Formula

C₇H₁₄N₂O₄Se

Average Mass

269.1600 Da

Monoisotopic Mass

270.01188 Da

IUPAC Name

2-amino-4-[(2-amino-2-carboxyethyl)selanyl]butanoic acid

Traditional Name

selenocystathionine

CAS Registry Number

Not Available

SMILES

NC(CC[Se]CC(N)C(O)=O)C(O)=O

InChI Identifier

InChI=1S/C7H14N2O4Se/c8-4(6(10)11)1-2-14-3-5(9)7(12)13/h4-5H,1-3,8-9H2,(H,10,11)(H,12,13)

InChI Key

ZNWYDQPOUQRDLY-UHFFFAOYSA-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
Astragalus pectinatus	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as alpha amino acids. These are amino acids in which the amino group is attached to the carbon atom immediately adjacent to the carboxylate group (alpha carbon).

Kingdom

Organic compounds

Super Class

Organic acids and derivatives

Class

Carboxylic acids and derivatives

Sub Class

Amino acids, peptides, and analogues

Direct Parent

Alpha amino acids

Alternative Parents

Substituents

Alpha-amino acid
Dicarboxylic acid or derivatives
Fatty acid
Amino acid
Carboxylic acid
Selenoether
Organic nitrogen compound
Hydrocarbon derivative
Organic oxide
Primary amine
Organoselenium compound
Organooxygen compound
Organonitrogen compound
Primary aliphatic amine
Organopnictogen compound
Organic oxygen compound
Carbonyl group
Amine
Aliphatic acyclic compound

Molecular Framework

Aliphatic acyclic compounds

External Descriptors

selenoamino acid (CHEBI:26630 )
cystathionines (CHEBI:26630 )

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	-4	ALOGPS
logP	-7.4	ChemAxon
logS	-0.49	ALOGPS
pKa (Strongest Acidic)	1.2	ChemAxon
pKa (Strongest Basic)	9.54	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	6	ChemAxon
Hydrogen Donor Count	4	ChemAxon
Polar Surface Area	126.64 Å²	ChemAxon
Rotatable Bond Count	7	ChemAxon
Refractivity	56.89 m³·mol⁻¹	ChemAxon
Polarizability	21.05 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

HMDB0006343

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

FDB023895

KNApSAcK ID

Not Available

Chemspider ID

88693

KEGG Compound ID

C05699

BioCyc ID

Not Available

BiGG ID

46314

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

98223

PDB ID

Not Available

ChEBI ID

26630

Good Scents ID

Not Available

References

General References

Esaki N, Nakamura T, Tanaka H, Suzuki T, Morino Y, Soda K: Enzymatic synthesis of selenocysteine in rat liver. Biochemistry. 1981 Jul 21;20(15):4492-6. doi: 10.1021/bi00518a039. [PubMed:6456763 ]
Freeman JL, Zhang LH, Marcus MA, Fakra S, McGrath SP, Pilon-Smits EA: Spatial imaging, speciation, and quantification of selenium in the hyperaccumulator plants Astragalus bisulcatus and Stanleya pinnata. Plant Physiol. 2006 Sep;142(1):124-34. doi: 10.1104/pp.106.081158. Epub 2006 Aug 18. [PubMed:16920881 ]
LOTUS database [Link]

Showing NP-Card for selenocystathionine (NP0250074)

MOL for NP0250074 (selenocystathionine)

3D MOL for NP0250074 (selenocystathionine)

3D SDF for NP0250074 (selenocystathionine)

3D-SDF for NP0250074 (selenocystathionine)

PDB for NP0250074 (selenocystathionine)

3D PDB for NP0250074 (selenocystathionine)

SMILES for NP0250074 (selenocystathionine)

INCHI for NP0250074 (selenocystathionine)

Structure for NP0250074 (selenocystathionine)

3D Structure for NP0250074 (selenocystathionine)