MiMeDB: Showing metabocard for Selenocystathionine (MMDBc0029826)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2021-11-17 23:43:18 UTC

Update Date

2024-04-30 19:42:31 UTC

Metabolite ID

MMDBc0029826

Metabolite Identification

Common Name

Selenocystathionine

Description

Selenocystathionine is formed from selenohomocysteine by the enzyme cystathionine beta-synthase (EC 4.2.1.22), as a by-product of cystathionine synthesis. It is an intermediate in selenoamine acid metabolism.

Structure

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>
MMDBc0029826

> <DATABASE_NAME>
MIME

> <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

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

Molecular Formula

C₇H₁₄N₂O₄Se

Average Mass

269.16

Monoisotopic Mass

270.011878774

IUPAC Name

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

Traditional Name

selenocystathionine

CAS Registry Number

2196-58-9

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

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 )

Functional Ontology

Not Available

Physical Properties

State

Solid

Predicted Properties

Property	Value	Source
Water Solubility	86.8 g/L	ALOGPS
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

Spectra

Spectrum Type	Description	Splash Key	Deposition Date	View
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	splash10-002f-9420000000-a9e99a8fd86be0c5402a	2016-09-22	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (2 TMS) - 70eV, Positive	splash10-006w-9610000000-67eb14a8bbb4d03ea463	2017-10-06	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-00fr-2290000000-f2bec65ba3fa54257a2a	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-004i-1490000000-c8e7ba1b974d80ad06fd	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-00ba-4900000000-44733d945ca0a2123bdd	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-014i-0910000000-949e30f57858894ebee4	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-0uy0-5980000000-44fdd01e4d44e8a390bd	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-00di-9600000000-a128c15c6924127ebb1b	2015-09-15	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 100 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 200 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 300 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 400 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 500 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 600 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 700 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 800 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 900 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, H₂O, predicted)		2022-08-18	View Spectrum

Biological Properties

Cellular Locations

Cytoplasm

Biospecimen Locations

Feces

Tissue Locations

Not Available

Associated OMIM IDs

114500 (Colorectal cancer)
610247 (Eosinophilic esophagitis)

Human Proteins and Enzymes

Protein ID	Protein Name	Protein Type	Uniprot ID	Species

Human Pathways

Pathways

Name	SMPDB/PathBank

Metabolic Reactions

Reactions

Reaction ID	Precursor	Product	Enzyme	Reaction Type	Data Source	Reference
MMDBr0002108	Selenocystathionine	2-Ketobutyric acid	cystathionine gamma-lyase		VMH	6461656
MMDBr0002109	Selenohomocysteine	Selenocystathionine	Not Available		VMH	6461656

Health Effects and Bioactivity

Health Outcome/Bioactivity	Metabolite Response/Effect	Evidence Type	Host and Biospecimen	Data Source	Reference

Microbial Sources

Superkingdom/Kingdom	Phylum	Total species	Hosts and Body Sites	Microbial Links
Bacteria	Proteobacteria	38	Human ; Human feces; Human feces; pleural fluid plaque; bal; Human stool	Unknown; Metabolic reconstruction
Bacteria	Firmicutes	78	Human feces; Human ; Human subgingival plaque	Metabolic reconstruction
Bacteria	Actinobacteria	27	Human feces; Human	Metabolic reconstruction
Bacteria	Bacteroidetes	6	Human feces; Human ; Human supragingival plaque; Human subgingival plaque; Human saliva	Metabolic reconstruction
Archaea	Euryarchaeota	1		Metabolic reconstruction
Eukaryota/Fungi	Ascomycota	1	Human feces; Human saliva	Unknown

Exposure Sources

Source Type	Source Sub-type	Species	Data Source	Reference

Host Biospecimen and Location

Host and Biospecimen	Status	Mean	Std	Min	Max	Units	Age	Sex	Health Condition	Data Source	Reference
Human Feces	Detected but not Quantified									HMDB

External Links

HMDB ID

HMDB0006343

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB 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

Food Biomarker Ontology

Not Available

References

Synthesis Reference

Not Available

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 ]
Neuhierl B, Thanbichler M, Lottspeich F, Bock A: A family of S-methylmethionine-dependent thiol/selenol methyltransferases. Role in selenium tolerance and evolutionary relation. J Biol Chem. 1999 Feb 26;274(9):5407-14. doi: 10.1074/jbc.274.9.5407. [PubMed:10026151 ]
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 ]

Showing metabocard for Selenocystathionine (MMDBc0029826)

MOL for #<Metabolite:0x00007fece8bdfe20>

3D MOL for #<Metabolite:0x00007fece8bdfe20>

3D SDF for #<Metabolite:0x00007fece8bdfe20>

3D-SDF for #<Metabolite:0x00007fece8bdfe20>

PDB for #<Metabolite:0x00007fece8bdfe20>

3D PDB for #<Metabolite:0x00007fece8bdfe20>

SMILES for #<Metabolite:0x00007fece8bdfe20>

INCHI for #<Metabolite:0x00007fece8bdfe20>

Structure for #<Metabolite:0x00007fece8bdfe20>

3D Structure for #<Metabolite:0x00007fece8bdfe20>