MiMeDB: Showing metabocard for Lanthionine (MMDBc0000766)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2020-12-10 18:54:29 UTC

Update Date

2024-04-30 19:33:38 UTC

Metabolite ID

MMDBc0000766

Metabolite Identification

Common Name

Lanthionine

Description

Lanthionine belongs to the class of organic compounds known as L-cysteine-S-conjugates. These are compounds containing L-cysteine where the thio-group is conjugated. Lanthionine is a uremic toxin (PMID: 30087103 ).

Structure

MOL 3D MOL SDF 3D SDF PDB 3D PDB SMILES InChI


  Mrv1652306042022272D          

 13 12  0  0  0  0            999 V2000
10000.849210002.0690    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
10000.134210002.4810    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10001.563910002.4810    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10000.849210001.2436    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
 9999.419410002.0690    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
10000.134210003.3059    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
10002.278710002.0690    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
10002.993310002.4810    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10003.710910002.0690    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
10004.424410002.4810    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10003.710910001.2436    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
10005.140010002.0690    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
10004.424410003.3059    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  1  3  1  0  0  0  0
  1  4  1  6  0  0  0
  2  5  1  0  0  0  0
  2  6  2  0  0  0  0
  3  7  1  0  0  0  0
  7  8  1  0  0  0  0
  8  9  1  0  0  0  0
  9 10  1  0  0  0  0
  9 11  1  1  0  0  0
 10 12  1  0  0  0  0
 10 13  2  0  0  0  0
M  END
> <DATABASE_ID>
MMDBc0000766

> <DATABASE_NAME>
MIME

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

> <INCHI_IDENTIFIER>
InChI=1S/C6H12N2O4S/c7-3(5(9)10)1-13-2-4(8)6(11)12/h3-4H,1-2,7-8H2,(H,9,10)(H,11,12)/t3-,4-/m0/s1

> <INCHI_KEY>
DWPCPZJAHOETAG-IMJSIDKUSA-N

> <FORMULA>
C6H12N2O4S

> <MOLECULAR_WEIGHT>
208.23

> <EXACT_MASS>
208.051778048

> <JCHEM_ACCEPTOR_COUNT>
6

> <JCHEM_ATOM_COUNT>
25

> <JCHEM_AVERAGE_POLARIZABILITY>
19.794967332949895

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2R)-2-amino-3-{[(2R)-2-amino-2-carboxyethyl]sulfanyl}propanoic acid

> <ALOGPS_LOGP>
-4.06

> <JCHEM_LOGP>
-6.03434669968463

> <ALOGPS_LOGS>
-1.11

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
2.4341299418536853

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.7056819646375265

> <JCHEM_PKA_STRONGEST_BASIC>
9.441859276427017

> <JCHEM_POLAR_SURFACE_AREA>
126.64000000000001

> <JCHEM_REFRACTIVITY>
46.8575

> <JCHEM_ROTATABLE_BOND_COUNT>
6

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.63e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
lanthionine

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 04-JUN-20   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   04-JUN-20         0                                  
HETATM    1  C   UNK     0    8668.2528670.529   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0    8666.9178671.298   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0    8669.5868671.298   0.000  0.00  0.00           C+0
HETATM    4  N   UNK     0    8668.2528668.988   0.000  0.00  0.00           N+0
HETATM    5  O   UNK     0    8665.5838670.529   0.000  0.00  0.00           O+0
HETATM    6  O   UNK     0    8666.9178672.838   0.000  0.00  0.00           O+0
HETATM    7  S   UNK     0    8670.9208670.529   0.000  0.00  0.00           S+0
HETATM    8  C   UNK     0    8672.2548671.298   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0    8673.5948670.529   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0    8674.9268671.298   0.000  0.00  0.00           C+0
HETATM   11  N   UNK     0    8673.5948668.988   0.000  0.00  0.00           N+0
HETATM   12  O   UNK     0    8676.2618670.529   0.000  0.00  0.00           O+0
HETATM   13  O   UNK     0    8674.9268672.838   0.000  0.00  0.00           O+0
CONECT    1    2    3    4                                                  
CONECT    2    1    5    6                                                  
CONECT    3    1    7                                                       
CONECT    4    1                                                            
CONECT    5    2                                                            
CONECT    6    2                                                            
CONECT    7    3    8                                                       
CONECT    8    7    9                                                       
CONECT    9    8   10   11                                                  
CONECT   10    9   12   13                                                  
CONECT   11    9                                                            
CONECT   12   10                                                            
CONECT   13   10                                                            
MASTER        0    0    0    0    0    0    0    0   13    0   24    0
END

Synonyms

Value	Source
(R)-S-(2-Amino-2-carboxyethyl)-L-cysteine	ChEBI
(R,R)-2,6-Diamino-4-thiaheptanedioic acid	ChEBI
(R,R)-3,3'-Thiobis-(2-aminopropanoic acid)	ChEBI
(R,R)-Bis(2-amino-2-carboxyethyl)sulfide	ChEBI
3,3'-Thiobis-L-alanine	ChEBI
3,3'-Thiodi-L-alanine	ChEBI
beta,Beta'-thiodi-L-alanine	ChEBI
(R,R)-2,6-Diamino-4-thiaheptanedioate	Generator
(R,R)-3,3'-Thiobis-(2-aminopropanoate)	Generator
(R,R)-Bis(2-amino-2-carboxyethyl)sulphide	Generator
b,Beta'-thiodi-L-alanine	Generator
Β,beta'-thiodi-L-alanine	Generator
3,3'-Thiodialanine	MeSH
Lanthionine, (L)-(R)-isomer	MeSH
Lanthionine	MeSH
L-Lanthionine	HMDB
S-[(2R)-2-Amino-2-carboxyethyl]-L-cysteine	HMDB

Molecular Formula

C₆H₁₂N₂O₄S

Average Mass

208.23

Monoisotopic Mass

208.051778048

IUPAC Name

(2R)-2-amino-3-{[(2R)-2-amino-2-carboxyethyl]sulfanyl}propanoic acid

Traditional Name

lanthionine

CAS Registry Number

Not Available

SMILES

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

InChI Identifier

InChI=1S/C6H12N2O4S/c7-3(5(9)10)1-13-2-4(8)6(11)12/h3-4H,1-2,7-8H2,(H,9,10)(H,11,12)/t3-,4-/m0/s1

InChI Key

DWPCPZJAHOETAG-IMJSIDKUSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as l-cysteine-s-conjugates. L-cysteine-S-conjugates are compounds containing L-cysteine where the thio-group is conjugated.

Kingdom

Organic compounds

Super Class

Organic acids and derivatives

Class

Carboxylic acids and derivatives

Sub Class

Amino acids, peptides, and analogues

Direct Parent

L-cysteine-S-conjugates

Alternative Parents

Substituents

L-cysteine-s-conjugate
Alpha-amino acid
L-alpha-amino acid
Dicarboxylic acid or derivatives
Amino acid
Carboxylic acid
Thioether
Sulfenyl compound
Dialkylthioether
Amine
Organic nitrogen compound
Primary amine
Organosulfur compound
Organooxygen compound
Organonitrogen compound
Primary aliphatic amine
Organic oxygen compound
Organic oxide
Carbonyl group
Organopnictogen compound
Hydrocarbon derivative
Aliphatic acyclic compound

Molecular Framework

Aliphatic acyclic compounds

External Descriptors

non-proteinogenic L-alpha-amino acid (CHEBI:21347 )
L-alanine derivative (CHEBI:21347 )
lanthionine (CHEBI:21347 )

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
Water Solubility	16.3 g/L	ALOGPS
logP	-4.1	ALOGPS
logP	-6	ChemAxon
logS	-1.1	ALOGPS
pKa (Strongest Acidic)	1.71	ChemAxon
pKa (Strongest Basic)	9.44	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	6	ChemAxon
Refractivity	46.86 m³·mol⁻¹	ChemAxon
Polarizability	19.79 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	Not Available	2021-10-12	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-00e9-5910000000-d6dba31a3ce2e863cd37	2021-09-23	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-001i-9500000000-e719314b45817c378178	2021-09-23	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-001i-9100000000-00d307236120c2a37eac	2021-09-23	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-004l-0900000000-3c74cf7eb702d7e244e4	2021-09-25	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-00di-4900000000-aa0102b721bc8704c354	2021-09-25	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-00di-9000000000-29ce92f1b06478fe32c3	2021-09-25	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)		2021-09-25	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 100 MHz, D₂O, predicted)		2021-09-25	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)		2021-09-25	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, D₂O, predicted)		2021-09-25	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)		2021-09-25	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 200 MHz, D₂O, predicted)		2021-09-25	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)		2021-09-25	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 300 MHz, D₂O, predicted)		2021-09-25	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)		2021-09-25	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 400 MHz, D₂O, predicted)		2021-09-25	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)		2021-09-25	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 500 MHz, D₂O, predicted)		2021-09-25	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)		2021-09-25	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 600 MHz, D₂O, predicted)		2021-09-25	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)		2021-09-25	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 700 MHz, D₂O, predicted)		2021-09-25	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)		2021-09-25	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 800 MHz, D₂O, predicted)		2021-09-25	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, predicted)		2021-09-25	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 900 MHz, D₂O, predicted)		2021-09-25	View Spectrum

Biological Properties

Cellular Locations

Not Available

Biospecimen Locations

Blood
Urine

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
MMDBp0192186	Cystathionine gamma-lyase	Enzyme	P32929	Homo sapiens
MMDBp0196724	Thiomorpholine-carboxylate dehydrogenase	Unknown	Q14894
MMDBp0197062	Ketimine reductase mu-crystallin	Unknown	Q28488	Macropus fuliginosus

Human Pathways

Pathways

Name	SMPDB/PathBank

Metabolic Reactions

Not Available

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	Firmicutes	1	Human stool	Indirect association between microbiota composition and metabolites measured in host biospecimen

Exposure Sources

Host Biospecimen and Location

Host and Biospecimen	Status	Mean	Std	Min	Max	Units	Age	Sex	Health Condition	Data Source	Reference
Human Urine	Detected but not Quantified						Adult (>18 years old)	Both	Normal	HMDB	30087103
Human Blood	Detected but not Quantified									HMDB

External Links

HMDB ID

Not Available

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

Not Available

KNApSAcK ID

Not Available

Chemspider ID

88959

KEGG Compound ID

Not Available

BioCyc ID

CPD-3736

BiGG ID

Not Available

Wikipedia Link

Lanthionine

METLIN ID

Not Available

PubChem Compound

98504

PDB ID

Not Available

ChEBI ID

21347

Food Biomarker Ontology

Not Available

References

Synthesis Reference

Not Available

General References

Mair RD, Sirich TL, Plummer NS, Meyer TW: Characteristics of Colon-Derived Uremic Solutes. Clin J Am Soc Nephrol. 2018 Sep 7;13(9):1398-1404. doi: 10.2215/CJN.03150318. Epub 2018 Aug 7. [PubMed:30087103 ]

Showing metabocard for Lanthionine (MMDBc0000766)

MOL for #<Metabolite:0x00007fdb4403b598>

3D MOL for #<Metabolite:0x00007fdb4403b598>

3D SDF for #<Metabolite:0x00007fdb4403b598>

3D-SDF for #<Metabolite:0x00007fdb4403b598>

PDB for #<Metabolite:0x00007fdb4403b598>

3D PDB for #<Metabolite:0x00007fdb4403b598>

SMILES for #<Metabolite:0x00007fdb4403b598>

INCHI for #<Metabolite:0x00007fdb4403b598>

Structure for #<Metabolite:0x00007fdb4403b598>

3D Structure for #<Metabolite:0x00007fdb4403b598>