NP-MRD: Showing NP-Card for (2s)-2-{[(2s)-2-amino-1,3-dihydroxypropylidene]amino}-4-(methylsulfanyl)butanoic acid (NP0205583)

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Record Information

Version

2.0

Created at

2022-09-05 01:31:53 UTC

Updated at

2022-09-05 01:31:53 UTC

NP-MRD ID

NP0205583

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(2s)-2-{[(2s)-2-amino-1,3-dihydroxypropylidene]amino}-4-(methylsulfanyl)butanoic acid

Description

Serylmethionine, also known as SM or L-ser-L-met, belongs to the class of organic compounds known as dipeptides. These are organic compounds containing a sequence of exactly two alpha-amino acids joined by a peptide bond. Serylmethionine is a very strong basic compound (based on its pKa). (2s)-2-{[(2s)-2-amino-1,3-dihydroxypropylidene]amino}-4-(methylsulfanyl)butanoic acid is found in Arabidopsis thaliana. It is an incomplete breakdown product of protein digestion or protein catabolism.

Structure

MOL 3D MOL SDF PDB SMILES InChI

     RDKit          3D

 31 30  0  0  0  0  0  0  0  0999 V2000
    4.0293   -2.0942    0.7991 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.8423   -0.4001    1.3845 S   0  0  0  0  0  0  0  0  0  0  0  0
    2.8418    0.5764    0.1840 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4378    0.0541    0.1443 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5612    0.8248   -0.7860 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.8101    0.2543   -0.7553 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8992    1.0119   -0.2612 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6677    2.1776    0.1484 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2906    0.5242   -0.1948 C   0  0  1  0  0  0  0  0  0  0  0  0
   -3.4398   -0.8256   -0.6898 N   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7379    0.5985    1.2711 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9639   -0.2530    2.0420 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.0670    0.7701   -2.1595 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3631    0.2140   -3.0639 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.2639    1.2882   -2.5443 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.0806   -2.3351    0.5283 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.4126   -2.3334   -0.0815 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.7567   -2.8377    1.5934 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.3740    0.5653   -0.7835 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8365    1.6108    0.5930 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4456   -1.0456   -0.0924 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.0312    0.1536    1.1833 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4764    1.8561   -0.3862 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8721   -0.7198   -1.1219 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0020    1.1644   -0.7780 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1448   -0.9248   -1.6785 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0713   -1.5525   -0.0482 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7103    1.6443    1.6202 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8210    0.3052    1.2592 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2984   -1.1840    1.9806 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.9091    0.9119   -3.2105 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  1  0
  4  5  1  0
  5  6  1  0
  6  7  1  0
  7  8  2  0
  7  9  1  0
  9 10  1  0
  9 11  1  0
 11 12  1  0
  5 13  1  0
 13 15  1  0
 13 14  2  0
  1 16  1  0
  1 17  1  0
  1 18  1  0
  3 19  1  0
  3 20  1  0
  4 21  1  0
  4 22  1  0
  5 23  1  1
  6 24  1  0
  9 25  1  6
 10 26  1  0
 10 27  1  0
 11 28  1  0
 11 29  1  0
 12 30  1  0
 15 31  1  0
M  END


  Mrv1652305181917152D          

 15 14  0  0  0  0            999 V2000
 2502.9811 2502.8808    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
 2502.9811 2502.0550    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
 2503.7022 2501.6556    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 2504.4172 2502.0674    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 2503.7022 2500.8300    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
 2502.9873 2500.4161    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 2502.2723 2500.8300    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 2504.4172 2500.4161    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
 2502.2661 2503.2924    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 2501.5512 2502.8808    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 2500.8362 2503.2924    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
 2500.1172 2502.8788    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 2503.6960 2503.2924    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 2504.4110 2502.8808    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 2503.6960 2504.1182    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  1  0  0  0
  1  9  1  0  0  0  0
  1 13  1  0  0  0  0
  2  3  1  0  0  0  0
  3  4  2  0  0  0  0
  5  3  1  1  0  0  0
  5  6  1  0  0  0  0
  5  8  1  0  0  0  0
  6  7  1  0  0  0  0
  9 10  1  0  0  0  0
 10 11  1  0  0  0  0
 11 12  1  0  0  0  0
 13 14  1  0  0  0  0
 13 15  2  0  0  0  0
M  END
> <DATABASE_ID>
NP0205583

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CSCC[C@H](NC(=O)[C@@H](N)CO)C(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C8H16N2O4S/c1-15-3-2-6(8(13)14)10-7(12)5(9)4-11/h5-6,11H,2-4,9H2,1H3,(H,10,12)(H,13,14)/t5-,6-/m0/s1

> <INCHI_KEY>
PBUXMVYWOSKHMF-WDSKDSINSA-N

> <FORMULA>
C8H16N2O4S

> <MOLECULAR_WEIGHT>
236.29

> <EXACT_MASS>
236.083078177

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_ATOM_COUNT>
31

> <JCHEM_AVERAGE_POLARIZABILITY>
23.649343781815887

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2S)-2-[(2S)-2-amino-3-hydroxypropanamido]-4-(methylsulfanyl)butanoic acid

> <ALOGPS_LOGP>
-2.35

> <JCHEM_LOGP>
-3.775785121039363

> <ALOGPS_LOGS>
-1.35

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
13.471066879685015

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.635452997434249

> <JCHEM_PKA_STRONGEST_BASIC>
7.849366949678391

> <JCHEM_POLAR_SURFACE_AREA>
112.65

> <JCHEM_REFRACTIVITY>
56.42710000000001

> <JCHEM_ROTATABLE_BOND_COUNT>
7

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.06e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(2S)-2-[(2S)-2-amino-3-hydroxypropanamido]-4-(methylsulfanyl)butanoic acid

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 18-MAY-19   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   18-MAY-19         0                                  
HETATM    1  C   UNK     0    4672.2314672.044   0.000  0.00  0.00           C+0
HETATM    2  N   UNK     0    4672.2314670.503   0.000  0.00  0.00           N+0
HETATM    3  C   UNK     0    4673.5774669.757   0.000  0.00  0.00           C+0
HETATM    4  O   UNK     0    4674.9124670.526   0.000  0.00  0.00           O+0
HETATM    5  C   UNK     0    4673.5774668.216   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0    4672.2434667.443   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0    4670.9084668.216   0.000  0.00  0.00           O+0
HETATM    8  N   UNK     0    4674.9124667.443   0.000  0.00  0.00           N+0
HETATM    9  C   UNK     0    4670.8974672.812   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0    4669.5624672.044   0.000  0.00  0.00           C+0
HETATM   11  S   UNK     0    4668.2284672.812   0.000  0.00  0.00           S+0
HETATM   12  C   UNK     0    4666.8854672.040   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0    4673.5664672.812   0.000  0.00  0.00           C+0
HETATM   14  O   UNK     0    4674.9014672.044   0.000  0.00  0.00           O+0
HETATM   15  O   UNK     0    4673.5664674.354   0.000  0.00  0.00           O+0
CONECT    1    2    9   13                                                  
CONECT    2    1    3                                                       
CONECT    3    2    4    5                                                  
CONECT    4    3                                                            
CONECT    5    3    6    8                                                  
CONECT    6    5    7                                                       
CONECT    7    6                                                            
CONECT    8    5                                                            
CONECT    9    1   10                                                       
CONECT   10    9   11                                                       
CONECT   11   10   12                                                       
CONECT   12   11                                                            
CONECT   13    1   14   15                                                  
CONECT   14   13                                                            
CONECT   15   13                                                            
MASTER        0    0    0    0    0    0    0    0   15    0   28    0
END

View in JSmol

Synonyms

Value	Source
L-Ser-L-met	ChEBI
N-L-Seryl-L-methionine	ChEBI
Serinyl-methionine	ChEBI
SM	ChEBI
L-Seryl-L-methionine	HMDB
Ser-met	HMDB
N-Serylmethionine	HMDB
S-m Dipeptide	HMDB
SM Dipeptide	HMDB
Serine methionine dipeptide	HMDB
Serine-methionine dipeptide	HMDB
Serinylmethionine	HMDB
Seryl-methionine	HMDB
Serylmethionine	ChEBI

Chemical Formula

C₈H₁₆N₂O₄S

Average Mass

236.2900 Da

Monoisotopic Mass

236.08308 Da

IUPAC Name

(2S)-2-[(2S)-2-amino-3-hydroxypropanamido]-4-(methylsulfanyl)butanoic acid

Traditional Name

(2S)-2-[(2S)-2-amino-3-hydroxypropanamido]-4-(methylsulfanyl)butanoic acid

CAS Registry Number

Not Available

SMILES

CSCC[C@H](NC(=O)[C@@H](N)CO)C(O)=O

InChI Identifier

InChI=1S/C8H16N2O4S/c1-15-3-2-6(8(13)14)10-7(12)5(9)4-11/h5-6,11H,2-4,9H2,1H3,(H,10,12)(H,13,14)/t5-,6-/m0/s1

InChI Key

PBUXMVYWOSKHMF-WDSKDSINSA-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
Arabidopsis thaliana	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as dipeptides. These are organic compounds containing a sequence of exactly two alpha-amino acids joined by a peptide bond.

Kingdom

Organic compounds

Super Class

Organic acids and derivatives

Class

Carboxylic acids and derivatives

Sub Class

Amino acids, peptides, and analogues

Direct Parent

Dipeptides

Alternative Parents

Substituents

Alpha-dipeptide
Methionine or derivatives
N-acyl-alpha-amino acid
N-acyl-alpha amino acid or derivatives
N-acyl-l-alpha-amino acid
Alpha-amino acid amide
Serine or derivatives
Alpha-amino acid or derivatives
Hydroxy fatty acid
Thia fatty acid
Fatty acyl
Fatty acid
Amino acid
Secondary carboxylic acid amide
Amino acid or derivatives
Carboxamide group
Dialkylthioether
Sulfenyl compound
Thioether
Carboxylic acid
Monocarboxylic acid or derivatives
Hydrocarbon derivative
Organonitrogen compound
Organic oxide
Organopnictogen compound
Organooxygen compound
Primary aliphatic amine
Alcohol
Organosulfur compound
Primary alcohol
Carbonyl group
Primary amine
Amine
Organic oxygen compound
Organic nitrogen compound
Aliphatic acyclic compound

Molecular Framework

Aliphatic acyclic compounds

External Descriptors

dipeptide (CHEBI:74817 )

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	-2.4	ALOGPS
logP	-3.8	ChemAxon
logS	-1.4	ALOGPS
pKa (Strongest Acidic)	3.64	ChemAxon
pKa (Strongest Basic)	7.85	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	5	ChemAxon
Hydrogen Donor Count	4	ChemAxon
Polar Surface Area	112.65 Å²	ChemAxon
Rotatable Bond Count	7	ChemAxon
Refractivity	56.43 m³·mol⁻¹	ChemAxon
Polarizability	23.65 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

HMDB0029045

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

151087

PDB ID

Not Available

ChEBI ID

74817

Good Scents ID

Not Available

References

General References

LOTUS database [Link]

Showing NP-Card for (2s)-2-{[(2s)-2-amino-1,3-dihydroxypropylidene]amino}-4-(methylsulfanyl)butanoic acid (NP0205583)

MOL for NP0205583 ((2s)-2-{[(2s)-2-amino-1,3-dihydroxypropylidene]amino}-4-(methylsulfanyl)butanoic acid)

3D MOL for NP0205583 ((2s)-2-{[(2s)-2-amino-1,3-dihydroxypropylidene]amino}-4-(methylsulfanyl)butanoic acid)

3D SDF for NP0205583 ((2s)-2-{[(2s)-2-amino-1,3-dihydroxypropylidene]amino}-4-(methylsulfanyl)butanoic acid)

3D-SDF for NP0205583 ((2s)-2-{[(2s)-2-amino-1,3-dihydroxypropylidene]amino}-4-(methylsulfanyl)butanoic acid)

PDB for NP0205583 ((2s)-2-{[(2s)-2-amino-1,3-dihydroxypropylidene]amino}-4-(methylsulfanyl)butanoic acid)

3D PDB for NP0205583 ((2s)-2-{[(2s)-2-amino-1,3-dihydroxypropylidene]amino}-4-(methylsulfanyl)butanoic acid)

SMILES for NP0205583 ((2s)-2-{[(2s)-2-amino-1,3-dihydroxypropylidene]amino}-4-(methylsulfanyl)butanoic acid)

INCHI for NP0205583 ((2s)-2-{[(2s)-2-amino-1,3-dihydroxypropylidene]amino}-4-(methylsulfanyl)butanoic acid)

Structure for NP0205583 ((2s)-2-{[(2s)-2-amino-1,3-dihydroxypropylidene]amino}-4-(methylsulfanyl)butanoic acid)

3D Structure for NP0205583 ((2s)-2-{[(2s)-2-amino-1,3-dihydroxypropylidene]amino}-4-(methylsulfanyl)butanoic acid)