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Record Information

Version

5.0

Status

Detected but not Quantified

Creation Date

2022-09-09 19:37:46 UTC

Update Date

2022-09-22 18:35:06 UTC

HMDB ID

HMDB0341196

Secondary Accession Numbers

None

Metabolite Identification

Common Name

Ser-Gly-Thr

Description

Ser-Gly-Thr belongs to the class of organic compounds known as oligopeptides. These are organic compounds containing a sequence of between three and ten alpha-amino acids joined by peptide bonds. Based on a literature review a small amount of articles have been published on Ser-Gly-Thr.

Structure

MOL SDF PDB SMILES InChI


  Mrv1652309092222162D          

 21 20  0  0  1  0            999 V2000
    4.1250   -1.4289    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.7125   -0.7145    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    4.5375   -0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3000   -1.4289    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.3000    0.0000    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.8875   -0.7145    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4750    0.0000    0.0000 N   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
    2.4750    1.4289    0.0000 O   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
    0.8250    0.0000    0.0000 N   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
   -0.4125    0.7145    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4125   -0.7145    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.4125   -0.7145    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000   -1.4289    0.0000 N   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
   -1.6500   -1.4289    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.7125    0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3000    1.4289    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.5375    0.7145    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  6  0  0  0
  2  3  1  0  0  0  0
  2  4  1  1  0  0  0
  2  5  1  0  0  0  0
  5  6  1  1  0  0  0
  5  7  1  6  0  0  0
  7  8  2  0  0  0  0
  8  9  1  4  0  0  0
  8 10  1  0  0  0  0
 11 10  1  4  0  0  0
 11 12  2  0  0  0  0
 12 13  1  0  0  0  0
 12 14  1  0  0  0  0
 14 15  1  6  0  0  0
 14 16  1  1  0  0  0
 14 17  1  0  0  0  0
 17 18  1  0  0  0  0
  5 19  1  0  0  0  0
 19 20  1  0  0  0  0
 19 21  2  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0341196

> <DATABASE_NAME>
hmdb

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

> <INCHI_IDENTIFIER>
InChI=1S/C9H17N3O6/c1-4(14)7(9(17)18)12-6(15)2-11-8(16)5(10)3-13/h4-5,7,13-14H,2-3,10H2,1H3,(H,11,16)(H,12,15)(H,17,18)/t4-,5+,7+/m1/s1

> <INCHI_KEY>
SFTZWNJFZYOLBD-ZDLURKLDSA-N

> <FORMULA>
C9H17N3O6

> <MOLECULAR_WEIGHT>
263.25

> <EXACT_MASS>
263.111735279

> <JCHEM_ACCEPTOR_COUNT>
9

> <JCHEM_ATOM_COUNT>
35

> <JCHEM_AVERAGE_POLARIZABILITY>
25.151237255784498

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
6

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2S,3R)-2-[(2-{[(2S)-2-amino-1,3-dihydroxypropylidene]amino}-1-hydroxyethylidene)amino]-3-hydroxybutanoic acid

> <JCHEM_LOGP>
-4.786433215564895

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
3.6076406835296044

> <JCHEM_PKA_STRONGEST_ACIDIC>
2.8509492684156332

> <JCHEM_PKA_STRONGEST_BASIC>
9.011101867668133

> <JCHEM_POLAR_SURFACE_AREA>
168.95999999999998

> <JCHEM_REFRACTIVITY>
59.1478

> <JCHEM_ROTATABLE_BOND_COUNT>
7

> <JCHEM_RULE_OF_FIVE>
0

> <JCHEM_TRADITIONAL_IUPAC>
(2S,3R)-2-[(2-{[(2S)-2-amino-1,3-dihydroxypropylidene]amino}-1-hydroxyethylidene)amino]-3-hydroxybutanoic acid

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 09-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   09-SEP-22         0                                  
HETATM    1  H   UNK     0       7.700  -2.667   0.000  0.00  0.00           H+0
HETATM    2  C   UNK     0       6.930  -1.334   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       8.470  -1.334   0.000  0.00  0.00           C+0
HETATM    4  O   UNK     0       6.160  -2.667   0.000  0.00  0.00           O+0
HETATM    5  C   UNK     0       6.160   0.000   0.000  0.00  0.00           C+0
HETATM    6  H   UNK     0       5.390  -1.334   0.000  0.00  0.00           H+0
HETATM    7  N   UNK     0       4.620   0.000   0.000  0.00  0.00           N+0
HETATM    8  C   UNK     0       3.850   1.334   0.000  0.00  0.00           C+0
HETATM    9  O   UNK     0       4.620   2.667   0.000  0.00  0.00           O+0
HETATM   10  C   UNK     0       2.310   1.334   0.000  0.00  0.00           C+0
HETATM   11  N   UNK     0       1.540   0.000   0.000  0.00  0.00           N+0
HETATM   12  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM   13  O   UNK     0      -0.770   1.334   0.000  0.00  0.00           O+0
HETATM   14  C   UNK     0      -0.770  -1.334   0.000  0.00  0.00           C+0
HETATM   15  H   UNK     0       0.770  -1.334   0.000  0.00  0.00           H+0
HETATM   16  N   UNK     0       0.000  -2.667   0.000  0.00  0.00           N+0
HETATM   17  C   UNK     0      -2.310  -1.334   0.000  0.00  0.00           C+0
HETATM   18  O   UNK     0      -3.080  -2.667   0.000  0.00  0.00           O+0
HETATM   19  C   UNK     0       6.930   1.334   0.000  0.00  0.00           C+0
HETATM   20  O   UNK     0       6.160   2.667   0.000  0.00  0.00           O+0
HETATM   21  O   UNK     0       8.470   1.334   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3    4    5                                             
CONECT    3    2                                                            
CONECT    4    2                                                            
CONECT    5    2    6    7   19                                             
CONECT    6    5                                                            
CONECT    7    5    8                                                       
CONECT    8    7    9   10                                                  
CONECT    9    8                                                            
CONECT   10    8   11                                                       
CONECT   11   10   12                                                       
CONECT   12   11   13   14                                                  
CONECT   13   12                                                            
CONECT   14   12   15   16   17                                             
CONECT   15   14                                                            
CONECT   16   14                                                            
CONECT   17   14   18                                                       
CONECT   18   17                                                            
CONECT   19    5   20   21                                                  
CONECT   20   19                                                            
CONECT   21   19                                                            
MASTER        0    0    0    0    0    0    0    0   21    0   40    0
END

View in JSmol View Stereo Labels

Synonyms

Not Available

Chemical Formula

C₉H₁₇N₃O₆

Average Molecular Weight

263.25

Monoisotopic Molecular Weight

263.111735279

IUPAC Name

(2S,3R)-2-[(2-{[(2S)-2-amino-1,3-dihydroxypropylidene]amino}-1-hydroxyethylidene)amino]-3-hydroxybutanoic acid

Traditional Name

(2S,3R)-2-[(2-{[(2S)-2-amino-1,3-dihydroxypropylidene]amino}-1-hydroxyethylidene)amino]-3-hydroxybutanoic acid

CAS Registry Number

Not Available

SMILES

[H][C@](C)(O)[C@]([H])(N=C(O)CN=C(O)[C@@]([H])(N)CO)C(O)=O

InChI Identifier

InChI=1S/C9H17N3O6/c1-4(14)7(9(17)18)12-6(15)2-11-8(16)5(10)3-13/h4-5,7,13-14H,2-3,10H2,1H3,(H,11,16)(H,12,15)(H,17,18)/t4-,5+,7+/m1/s1

InChI Key

SFTZWNJFZYOLBD-ZDLURKLDSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as oligopeptides. These are organic compounds containing a sequence of between three and ten alpha-amino acids joined by peptide bonds.

Kingdom

Organic compounds

Super Class

Organic acids and derivatives

Class

Carboxylic acids and derivatives

Sub Class

Amino acids, peptides, and analogues

Direct Parent

Oligopeptides

Alternative Parents

Substituents

Alpha-oligopeptide
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
N-substituted-alpha-amino acid
Alpha-amino acid or derivatives
Short-chain hydroxy acid
Beta-hydroxy acid
Fatty acid
Hydroxy acid
Amino acid
Amino acid or derivatives
Secondary alcohol
Carboxamide group
Secondary carboxylic acid amide
Monocarboxylic acid or derivatives
Carboxylic acid
Alcohol
Primary aliphatic amine
Organonitrogen compound
Organooxygen compound
Primary alcohol
Carbonyl group
Primary amine
Hydrocarbon derivative
Amine
Organic oxide
Organic oxygen compound
Organic nitrogen compound
Aliphatic acyclic compound

Molecular Framework

Aliphatic acyclic compounds

External Descriptors

Not Available

Ontology

Not Available

Physical Properties

State

Not Available

Experimental Molecular 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

Experimental Chromatographic Properties

Not Available

Predicted Molecular Properties

Property	Value	Source
logP	-4.8	ChemAxon
pKa (Strongest Acidic)	2.85	ChemAxon
pKa (Strongest Basic)	9.01	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	9	ChemAxon
Hydrogen Donor Count	6	ChemAxon
Polar Surface Area	168.96 Å²	ChemAxon
Rotatable Bond Count	7	ChemAxon
Refractivity	59.15 m³·mol⁻¹	ChemAxon
Polarizability	25.15 Å³	ChemAxon
Number of Rings	0	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	No	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

Predicted Chromatographic Properties

Predicted Kovats Retention Indices

Not Available

Spectra

Biological Properties

Cellular Locations

Not Available

Biospecimen Locations

Blood
Urine

Tissue Locations

Not Available

Pathways

Not Available

Name	SMPDB/PathBank	KEGG

Normal Concentrations

Biospecimen	Status	Value	Age	Sex	Condition	Reference	Details
Blood	Expected but not Quantified	Not Quantified	Not Specified	Not Specified	Normal	34436864	details
Urine	Detected but not Quantified	Not Quantified	Not Specified	Not Specified	Normal	34436864	details

Abnormal Concentrations

Not Available

Associated Disorders and Diseases

Disease References

None

Associated OMIM IDs

None

External Links

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

Not Available

KNApSAcK ID

Not Available

Chemspider ID

8140710

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

9965117

PDB ID

Not Available

ChEBI ID

163129

Food Biomarker Ontology

Not Available

VMH ID

Not Available

MarkerDB ID

Not Available

Good Scents ID

Not Available

References

Synthesis Reference

Not Available

Material Safety Data Sheet (MSDS)

Not Available

General References

Neto FC, Raftery D: Expanding Urinary Metabolite Annotation through Integrated Mass Spectral Similarity Networking. Anal Chem. 2021 Sep 7;93(35):12001-12010. doi: 10.1021/acs.analchem.1c02041. Epub 2021 Aug 26. [PubMed:34436864 ]

Showing metabocard for Ser-Gly-Thr (HMDB0341196)

MOL for HMDB0341196 (Ser-Gly-Thr)

3D MOL for HMDB0341196 (Ser-Gly-Thr)

3D SDF for HMDB0341196 (Ser-Gly-Thr)

3D-SDF for HMDB0341196 (Ser-Gly-Thr)

PDB for HMDB0341196 (Ser-Gly-Thr)

3D PDB for HMDB0341196 (Ser-Gly-Thr)

SMILES for HMDB0341196 (Ser-Gly-Thr)

INCHI for HMDB0341196 (Ser-Gly-Thr)

Structure for HMDB0341196 (Ser-Gly-Thr)

3D Structure for HMDB0341196 (Ser-Gly-Thr)

Predicted Kovats Retention Indices