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Showing metabocard for D-Threonine (HMDB0250801)

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Record Information
Version5.0
StatusDetected but not Quantified
Creation Date2021-09-11 07:54:36 UTC
Update Date2021-09-26 23:02:28 UTC
HMDB IDHMDB0250801
Secondary Accession NumbersNone
Metabolite Identification
Common NameD-Threonine
Descriptionalpha-Amino-beta-hydroxybutyric acid, also known as a-amino-b-hydroxybutyrate, 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). alpha-Amino-beta-hydroxybutyric acid has been detected, but not quantified in, peanuts (Arachis hypogaea). This could make alpha-amino-beta-hydroxybutyric acid a potential biomarker for the consumption of these foods. alpha-Amino-beta-hydroxybutyric acid is a secondary metabolite. Secondary metabolites are metabolically or physiologically non-essential metabolites that may serve a role as defense or signalling molecules. In some cases they are simply molecules that arise from the incomplete metabolism of other secondary metabolites. Based on a literature review very few articles have been published on alpha-Amino-beta-hydroxybutyric acid. This compound has been identified in human blood as reported by (PMID: 31557052 ). D-threonine is not a naturally occurring metabolite and is only found in those individuals exposed to this compound or its derivatives. Technically D-Threonine is part of the human exposome. The exposome can be defined as the collection of all the exposures of an individual in a lifetime and how those exposures relate to health. An individual's exposure begins before birth and includes insults from environmental and occupational sources.
Structure
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MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0250801 (D-Threonine)

  Mrv1652310071709022D          

  8  7  0  0  0  0            999 V2000
    1.2375    2.1434    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8250    1.4289    0.0000 C   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 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0625    0.7145    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0000    1.4289    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.2375   -0.7145    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  0  0  0  0
  3  2  1  0  0  0  0
  4  3  1  0  0  0  0
  5  3  1  0  0  0  0
  6  2  1  0  0  0  0
  7  4  2  0  0  0  0
  8  4  1  0  0  0  0
M  END
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3D MOL for HMDB0250801 (D-Threonine)

HMDB0250801
     RDKit          3D
D-Threonine
 17 16  0  0  0  0  0  0  0  0999 V2000
   -1.8721    0.0070    0.3343 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4944   -0.5185    0.0200 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4562   -1.1422   -1.1977 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.5411    0.5589    0.1928 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4496    1.6220   -0.7456 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.8669   -0.0886    0.2376 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8450    0.2336   -0.4637 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.0251   -1.1450    1.1421 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1964    0.6203   -0.5247 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8520    0.5975    1.2678 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5739   -0.8387    0.4591 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2621   -1.3017    0.7981 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3586   -1.4376   -1.4595 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3606    1.0016    1.2162 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5337    1.3636   -1.7294 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1864    2.3884   -0.5130 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.6301   -1.9207    0.9656 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  2  4  1  0
  4  5  1  0
  4  6  1  0
  6  7  2  0
  6  8  1  0
  1  9  1  0
  1 10  1  0
  1 11  1  0
  2 12  1  0
  3 13  1  0
  4 14  1  0
  5 15  1  0
  5 16  1  0
  8 17  1  0
M  END
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3D SDF for HMDB0250801 (D-Threonine)

  Mrv1652310071709022D          

  8  7  0  0  0  0            999 V2000
    1.2375    2.1434    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8250    1.4289    0.0000 C   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 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0625    0.7145    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0000    1.4289    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.2375   -0.7145    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  0  0  0  0
  3  2  1  0  0  0  0
  4  3  1  0  0  0  0
  5  3  1  0  0  0  0
  6  2  1  0  0  0  0
  7  4  2  0  0  0  0
  8  4  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0250801

> <DATABASE_NAME>
hmdb

> <SMILES>
CC(O)C(N)C(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C4H9NO3/c1-2(6)3(5)4(7)8/h2-3,6H,5H2,1H3,(H,7,8)

> <INCHI_KEY>
AYFVYJQAPQTCCC-UHFFFAOYSA-N

> <FORMULA>
C4H9NO3

> <MOLECULAR_WEIGHT>
119.1192

> <EXACT_MASS>
119.058243159

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_ATOM_COUNT>
17

> <JCHEM_AVERAGE_POLARIZABILITY>
11.213705882336926

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
2-amino-3-hydroxybutanoic acid

> <ALOGPS_LOGP>
-3.01

> <JCHEM_LOGP>
-3.4709635238772347

> <ALOGPS_LOGS>
0.60

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
14.95336930566473

> <JCHEM_PKA_STRONGEST_ACIDIC>
2.207432028688764

> <JCHEM_PKA_STRONGEST_BASIC>
9.002504827404067

> <JCHEM_POLAR_SURFACE_AREA>
83.55

> <JCHEM_REFRACTIVITY>
26.4598

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
4.77e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
threonine(L)

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for HMDB0250801 (D-Threonine)

HMDB0250801
     RDKit          3D
D-Threonine
 17 16  0  0  0  0  0  0  0  0999 V2000
   -1.8721    0.0070    0.3343 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4944   -0.5185    0.0200 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4562   -1.1422   -1.1977 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.5411    0.5589    0.1928 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4496    1.6220   -0.7456 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.8669   -0.0886    0.2376 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8450    0.2336   -0.4637 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.0251   -1.1450    1.1421 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1964    0.6203   -0.5247 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8520    0.5975    1.2678 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5739   -0.8387    0.4591 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2621   -1.3017    0.7981 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3586   -1.4376   -1.4595 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3606    1.0016    1.2162 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5337    1.3636   -1.7294 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1864    2.3884   -0.5130 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.6301   -1.9207    0.9656 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  2  4  1  0
  4  5  1  0
  4  6  1  0
  6  7  2  0
  6  8  1  0
  1  9  1  0
  1 10  1  0
  1 11  1  0
  2 12  1  0
  3 13  1  0
  4 14  1  0
  5 15  1  0
  5 16  1  0
  8 17  1  0
M  END
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PDB for HMDB0250801 (D-Threonine)

HEADER    PROTEIN                                 07-OCT-17   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   07-OCT-17         0                                  
HETATM    1  C   UNK     0       2.310   4.001   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       1.540   2.667   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       2.310   1.334   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       1.540   0.000   0.000  0.00  0.00           C+0
HETATM    5  N   UNK     0       3.850   1.334   0.000  0.00  0.00           N+0
HETATM    6  O   UNK     0      -0.000   2.667   0.000  0.00  0.00           O+0
HETATM    7  O   UNK     0       2.310  -1.334   0.000  0.00  0.00           O+0
HETATM    8  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3    6                                                  
CONECT    3    2    4    5                                                  
CONECT    4    3    7    8                                                  
CONECT    5    3                                                            
CONECT    6    2                                                            
CONECT    7    4                                                            
CONECT    8    4                                                            
MASTER        0    0    0    0    0    0    0    0    8    0   14    0
END
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3D PDB for HMDB0250801 (D-Threonine)

COMPND    HMDB0250801
HETATM    1  C1  UNL     1      -1.872   0.007   0.334  1.00  0.00           C  
HETATM    2  C2  UNL     1      -0.494  -0.518   0.020  1.00  0.00           C  
HETATM    3  O1  UNL     1      -0.456  -1.142  -1.198  1.00  0.00           O  
HETATM    4  C3  UNL     1       0.541   0.559   0.193  1.00  0.00           C  
HETATM    5  N1  UNL     1       0.450   1.622  -0.746  1.00  0.00           N  
HETATM    6  C4  UNL     1       1.867  -0.089   0.238  1.00  0.00           C  
HETATM    7  O2  UNL     1       2.845   0.234  -0.464  1.00  0.00           O  
HETATM    8  O3  UNL     1       2.025  -1.145   1.142  1.00  0.00           O  
HETATM    9  H1  UNL     1      -2.196   0.620  -0.525  1.00  0.00           H  
HETATM   10  H2  UNL     1      -1.852   0.598   1.268  1.00  0.00           H  
HETATM   11  H3  UNL     1      -2.574  -0.839   0.459  1.00  0.00           H  
HETATM   12  H4  UNL     1      -0.262  -1.302   0.798  1.00  0.00           H  
HETATM   13  H5  UNL     1      -1.359  -1.438  -1.459  1.00  0.00           H  
HETATM   14  H6  UNL     1       0.361   1.002   1.216  1.00  0.00           H  
HETATM   15  H7  UNL     1       0.534   1.364  -1.729  1.00  0.00           H  
HETATM   16  H8  UNL     1      -0.186   2.388  -0.513  1.00  0.00           H  
HETATM   17  H9  UNL     1       2.630  -1.921   0.966  1.00  0.00           H  
CONECT    1    2    9   10   11
CONECT    2    3    4   12
CONECT    3   13
CONECT    4    5    6   14
CONECT    5   15   16
CONECT    6    7    7    8
CONECT    8   17
END
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SMILES for HMDB0250801 (D-Threonine)

CC(O)C(N)C(O)=O
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INCHI for HMDB0250801 (D-Threonine)

InChI=1S/C4H9NO3/c1-2(6)3(5)4(7)8/h2-3,6H,5H2,1H3,(H,7,8)
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View in JSmolView Stereo Labels
Synonyms
ValueSource
a-Amino-b-hydroxybutyrateGenerator
a-Amino-b-hydroxybutyric acidGenerator
alpha-Amino-beta-hydroxybutyrateGenerator
Α-amino-β-hydroxybutyrateGenerator
Α-amino-β-hydroxybutyric acidGenerator
Chemical FormulaC4H9NO3
Average Molecular Weight119.1192
Monoisotopic Molecular Weight119.058243159
IUPAC Name2-amino-3-hydroxybutanoic acid
Traditional Namethreonine(L)
CAS Registry NumberNot Available
SMILES
CC(O)C(N)C(O)=O
InChI Identifier
InChI=1S/C4H9NO3/c1-2(6)3(5)4(7)8/h2-3,6H,5H2,1H3,(H,7,8)
InChI KeyAYFVYJQAPQTCCC-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).
KingdomOrganic compounds
Super ClassOrganic acids and derivatives
ClassCarboxylic acids and derivatives
Sub ClassAmino acids, peptides, and analogues
Direct ParentAlpha amino acids
Alternative Parents
Substituents
  • Alpha-amino acid
  • Beta-hydroxy acid
  • Short-chain hydroxy acid
  • Hydroxy acid
  • Fatty acid
  • Amino acid
  • Secondary alcohol
  • Carboxylic acid
  • Monocarboxylic acid or derivatives
  • Alcohol
  • Primary amine
  • Organooxygen compound
  • Organonitrogen compound
  • Hydrocarbon derivative
  • Primary aliphatic amine
  • Organic oxide
  • Organopnictogen compound
  • Carbonyl group
  • Organic oxygen compound
  • Amine
  • Organic nitrogen compound
  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic compounds
External Descriptors
Ontology
Physiological effectNot Available
Disposition
Biological locationSource
ProcessNot Available
RoleNot Available
Physical Properties
StateNot Available
Experimental Molecular Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
Predicted Chromatographic Properties
Spectra
Biological Properties
Cellular LocationsNot Available
Biospecimen Locations
  • Blood
Tissue LocationsNot Available
Pathways
Normal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
BloodDetected but not QuantifiedNot QuantifiedNot SpecifiedNot SpecifiedNormal details
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDFDB004013
KNApSAcK IDNot Available
Chemspider ID200
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound205
PDB IDNot Available
ChEBI ID38263
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDNot Available
Good Scents IDNot Available
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Not Available
General References
  1. Barupal DK, Fiehn O: Generating the Blood Exposome Database Using a Comprehensive Text Mining and Database Fusion Approach. Environ Health Perspect. 2019 Sep;127(9):97008. doi: 10.1289/EHP4713. Epub 2019 Sep 26. [PubMed:31557052 ]