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Showing NP-Card for L-Homoserine (NP0000715)

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Record Information
Version2.0
Created at2005-11-16 15:48:42 UTC
Updated at2021-08-19 23:58:23 UTC
NP-MRD IDNP0000715
Secondary Accession NumbersNone
Natural Product Identification
Common NameL-Homoserine
DescriptionHomoserine is a more reactive variant of the amino acid serine. In this variant, the hydroxyl side chain contains an additional CH2 group which brings the hydroxyl group closer to its own carboxyl group, allowing it to chemically react to form a five-membered ring. This occurs at the point that amino acids normally join to their neighbours in a peptide bond. Homoserine is therefore unsuitable for forming proteins and has been eliminated from the repertoire of amino acids used by living things. Homoserine is the final product on the C-terminal end of the N-terminal fragment following a cyanogen bromide cleavage. (Wikipedia).
Structure
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MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for NP0000715 (L-Homoserine)


  Mrv1652309042000062D          

  8  7  0  0  1  0            999 V2000
    1.9520    1.9520    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.9520    1.1270    0.0000 C   0  0  1  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
    0.5230    1.1270    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1914    0.7145    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.6664    0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3809    1.1270    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.6664   -0.1105    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
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  2  6  1  0  0  0  0
  6  7  1  0  0  0  0
  6  8  2  0  0  0  0
M  END
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3D MOL for NP0000715 (L-Homoserine)

HMDB0000719
     RDKit          3D
L-Homoserine
 17 16  0  0  0  0  0  0  0  0999 V2000
   -1.5027    1.3775   -0.2642 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6651    0.2448   -0.6080 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.7316    0.4466   -0.1212 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6854   -0.6504   -0.4150 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9530   -0.3506    0.0855 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3218   -0.9768   -0.1869 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8478   -2.1255   -0.3475 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5541   -0.9328    0.4384 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3720    1.0996    0.2471 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9580    2.0130    0.3695 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6055    0.2668   -1.7390 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1610    1.3917   -0.5153 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6859    0.5784    0.9847 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4135   -1.6355   -0.0287 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8315   -0.7809   -1.5264 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.0045    0.6473    0.2037 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6395   -0.6131    1.4103 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
  2  6  1  0
  6  7  2  0
  6  8  1  0
  1  9  1  0
  1 10  1  0
  2 11  1  6
  3 12  1  0
  3 13  1  0
  4 14  1  0
  4 15  1  0
  5 16  1  0
  8 17  1  0
M  END
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3D SDF for NP0000715 (L-Homoserine)


  Mrv1652309042000062D          

  8  7  0  0  1  0            999 V2000
    1.9520    1.9520    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.9520    1.1270    0.0000 C   0  0  1  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
    0.5230    1.1270    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1914    0.7145    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.6664    0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3809    1.1270    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.6664   -0.1105    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
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  2  6  1  0  0  0  0
  6  7  1  0  0  0  0
  6  8  2  0  0  0  0
M  END
> <DATABASE_ID>
NP0000715

> <DATABASE_NAME>
NP-MRD

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

> <INCHI_IDENTIFIER>
InChI=1S/C4H9NO3/c5-3(1-2-6)4(7)8/h3,6H,1-2,5H2,(H,7,8)/t3-/m0/s1

> <INCHI_KEY>
UKAUYVFTDYCKQA-VKHMYHEASA-N

> <FORMULA>
C4H9NO3

> <MOLECULAR_WEIGHT>
119.1192

> <EXACT_MASS>
119.058243159

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_ATOM_COUNT>
17

> <JCHEM_AVERAGE_POLARIZABILITY>
11.439148714602187

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2S)-2-amino-4-hydroxybutanoic acid

> <ALOGPS_LOGP>
-3.31

> <JCHEM_LOGP>
-3.8277325124850385

> <ALOGPS_LOGS>
0.55

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
15.933083327320805

> <JCHEM_PKA_STRONGEST_ACIDIC>
2.223319649729163

> <JCHEM_PKA_STRONGEST_BASIC>
9.159110100742131

> <JCHEM_POLAR_SURFACE_AREA>
83.55000000000001

> <JCHEM_REFRACTIVITY>
26.906399999999998

> <JCHEM_ROTATABLE_BOND_COUNT>
3

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
4.23e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
L-homoserine

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for NP0000715 (L-Homoserine)

HMDB0000719
     RDKit          3D
L-Homoserine
 17 16  0  0  0  0  0  0  0  0999 V2000
   -1.5027    1.3775   -0.2642 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6651    0.2448   -0.6080 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.7316    0.4466   -0.1212 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6854   -0.6504   -0.4150 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9530   -0.3506    0.0855 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3218   -0.9768   -0.1869 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8478   -2.1255   -0.3475 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5541   -0.9328    0.4384 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3720    1.0996    0.2471 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9580    2.0130    0.3695 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6055    0.2668   -1.7390 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1610    1.3917   -0.5153 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6859    0.5784    0.9847 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4135   -1.6355   -0.0287 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8315   -0.7809   -1.5264 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.0045    0.6473    0.2037 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6395   -0.6131    1.4103 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
  2  6  1  0
  6  7  2  0
  6  8  1  0
  1  9  1  0
  1 10  1  0
  2 11  1  6
  3 12  1  0
  3 13  1  0
  4 14  1  0
  4 15  1  0
  5 16  1  0
  8 17  1  0
M  END
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PDB for NP0000715 (L-Homoserine)

HEADER    PROTEIN                                 04-SEP-20   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   04-SEP-20         0                                  
HETATM    1  N   UNK     0       3.644   3.644   0.000  0.00  0.00           N+0
HETATM    2  C   UNK     0       3.644   2.104   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       0.976   2.104   0.000  0.00  0.00           C+0
HETATM    5  O   UNK     0      -0.357   1.334   0.000  0.00  0.00           O+0
HETATM    6  C   UNK     0       4.977   1.334   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0       6.311   2.104   0.000  0.00  0.00           O+0
HETATM    8  O   UNK     0       4.977  -0.206   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3    6                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4                                                            
CONECT    6    2    7    8                                                  
CONECT    7    6                                                            
CONECT    8    6                                                            
MASTER        0    0    0    0    0    0    0    0    8    0   14    0
END
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3D PDB for NP0000715 (L-Homoserine)

COMPND    HMDB0000719
HETATM    1  N1  UNL     1      -1.503   1.378  -0.264  1.00  0.00           N  
HETATM    2  C1  UNL     1      -0.665   0.245  -0.608  1.00  0.00           C  
HETATM    3  C2  UNL     1       0.732   0.447  -0.121  1.00  0.00           C  
HETATM    4  C3  UNL     1       1.685  -0.650  -0.415  1.00  0.00           C  
HETATM    5  O1  UNL     1       2.953  -0.351   0.086  1.00  0.00           O  
HETATM    6  C4  UNL     1      -1.322  -0.977  -0.187  1.00  0.00           C  
HETATM    7  O2  UNL     1      -0.848  -2.126  -0.347  1.00  0.00           O  
HETATM    8  O3  UNL     1      -2.554  -0.933   0.438  1.00  0.00           O  
HETATM    9  H1  UNL     1      -2.372   1.100   0.247  1.00  0.00           H  
HETATM   10  H2  UNL     1      -0.958   2.013   0.369  1.00  0.00           H  
HETATM   11  H3  UNL     1      -0.606   0.267  -1.739  1.00  0.00           H  
HETATM   12  H4  UNL     1       1.161   1.392  -0.515  1.00  0.00           H  
HETATM   13  H5  UNL     1       0.686   0.578   0.985  1.00  0.00           H  
HETATM   14  H6  UNL     1       1.414  -1.635  -0.029  1.00  0.00           H  
HETATM   15  H7  UNL     1       1.831  -0.781  -1.526  1.00  0.00           H  
HETATM   16  H8  UNL     1       3.005   0.647   0.204  1.00  0.00           H  
HETATM   17  H9  UNL     1      -2.640  -0.613   1.410  1.00  0.00           H  
CONECT    1    2    9   10
CONECT    2    3    6   11
CONECT    3    4   12   13
CONECT    4    5   14   15
CONECT    5   16
CONECT    6    7    7    8
CONECT    8   17
END
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SMILES for NP0000715 (L-Homoserine)

N[C@@H](CCO)C(O)=O
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INCHI for NP0000715 (L-Homoserine)

InChI=1S/C4H9NO3/c5-3(1-2-6)4(7)8/h3,6H,1-2,5H2,(H,7,8)/t3-/m0/s1
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View in JSmol
Synonyms
ValueSource
(2S)-2-Amino-4-hydroxybutanoic acidChEBI
2-Amino-4-hydroxybutanoic acidChEBI
2-Amino-4-hydroxybutyric acidChEBI
HomoserineChEBI
(2S)-2-Amino-4-hydroxybutanoateGenerator
2-Amino-4-hydroxybutanoateGenerator
2-Amino-4-hydroxybutyrateGenerator
(S)-2-Amino-4-hydroxy-butanoateHMDB
(S)-2-Amino-4-hydroxy-butanoic acidHMDB
(S)-2-Amino-4-hydroxybutanoateHMDB
(S)-2-Amino-4-hydroxybutanoic acidHMDB
(S)-HomoserineHMDB
2-Amino-4-hydroxy-butyrateHMDB
2-Amino-4-hydroxy-butyric acidHMDB
2-Amino-4-hydroxy-L-butyrateHMDB
2-Amino-4-hydroxy-L-butyric acidHMDB
Homoserine L-isomerHMDB
L Isomer OF homoserineHMDB
L-Isomer OF homoserineHMDB
Chemical FormulaC4H9NO3
Average Mass119.1192 Da
Monoisotopic Mass119.05824 Da
IUPAC Name(2S)-2-amino-4-hydroxybutanoic acid
Traditional NameL-homoserine
CAS Registry Number672-15-1
SMILES
N[C@@H](CCO)C(O)=O
InChI Identifier
InChI=1S/C4H9NO3/c5-3(1-2-6)4(7)8/h3,6H,1-2,5H2,(H,7,8)/t3-/m0/s1
InChI KeyUKAUYVFTDYCKQA-VKHMYHEASA-N
Experimental Spectra
Spectrum TypeDescriptionDepositor EmailDepositor OrganizationDepositorDeposition DateView
1D NMR1H NMR Spectrum (1D, 500 MHz, H2O, experimental)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
2D NMR[1H, 13C]-HSQC NMR Spectrum (2D, 600 MHz, H2O, experimental)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
Predicted Spectra
Not Available
Chemical Shift Submissions
Spectrum TypeDescriptionDepositor EmailDepositor OrganizationDepositorDeposition DateView
1D NMR13C NMR Spectrum (1D, 400 MHz, H2O, simulated)v.dorna83@yahoo.comNot AvailableNot Available2021-08-07View Spectrum
Species
Species of Origin
Species NameSourceReference
Arabidopsis thalianaKNApSAcK Database
Cannabis sativaCannabisDB
      Not Available
Chlamydomonas reinhardtiiLOTUS Database
Coffea arabica L.FooDB
    • Shmuel Yannai Dictionary of Food Compounds with CD-ROM: Additives, Flavors, and Ingredients. Chap...
Coffea canephoraFooDB
    • Shmuel Yannai Dictionary of Food Compounds with CD-ROM: Additives, Flavors, and Ingredients. Chap...
Lathyrus latifoliusLOTUS Database
Lotus corniculatusLOTUS Database
Lotus uliginosusLOTUS Database
Pisum sativumKNApSAcK Database
Salmonella entericaLOTUS Database
Thalassiosira pseudonanaLOTUS Database
Trypanosoma bruceiLOTUS Database
Species Where Detected
Species NameSourceReference
Escherichia coli K12KNApSAcK Database
Chemical Taxonomy
Description Belongs to the class of organic compounds known as l-alpha-amino acids. These are alpha amino acids which have the L-configuration of the alpha-carbon atom.
KingdomOrganic compounds
Super ClassOrganic acids and derivatives
ClassCarboxylic acids and derivatives
Sub ClassAmino acids, peptides, and analogues
Direct ParentL-alpha-amino acids
Alternative Parents
Substituents
  • L-alpha-amino acid
  • Short-chain hydroxy acid
  • Fatty acid
  • 1,3-aminoalcohol
  • Amino acid
  • Carboxylic acid
  • Monocarboxylic acid or derivatives
  • Organic nitrogen compound
  • Hydrocarbon derivative
  • Organic oxide
  • Primary amine
  • Primary alcohol
  • Organooxygen compound
  • Organonitrogen compound
  • Organopnictogen compound
  • Primary aliphatic amine
  • Organic oxygen compound
  • Carbonyl group
  • Amine
  • Alcohol
  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic compounds
External Descriptors
Physical Properties
StateSolid
Experimental Properties
PropertyValueReference
Melting Point203 °CNot Available
Boiling Point368.72 °C. @ 760.00 mm Hg (est)The Good Scents Company Information System
Water Solubility1000 mg/mLNot Available
LogP-1.289 (est)The Good Scents Company Information System
Predicted Properties
PropertyValueSource
Water Solubility423 g/LALOGPS
logP-3.3ALOGPS
logP-3.8ChemAxon
logS0.55ALOGPS
pKa (Strongest Acidic)2.22ChemAxon
pKa (Strongest Basic)9.16ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count4ChemAxon
Hydrogen Donor Count3ChemAxon
Polar Surface Area83.55 ŲChemAxon
Rotatable Bond Count3ChemAxon
Refractivity26.91 m³·mol⁻¹ChemAxon
Polarizability11.44 ųChemAxon
Number of Rings0ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
HMDB IDHMDB0000719
DrugBank IDDB04193
Phenol Explorer Compound IDNot Available
FoodDB IDFDB006683
KNApSAcK IDC00001366
Chemspider ID12126
KEGG Compound IDC00263
BioCyc IDHOMO-SER
BiGG ID34437
Wikipedia LinkHomoserine
METLIN ID5687
PubChem Compound12647
PDB IDNot Available
ChEBI ID15699
Good Scents IDrw1253711
References
General References
  1. Gazarian KG, Gening LV, Gazarian TG: L-Homoserine: a novel excreted metabolic marker of hepatitis B abnormally produced in liver from methionine. Med Hypotheses. 2002 Apr;58(4):279-83. [PubMed:12027520 ]
  2. Compagnini A, Cunsolo V, Foti S, Saletti R: Improved accuracy in the matrix-assisted laser desorption/ionization-mass spectrometry determination of the molecular mass of cyanogen bromide fragments of proteins by post-cleavage reaction with tris(hydroxymethyl)aminomethane. Proteomics. 2001 Aug;1(8):967-74. [PubMed:11683513 ]