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Showing NP-Card for 2-hydroxymethylserine (NP0279439)

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Record Information
Version2.0
Created at2022-09-09 04:50:10 UTC
Updated at2022-09-09 04:50:10 UTC
NP-MRD IDNP0279439
Secondary Accession NumbersNone
Natural Product Identification
Common Name2-hydroxymethylserine
DescriptionAlpha-(hydroxymethyl)serine 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. 2-hydroxymethylserine is found in Vicia pseudo-orobus. 2-hydroxymethylserine was first documented in 1962 (PMID: 14021091). Alpha-(hydroxymethyl)serine is a very strong basic compound (based on its pKa) (PMID: 18646253) (PMID: 24314397) (PMID: 6669377) (PMID: 9523755).
Structure
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MOL3D MOLSDFPDBSMILESInChI

MOL for NP0279439 (2-hydroxymethylserine)


  Mrv1533004161518402D          

  9  8  0  0  0  0            999 V2000
    1.6500   -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
    1.9520   -0.3020    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9520    0.5230    0.0000 O   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
    0.5230   -1.9520    0.0000 O   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
    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
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  2  5  1  0  0  0  0
  5  6  1  0  0  0  0
  2  7  1  0  0  0  0
  7  8  2  0  0  0  0
  7  9  1  0  0  0  0
M  END
Download

3D MOL for NP0279439 (2-hydroxymethylserine)

     RDKit          3D

 18 17  0  0  0  0  0  0  0  0999 V2000
   -0.8555    0.8533   -1.0847 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0191    0.0370   -0.2000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4341   -1.4053   -0.4560 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7808   -1.5983   -0.1702 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3398    0.4404    1.2042 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0798    1.7727    1.4263 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.3762    0.2846   -0.5914 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7171    1.0660   -1.5235 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.4155   -0.3621    0.0816 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6365    0.6086   -2.0890 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5587    1.8485   -0.9791 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2937   -1.6834   -1.5190 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2063   -2.1084    0.1355 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9358   -2.1592    0.6182 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4216    0.2373    1.3677 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2054   -0.1780    1.9560 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8876    2.2816    1.5975 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.3225    0.0647    0.2258 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
  2  5  1  0
  5  6  1  0
  2  7  1  0
  7  9  1  0
  7  8  2  0
  1 10  1  0
  1 11  1  0
  3 12  1  0
  3 13  1  0
  4 14  1  0
  5 15  1  0
  5 16  1  0
  6 17  1  0
  9 18  1  0
M  END
Download

3D SDF for NP0279439 (2-hydroxymethylserine)


  Mrv1533004161518402D          

  9  8  0  0  0  0            999 V2000
    1.6500   -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
    1.9520   -0.3020    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9520    0.5230    0.0000 O   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
    0.5230   -1.9520    0.0000 O   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
    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
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  2  5  1  0  0  0  0
  5  6  1  0  0  0  0
  2  7  1  0  0  0  0
  7  8  2  0  0  0  0
  7  9  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0279439

> <DATABASE_NAME>
NP-MRD

> <SMILES>
NC(CO)(CO)C(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C4H9NO4/c5-4(1-6,2-7)3(8)9/h6-7H,1-2,5H2,(H,8,9)

> <INCHI_KEY>
ZRPDXDBGEYHEBJ-UHFFFAOYSA-N

> <FORMULA>
C4H9NO4

> <MOLECULAR_WEIGHT>
135.119

> <EXACT_MASS>
135.053157774

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_ATOM_COUNT>
18

> <JCHEM_AVERAGE_POLARIZABILITY>
12.097160199016253

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
2-amino-3-hydroxy-2-(hydroxymethyl)propanoic acid

> <ALOGPS_LOGP>
-3.26

> <JCHEM_LOGP>
-4.501621082748541

> <ALOGPS_LOGS>
0.56

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
14.442160405901365

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.8651612862760043

> <JCHEM_PKA_STRONGEST_BASIC>
8.660437614857479

> <JCHEM_POLAR_SURFACE_AREA>
103.78000000000002

> <JCHEM_REFRACTIVITY>
28.298000000000002

> <JCHEM_ROTATABLE_BOND_COUNT>
3

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
4.93e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
2-hydroxymethylserine

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for NP0279439 (2-hydroxymethylserine)

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PDB for NP0279439 (2-hydroxymethylserine)
HEADER    PROTEIN                                 16-APR-15   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   16-APR-15         0                                  
HETATM    1  N   UNK     0       3.080  -2.667   0.000  0.00  0.00           N+0
HETATM    2  C   UNK     0       2.310  -1.334   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       3.644  -0.564   0.000  0.00  0.00           C+0
HETATM    4  O   UNK     0       3.644   0.976   0.000  0.00  0.00           O+0
HETATM    5  C   UNK     0       0.976  -2.104   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0       0.976  -3.644   0.000  0.00  0.00           O+0
HETATM    7  C   UNK     0       1.540   0.000   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0       2.310   1.334   0.000  0.00  0.00           O+0
HETATM    9  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3    5    7                                             
CONECT    3    2    4                                                       
CONECT    4    3                                                            
CONECT    5    2    6                                                       
CONECT    6    5                                                            
CONECT    7    2    8    9                                                  
CONECT    8    7                                                            
CONECT    9    7                                                            
MASTER        0    0    0    0    0    0    0    0    9    0   16    0
END

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3D PDB for NP0279439 (2-hydroxymethylserine)
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SMILES for NP0279439 (2-hydroxymethylserine)
NC(CO)(CO)C(O)=O
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INCHI for NP0279439 (2-hydroxymethylserine)
InChI=1S/C4H9NO4/c5-4(1-6,2-7)3(8)9/h6-7H,1-2,5H2,(H,8,9)
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Synonyms
ValueSource
(Hydroxymethyl)serineChEBI
2-HydroxymethylserineChEBI
HydroxymethylserineChEBI
a-(Hydroxymethyl)serineGenerator
Α-(hydroxymethyl)serineGenerator
Chemical FormulaC4H9NO4
Average Mass135.1190 Da
Monoisotopic Mass135.05316 Da
IUPAC Name2-amino-3-hydroxy-2-(hydroxymethyl)propanoic acid
Traditional Name2-hydroxymethylserine
CAS Registry NumberNot Available
SMILES
NC(CO)(CO)C(O)=O
InChI Identifier
InChI=1S/C4H9NO4/c5-4(1-6,2-7)3(8)9/h6-7H,1-2,5H2,(H,8,9)
InChI KeyZRPDXDBGEYHEBJ-UHFFFAOYSA-N
Experimental Spectra
Not Available
Predicted Spectra
Spectrum TypeDescriptionDepositor IDDepositor OrganizationDepositorDeposition DateView
1D NMR13C NMR Spectrum (1D, 25 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 100 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 252 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 1000 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 50 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 200 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 75 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 300 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 101 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 400 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 126 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 500 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 151 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 600 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 176 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 700 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 201 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 800 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 226 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 900 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
Chemical Shift Submissions
Not Available
Species
Species of Origin
Species NameSourceReference
Vicia pseudo-orobusLOTUS 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
  • D-alpha-amino acid
    • 

  • L-alpha-amino acid
    • 

  • Beta-hydroxy acid
    • 

  • Hydroxy acid
    • 

  • Amino acid
    • 

  • Carboxylic acid
    • 

  • Monocarboxylic acid or derivatives
    • 

  • Alcohol
    • 

  • Hydrocarbon derivative
    • 

  • Primary amine
    • 

  • Primary alcohol
    • 

  • Organooxygen compound
    • 

  • Organonitrogen compound
    • 

  • Organic oxide
    • 

  • Primary aliphatic amine
    • 

  • Organopnictogen compound
    • 

  • Organic oxygen compound
    • 

  • Carbonyl group
    • 

  • Organic nitrogen compound
    • 

  • Amine
    • 

  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic compounds
External Descriptors
Physical Properties
StateNot Available
Experimental Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Predicted Properties
PropertyValueSource
logP-3.3ALOGPS
logP-4.5ChemAxon
logS0.56ALOGPS
pKa (Strongest Acidic)1.87ChemAxon
pKa (Strongest Basic)8.66ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count5ChemAxon
Hydrogen Donor Count4ChemAxon
Polar Surface Area103.78 ŲChemAxon
Rotatable Bond Count3ChemAxon
Refractivity28.3 m³·mol⁻¹ChemAxon
Polarizability12.1 ųChemAxon
Number of Rings0ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
HMDB IDNot Available
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FoodDB IDNot Available
KNApSAcK IDNot Available
Chemspider IDNot Available
KEGG Compound IDC03059  
BioCyc IDOH-CH3-SER  
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound439893  
PDB IDNot Available
ChEBI ID28187  
Good Scents IDNot Available
References
General References
  1. CHRISTENSEN HN, CLIFFORD J: Test for metabolic attack on tris(hydroxymethyl)aminomethane and alpha-hydroxymethylserine in the rat. Proc Soc Exp Biol Med. 1962 Oct;111:140-3. doi: 10.3181/00379727-111-27728. [PubMed:14021091  ] 
  2. Stasiak M, Slomczynska U, Olma A, Leplawy MT: Chemistry of alpha-hydroxymethylserine: problems and solutions. J Pept Sci. 2008 Nov;14(11):1163-72. doi: 10.1002/psc.1054. [PubMed:18646253  ] 
  3. Harty M, Nagar M, Atkinson L, Legay CM, Derksen DJ, Bearne SL: Inhibition of serine and proline racemases by substrate-product analogues. Bioorg Med Chem Lett. 2014 Jan 1;24(1):390-3. doi: 10.1016/j.bmcl.2013.10.061.  Epub 2013 Nov 4. [PubMed:24314397  ] 
  4. Ivanov CP, Ivanov OC: A study of the interaction of glycine and its oligohomopeptides with formaldehyde and acetaldehyde under possible primitive earth conditions. Orig Life. 1983 Dec;13(2):97-108. doi: 10.1007/BF00928887. [PubMed:6669377  ] 
  5. Stasiak M, Wolf WM, Leplawy MT: Alpha-hydroxymethylserine as a peptide building block: synthetic and structural aspects. J Pept Sci. 1998 Feb;4(1):46-57. doi:  10.1002/(SICI)1099-1387(199802)4:1%3C46::AID-PSC128%3E3.0.CO;2-L. [PubMed:9523755  ] 
  6. LOTUS database [Link]