Np mrd loader

Showing NP-Card for (2s)-2-[(2-amino-1-hydroxyethylidene)amino]-3-hydroxypropanoic acid (NP0212770)

Jump To Section:
IdentificationSpectraBioTaxonomyChemoTaxonomyPhysical propertiesLinksReferencesXML
Record Information
Version2.0
Created at2022-09-05 11:32:14 UTC
Updated at2022-09-05 11:32:14 UTC
NP-MRD IDNP0212770
Secondary Accession NumbersNone
Natural Product Identification
Common Name(2s)-2-[(2-amino-1-hydroxyethylidene)amino]-3-hydroxypropanoic acid
DescriptionGly-Ser, also known as G-S or gly-L-ser, belongs to the class of organic compounds known as peptides. Peptides are compounds containing an amide derived from two or more amino carboxylic acid molecules (the same or different) by formation of a covalent bond from the carbonyl carbon of one to the nitrogen atom of another. Gly-Ser 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. (2s)-2-[(2-amino-1-hydroxyethylidene)amino]-3-hydroxypropanoic acid is found in Trypanosoma brucei. (2s)-2-[(2-amino-1-hydroxyethylidene)amino]-3-hydroxypropanoic acid was first documented in 2022 (PMID: 35969667). Based on a literature review a small amount of articles have been published on Gly-Ser (PMID: 35407334) (PMID: 35260726) (PMID: 35788005).
Structure
Thumb
MOL3D MOLSDFPDBSMILESInChI

MOL for NP0212770 ((2s)-2-[(2-amino-1-hydroxyethylidene)amino]-3-hydroxypropanoic acid)


  Mrv1652309052213322D          

 11 10  0  0  1  0            999 V2000
    2.0625    0.7145    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
    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 N   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
   -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
    0.0000   -1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4125   -2.1434    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.8250   -1.4289    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  4  0  0  0
  3  5  2  0  0  0  0
  6  5  1  6  0  0  0
  6  7  1  0  0  0  0
  7  8  1  0  0  0  0
  6  9  1  0  0  0  0
  9 10  2  0  0  0  0
  9 11  1  0  0  0  0
M  END
Download

3D MOL for NP0212770 ((2s)-2-[(2-amino-1-hydroxyethylidene)amino]-3-hydroxypropanoic acid)

     RDKit          3D

 21 20  0  0  0  0  0  0  0  0999 V2000
    3.3966   -0.5246   -0.0200 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.2868   -0.4057   -0.9483 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0984    0.2388   -0.3029 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2506    1.5181    0.1982 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0185   -0.4285   -0.2535 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2138    0.0119    0.3181 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.9383    0.9010   -0.6760 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1561    1.3333   -0.1062 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0811   -1.1007    0.7716 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1862   -0.8197    1.2888 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7196   -2.4250    0.6464 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.0307   -0.7818    0.9299 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.9187    0.3614   -0.0260 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0603   -1.4160   -1.3162 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.6533    0.2372   -1.7876 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7132    1.6698    1.0849 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9757    0.6651    1.2002 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1005    0.3843   -1.6416 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3618    1.8236   -0.8655 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9450    1.4670    0.8659 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7490   -2.7094    0.6400 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
  3  5  2  0
  5  6  1  0
  6  7  1  0
  7  8  1  0
  6  9  1  0
  9 11  1  0
  9 10  2  0
  1 12  1  0
  1 13  1  0
  2 14  1  0
  2 15  1  0
  4 16  1  0
  6 17  1  1
  7 18  1  0
  7 19  1  0
  8 20  1  0
 11 21  1  0
M  END
Download

3D SDF for NP0212770 ((2s)-2-[(2-amino-1-hydroxyethylidene)amino]-3-hydroxypropanoic acid)


  Mrv1652309052213322D          

 11 10  0  0  1  0            999 V2000
    2.0625    0.7145    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
    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 N   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
   -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
    0.0000   -1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4125   -2.1434    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.8250   -1.4289    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  4  0  0  0
  3  5  2  0  0  0  0
  6  5  1  6  0  0  0
  6  7  1  0  0  0  0
  7  8  1  0  0  0  0
  6  9  1  0  0  0  0
  9 10  2  0  0  0  0
  9 11  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0212770

> <DATABASE_NAME>
NP-MRD

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

> <INCHI_IDENTIFIER>
InChI=1S/C5H10N2O4/c6-1-4(9)7-3(2-8)5(10)11/h3,8H,1-2,6H2,(H,7,9)(H,10,11)/t3-/m0/s1

> <INCHI_KEY>
BCCRXDTUTZHDEU-VKHMYHEASA-N

> <FORMULA>
C5H10N2O4

> <MOLECULAR_WEIGHT>
162.145

> <EXACT_MASS>
162.06405681

> <JCHEM_ACCEPTOR_COUNT>
6

> <JCHEM_ATOM_COUNT>
21

> <JCHEM_AVERAGE_POLARIZABILITY>
14.863988396203588

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2S)-2-[(2-amino-1-hydroxyethylidene)amino]-3-hydroxypropanoic acid

> <JCHEM_LOGP>
-4.470235385576427

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
4.060964383388095

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.2370041340756477

> <JCHEM_PKA_STRONGEST_BASIC>
9.33426191509402

> <JCHEM_POLAR_SURFACE_AREA>
116.14

> <JCHEM_REFRACTIVITY>
35.3662

> <JCHEM_ROTATABLE_BOND_COUNT>
4

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
(2S)-2-[(2-amino-1-hydroxyethylidene)amino]-3-hydroxypropanoic acid

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for NP0212770 ((2s)-2-[(2-amino-1-hydroxyethylidene)amino]-3-hydroxypropanoic acid)

Download
PDB for NP0212770 ((2s)-2-[(2-amino-1-hydroxyethylidene)amino]-3-hydroxypropanoic acid)
HEADER    PROTEIN                                 05-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   05-SEP-22         0                                  
HETATM    1  N   UNK     0       3.850   1.334   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       1.540   0.000   0.000  0.00  0.00           C+0
HETATM    4  O   UNK     0       2.310  -1.334   0.000  0.00  0.00           O+0
HETATM    5  N   UNK     0       0.000   0.000   0.000  0.00  0.00           N+0
HETATM    6  C   UNK     0      -0.770  -1.334   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      -2.310  -1.334   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0      -3.080  -2.667   0.000  0.00  0.00           O+0
HETATM    9  C   UNK     0       0.000  -2.667   0.000  0.00  0.00           C+0
HETATM   10  O   UNK     0      -0.770  -4.001   0.000  0.00  0.00           O+0
HETATM   11  O   UNK     0       1.540  -2.667   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4    5                                                  
CONECT    4    3                                                            
CONECT    5    3    6                                                       
CONECT    6    5    7    9                                                  
CONECT    7    6    8                                                       
CONECT    8    7                                                            
CONECT    9    6   10   11                                                  
CONECT   10    9                                                            
CONECT   11    9                                                            
MASTER        0    0    0    0    0    0    0    0   11    0   20    0
END

Download
3D PDB for NP0212770 ((2s)-2-[(2-amino-1-hydroxyethylidene)amino]-3-hydroxypropanoic acid)
Download
SMILES for NP0212770 ((2s)-2-[(2-amino-1-hydroxyethylidene)amino]-3-hydroxypropanoic acid)
NCC(O)=N[C@@H](CO)C(O)=O
Download
INCHI for NP0212770 ((2s)-2-[(2-amino-1-hydroxyethylidene)amino]-3-hydroxypropanoic acid)
InChI=1S/C5H10N2O4/c6-1-4(9)7-3(2-8)5(10)11/h3,8H,1-2,6H2,(H,7,9)(H,10,11)/t3-/m0/s1
Download
View in JSmol
Synonyms
ValueSource
G-SChEBI
Gly-L-serChEBI
GSChEBI
Chemical FormulaC5H10N2O4
Average Mass162.1450 Da
Monoisotopic Mass162.06406 Da
IUPAC Name(2S)-2-[(2-amino-1-hydroxyethylidene)amino]-3-hydroxypropanoic acid
Traditional Name(2S)-2-[(2-amino-1-hydroxyethylidene)amino]-3-hydroxypropanoic acid
CAS Registry NumberNot Available
SMILES
NCC(O)=N[C@@H](CO)C(O)=O
InChI Identifier
InChI=1S/C5H10N2O4/c6-1-4(9)7-3(2-8)5(10)11/h3,8H,1-2,6H2,(H,7,9)(H,10,11)/t3-/m0/s1
InChI KeyBCCRXDTUTZHDEU-VKHMYHEASA-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
Trypanosoma bruceiLOTUS Database
Chemical Taxonomy
Description Belongs to the class of organic compounds known as peptides. Peptides are compounds containing an amide derived from two or more amino carboxylic acid molecules (the same or different) by formation of a covalent bond from the carbonyl carbon of one to the nitrogen atom of another.
KingdomOrganic compounds  
Super ClassOrganic acids and derivatives  
ClassCarboxylic acids and derivatives  
Sub ClassAmino acids, peptides, and analogues  
Direct ParentPeptides  
Alternative Parents
Substituents
  • Alpha peptide
    • 

  • N-acyl-alpha-amino acid
    • 

  • N-acyl-alpha amino acid or derivatives
    • 

  • Serine or derivatives
    • 

  • Alpha-amino acid or derivatives
    • 

  • Beta-hydroxy acid
    • 

  • Hydroxy acid
    • 

  • Amino acid or derivatives
    • 

  • Amino acid
    • 

  • Carboximidic acid
    • 

  • Carboximidic acid derivative
    • 

  • Carboxylic acid
    • 

  • Monocarboxylic acid or derivatives
    • 

  • Organic 1,3-dipolar compound
    • 

  • Propargyl-type 1,3-dipolar organic compound
    • 

  • Hydrocarbon derivative
    • 

  • Amine
    • 

  • Primary aliphatic amine
    • 

  • Organic oxide
    • 

  • Organic nitrogen compound
    • 

  • Alcohol
    • 

  • Carbonyl group
    • 

  • Organic oxygen compound
    • 

  • Organonitrogen compound
    • 

  • Organooxygen compound
    • 

  • Organopnictogen compound
    • 

  • Primary alcohol
    • 

  • Primary 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-4.5ChemAxon
pKa (Strongest Acidic)3.24ChemAxon
pKa (Strongest Basic)9.33ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count6ChemAxon
Hydrogen Donor Count4ChemAxon
Polar Surface Area116.14 ŲChemAxon
Rotatable Bond Count4ChemAxon
Refractivity35.37 m³·mol⁻¹ChemAxon
Polarizability14.86 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 ID65873  
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound73086  
PDB IDNot Available
ChEBI ID73516  
Good Scents IDNot Available
References
General References
  1. Hojo K, Manabe Y, Uda T, Tsuda Y: Water-Based Solid-Phase Peptide Synthesis without Hydroxy Side Chain Protection. J Org Chem. 2022 Sep 2;87(17):11362-11368. doi: 10.1021/acs.joc.2c00828. Epub 2022 Aug 15. [PubMed:35969667  ] 
  2. Schieber R, Mas-Moruno C, Lasserre F, Roa JJ, Ginebra MP, Mucklich F, Pegueroles M: Effectiveness of Direct Laser Interference Patterning and Peptide Immobilization on Endothelial Cell Migration for Cardio-Vascular Applications: An In Vitro Study. Nanomaterials (Basel). 2022 Apr 5;12(7). pii: nano12071217. doi: 10.3390/nano12071217. [PubMed:35407334  ] 
  3. Alharthi S, Ali A, Iqbal M, Ibrar A, Ahmad B, Nisa S, Mabood F: Preparation of mixed-mode stationary phase for separation of peptides and proteins in high performance liquid chromatography. Sci Rep. 2022 Mar 8;12(1):4061. doi: 10.1038/s41598-022-08074-7. [PubMed:35260726  ] 
  4. Asakura T, Naito A: Structure of silk I (Bombyx mori silk fibroin before spinning) in the dry and hydrated states studied using (13)C solid-state NMR spectroscopy. Int J Biol Macromol. 2022 Sep 1;216:282-290. doi: 10.1016/j.ijbiomac.2022.06.192.  Epub 2022 Jul 2. [PubMed:35788005  ] 
  5. LOTUS database [Link]