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Showing NP-Card for (2s)-2-amino-3-[(c-hydroxycarbonimidoylamino)oxy]propanoic acid (NP0286294)

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Record Information
Version2.0
Created at2022-09-09 14:48:35 UTC
Updated at2022-09-09 14:48:35 UTC
NP-MRD IDNP0286294
Secondary Accession NumbersNone
Natural Product Identification
Common Name(2s)-2-amino-3-[(c-hydroxycarbonimidoylamino)oxy]propanoic acid
DescriptionO-ureido-L-serine zwitterion, also known as O-ureido-L-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. (2s)-2-amino-3-[(c-hydroxycarbonimidoylamino)oxy]propanoic acid is found in Streptomyces lavendulae. (2s)-2-amino-3-[(c-hydroxycarbonimidoylamino)oxy]propanoic acid was first documented in 2010 (PMID: 20086163). Based on a literature review very few articles have been published on O-ureido-L-serine zwitterion (PMID: 23529730).
Structure
Thumb
MOL3D MOLSDFPDBSMILESInChI

MOL for NP0286294 ((2s)-2-amino-3-[(c-hydroxycarbonimidoylamino)oxy]propanoic acid)


  Mrv1652309092216482D          

 11 10  0  0  1  0            999 V2000
    1.0461    1.4289    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.7605    1.8414    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7605    2.6664    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.4750    1.4289    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.1895    1.8414    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.9039    1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.6184    1.8414    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    4.6184    2.6664    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    5.3329    1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.0474    1.8414    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.3329    0.6039    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0  0  0  0
  2  3  1  0  0  0  0
  2  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  1  0  0  0  0
  7  8  1  6  0  0  0
  7  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 NP0286294 ((2s)-2-amino-3-[(c-hydroxycarbonimidoylamino)oxy]propanoic acid)

     RDKit          3D

 20 19  0  0  0  0  0  0  0  0999 V2000
    4.1672   -1.9136   -0.2755 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.0904   -0.8731   -0.2630 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.9630   -0.2583   -0.2266 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9439    1.1216   -0.2121 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.7553   -1.0018   -0.2018 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.6158   -0.4712   -0.6991 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1044    0.0350    0.3625 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4116    0.6641   -0.0441 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.0460    1.1443    1.1672 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3120   -0.2754   -0.7191 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9691   -0.8127   -1.7847 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5447   -0.5631   -0.1679 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.5556    1.6872    0.3607 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7598   -1.9615    0.2049 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2881   -0.7449    1.0996 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5107    0.8452    0.8228 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2694    1.5351   -0.7106 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0422    1.4252    1.0146 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0419    0.3473    1.8623 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3324    0.0708   -0.1819 H   0  0  0  0  0  0  0  0  0  0  0  0
  9  8  1  0
  8  7  1  0
  7  6  1  0
  6  5  1  0
  5  3  1  0
  3  4  1  0
  3  2  2  0
  8 10  1  0
 10 12  1  0
 10 11  2  0
  9 18  1  0
  9 19  1  0
  8 17  1  6
  7 15  1  0
  7 16  1  0
  5 14  1  0
  4 13  1  0
  2  1  1  0
 12 20  1  0
M  END
Download

3D SDF for NP0286294 ((2s)-2-amino-3-[(c-hydroxycarbonimidoylamino)oxy]propanoic acid)


  Mrv1652309092216482D          

 11 10  0  0  1  0            999 V2000
    1.0461    1.4289    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.7605    1.8414    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7605    2.6664    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.4750    1.4289    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.1895    1.8414    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.9039    1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.6184    1.8414    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    4.6184    2.6664    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    5.3329    1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.0474    1.8414    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.3329    0.6039    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0  0  0  0
  2  3  1  0  0  0  0
  2  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  1  0  0  0  0
  7  8  1  6  0  0  0
  7  9  1  0  0  0  0
  9 10  2  0  0  0  0
  9 11  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0286294

> <DATABASE_NAME>
NP-MRD

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

> <INCHI_IDENTIFIER>
InChI=1S/C4H9N3O4/c5-2(3(8)9)1-11-7-4(6)10/h2H,1,5H2,(H,8,9)(H3,6,7,10)/t2-/m0/s1

> <INCHI_KEY>
ZFLDWYJOQSXISF-REOHCLBHSA-N

> <FORMULA>
C4H9N3O4

> <MOLECULAR_WEIGHT>
163.133

> <EXACT_MASS>
163.059305782

> <JCHEM_ACCEPTOR_COUNT>
7

> <JCHEM_ATOM_COUNT>
20

> <JCHEM_AVERAGE_POLARIZABILITY>
14.320797583326499

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
5

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2S)-2-amino-3-{[(C-hydroxycarbonimidoyl)amino]oxy}propanoic acid

> <JCHEM_LOGP>
-5.055157494407727

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
1.8951863510122795

> <JCHEM_PKA_STRONGEST_ACIDIC>
-3.2121885359726177

> <JCHEM_PKA_STRONGEST_BASIC>
15.000000027444418

> <JCHEM_POLAR_SURFACE_AREA>
128.66

> <JCHEM_REFRACTIVITY>
54.72070000000001

> <JCHEM_ROTATABLE_BOND_COUNT>
4

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
(2S)-2-amino-3-[(C-hydroxycarbonimidoylamino)oxy]propanoic acid

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for NP0286294 ((2s)-2-amino-3-[(c-hydroxycarbonimidoylamino)oxy]propanoic acid)

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PDB for NP0286294 ((2s)-2-amino-3-[(c-hydroxycarbonimidoylamino)oxy]propanoic acid)
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  N   UNK     0       1.953   2.667   0.000  0.00  0.00           N+0
HETATM    2  C   UNK     0       3.286   3.437   0.000  0.00  0.00           C+0
HETATM    3  O   UNK     0       3.286   4.977   0.000  0.00  0.00           O+0
HETATM    4  N   UNK     0       4.620   2.667   0.000  0.00  0.00           N+0
HETATM    5  O   UNK     0       5.954   3.437   0.000  0.00  0.00           O+0
HETATM    6  C   UNK     0       7.287   2.667   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       8.621   3.437   0.000  0.00  0.00           C+0
HETATM    8  N   UNK     0       8.621   4.977   0.000  0.00  0.00           N+0
HETATM    9  C   UNK     0       9.955   2.667   0.000  0.00  0.00           C+0
HETATM   10  O   UNK     0      11.288   3.437   0.000  0.00  0.00           O+0
HETATM   11  O   UNK     0       9.955   1.127   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3    4                                                  
CONECT    3    2                                                            
CONECT    4    2    5                                                       
CONECT    5    4    6                                                       
CONECT    6    5    7                                                       
CONECT    7    6    8    9                                                  
CONECT    8    7                                                            
CONECT    9    7   10   11                                                  
CONECT   10    9                                                            
CONECT   11    9                                                            
MASTER        0    0    0    0    0    0    0    0   11    0   20    0
END

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3D PDB for NP0286294 ((2s)-2-amino-3-[(c-hydroxycarbonimidoylamino)oxy]propanoic acid)
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SMILES for NP0286294 ((2s)-2-amino-3-[(c-hydroxycarbonimidoylamino)oxy]propanoic acid)
N[C@@H](CONC(O)=N)C(O)=O
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INCHI for NP0286294 ((2s)-2-amino-3-[(c-hydroxycarbonimidoylamino)oxy]propanoic acid)
InChI=1S/C4H9N3O4/c5-2(3(8)9)1-11-7-4(6)10/h2H,1,5H2,(H,8,9)(H3,6,7,10)/t2-/m0/s1
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View in JSmol
Synonyms
ValueSource
(2S)-2-Ammonio-3-[(carbamoylamino)oxy]propanoateChEBI
O-Ureido-L-serineChEBI
(2S)-2-Ammonio-3-[(carbamoylamino)oxy]propanoic acidGenerator
Chemical FormulaC4H9N3O4
Average Mass163.1330 Da
Monoisotopic Mass163.05931 Da
IUPAC Name(2S)-2-amino-3-{[(C-hydroxycarbonimidoyl)amino]oxy}propanoic acid
Traditional Name(2S)-2-amino-3-[(C-hydroxycarbonimidoylamino)oxy]propanoic acid
CAS Registry NumberNot Available
SMILES
N[C@@H](CONC(O)=N)C(O)=O
InChI Identifier
InChI=1S/C4H9N3O4/c5-2(3(8)9)1-11-7-4(6)10/h2H,1,5H2,(H,8,9)(H3,6,7,10)/t2-/m0/s1
InChI KeyZFLDWYJOQSXISF-REOHCLBHSA-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
Streptomyces lavendulaeLOTUS 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
    • 

  • Carbonic acid derivative
    • 

  • Amino acid
    • 

  • Carboxylic acid
    • 

  • Monocarboxylic acid or derivatives
    • 

  • Amine
    • 

  • Hydrocarbon derivative
    • 

  • Organic oxide
    • 

  • Primary amine
    • 

  • Organooxygen compound
    • 

  • Organonitrogen compound
    • 

  • Organopnictogen compound
    • 

  • Organic oxygen compound
    • 

  • Primary aliphatic amine
    • 

  • Organic nitrogen compound
    • 

  • Carbonyl group
    • 

  • 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-5.1ChemAxon
pKa (Strongest Acidic)-3.2ChemAxon
pKa (Strongest Basic)15ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count7ChemAxon
Hydrogen Donor Count5ChemAxon
Polar Surface Area128.66 ŲChemAxon
Rotatable Bond Count4ChemAxon
Refractivity54.72 m³·mol⁻¹ChemAxon
Polarizability14.32 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 ID26996867  
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound57328746  
PDB IDNot Available
ChEBI ID73389  
Good Scents IDNot Available
References
General References
  1. Kumagai T, Koyama Y, Oda K, Noda M, Matoba Y, Sugiyama M: Molecular cloning and heterologous expression of a biosynthetic gene cluster for the antitubercular agent D-cycloserine produced by Streptomyces lavendulae. Antimicrob Agents Chemother. 2010 Mar;54(3):1132-9. doi: 10.1128/AAC.01226-09. Epub 2010 Jan 19. [PubMed:20086163  ] 
  2. Uda N, Matoba Y, Kumagai T, Oda K, Noda M, Sugiyama M: Establishment of an in vitro D-cycloserine-synthesizing system by using O-ureido-L-serine synthase and D-cycloserine synthetase found in the biosynthetic pathway. Antimicrob Agents Chemother. 2013 Jun;57(6):2603-12. doi: 10.1128/AAC.02291-12. Epub 2013 Mar 25. [PubMed:23529730  ] 
  3. LOTUS database [Link]