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Showing NP-Card for 3,4,5-trihydroxypiperidine-2-carboxylic acid (NP0266791)

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Record Information
Version2.0
Created at2022-09-08 11:21:40 UTC
Updated at2022-09-08 11:21:40 UTC
NP-MRD IDNP0266791
Secondary Accession NumbersNone
Natural Product Identification
Common Name3,4,5-trihydroxypiperidine-2-carboxylic acid
DescriptionSCHEMBL971521 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). 3,4,5-trihydroxypiperidine-2-carboxylic acid is found in Baphia racemosa. SCHEMBL971521 is a very strong basic compound (based on its pKa).
Structure
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MOL3D MOLSDFPDBSMILESInChI

MOL for NP0266791 (3,4,5-trihydroxypiperidine-2-carboxylic acid)


  Mrv1533004191513152D          

 12 12  0  0  0  0            999 V2000
    0.7145    2.0625    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -0.0000    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145   -0.4125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145    1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -1.6500    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0000   -1.6500    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
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  1  0  0  0  0
  6  8  1  0  0  0  0
  2  8  1  0  0  0  0
  8  9  1  0  0  0  0
  5 10  1  0  0  0  0
 10 11  2  0  0  0  0
 10 12  1  0  0  0  0
M  END
Download

3D MOL for NP0266791 (3,4,5-trihydroxypiperidine-2-carboxylic acid)

     RDKit          3D

 23 23  0  0  0  0  0  0  0  0999 V2000
   -3.1133    0.6390    1.0450 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4577    0.6479   -0.0266 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0644    1.1881   -1.1498 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0992    0.0988   -0.0594 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.7165   -0.3954    1.2404 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.4276   -1.3088    1.1168 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2471   -0.9950   -0.1123 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.5494   -1.4273    0.1285 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.2937    0.5107   -0.2466 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.2575    0.8455   -1.1698 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0722    1.0765   -0.5934 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.2527    2.3608   -0.1035 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4319    0.5292   -1.8560 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0799   -0.7744   -0.7704 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5166   -0.9391    1.6339 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0621   -2.3596    1.1007 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.0760   -1.1009    1.9939 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8750   -1.4927   -1.0199 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.7563   -2.2438   -0.3806 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5846    0.9013    0.7664 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.1518    0.7369   -0.7296 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1655    1.1078   -1.6868 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3109    2.3944    0.8790 H   0  0  0  0  0  0  0  0  0  0  0  0
  8  7  1  0
  7  6  1  0
  6  5  1  0
  5  4  1  0
  4 11  1  0
 11 12  1  0
 11  9  1  0
  9 10  1  0
  4  2  1  0
  2  3  1  0
  2  1  2  0
  9  7  1  0
  8 19  1  0
  7 18  1  6
  6 16  1  0
  6 17  1  0
  5 15  1  0
  4 14  1  6
 11 22  1  6
 12 23  1  0
  9 20  1  1
 10 21  1  0
  3 13  1  0
M  END
Download

3D SDF for NP0266791 (3,4,5-trihydroxypiperidine-2-carboxylic acid)


  Mrv1533004191513152D          

 12 12  0  0  0  0            999 V2000
    0.7145    2.0625    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -0.0000    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145   -0.4125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145    1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -1.6500    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0000   -1.6500    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
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  1  0  0  0  0
  6  8  1  0  0  0  0
  2  8  1  0  0  0  0
  8  9  1  0  0  0  0
  5 10  1  0  0  0  0
 10 11  2  0  0  0  0
 10 12  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0266791

> <DATABASE_NAME>
NP-MRD

> <SMILES>
OC1CNC(C(O)C1O)C(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C6H11NO5/c8-2-1-7-3(6(11)12)5(10)4(2)9/h2-5,7-10H,1H2,(H,11,12)

> <INCHI_KEY>
ZHFMVVUVCALAMY-UHFFFAOYSA-N

> <FORMULA>
C6H11NO5

> <MOLECULAR_WEIGHT>
177.156

> <EXACT_MASS>
177.063722458

> <JCHEM_ACCEPTOR_COUNT>
6

> <JCHEM_ATOM_COUNT>
23

> <JCHEM_AVERAGE_POLARIZABILITY>
15.823167030099288

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
5

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
3,4,5-trihydroxypiperidine-2-carboxylic acid

> <ALOGPS_LOGP>
-3.24

> <JCHEM_LOGP>
-5.035507561979963

> <ALOGPS_LOGS>
0.16

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
12.94033482428112

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.358348747709111

> <JCHEM_PKA_STRONGEST_BASIC>
8.62977883945482

> <JCHEM_POLAR_SURFACE_AREA>
110.02

> <JCHEM_REFRACTIVITY>
36.4418

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
2.58e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
3,4,5-trihydroxypiperidine-2-carboxylic acid

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for NP0266791 (3,4,5-trihydroxypiperidine-2-carboxylic acid)

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PDB for NP0266791 (3,4,5-trihydroxypiperidine-2-carboxylic acid)
HEADER    PROTEIN                                 19-APR-15   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   19-APR-15         0                                  
HETATM    1  O   UNK     0       1.334   3.850   0.000  0.00  0.00           O+0
HETATM    2  C   UNK     0       1.334   2.310   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       2.667   1.540   0.000  0.00  0.00           C+0
HETATM    4  N   UNK     0       2.667  -0.000   0.000  0.00  0.00           N+0
HETATM    5  C   UNK     0       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0      -1.334  -0.770   0.000  0.00  0.00           O+0
HETATM    8  C   UNK     0       0.000   1.540   0.000  0.00  0.00           C+0
HETATM    9  O   UNK     0      -1.334   2.310   0.000  0.00  0.00           O+0
HETATM   10  C   UNK     0       1.334  -2.310   0.000  0.00  0.00           C+0
HETATM   11  O   UNK     0       2.667  -3.080   0.000  0.00  0.00           O+0
HETATM   12  O   UNK     0      -0.000  -3.080   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3    8                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4    6   10                                                  
CONECT    6    5    7    8                                                  
CONECT    7    6                                                            
CONECT    8    6    2    9                                                  
CONECT    9    8                                                            
CONECT   10    5   11   12                                                  
CONECT   11   10                                                            
CONECT   12   10                                                            
MASTER        0    0    0    0    0    0    0    0   12    0   24    0
END

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3D PDB for NP0266791 (3,4,5-trihydroxypiperidine-2-carboxylic acid)
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SMILES for NP0266791 (3,4,5-trihydroxypiperidine-2-carboxylic acid)
OC1CNC(C(O)C1O)C(O)=O
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INCHI for NP0266791 (3,4,5-trihydroxypiperidine-2-carboxylic acid)
InChI=1S/C6H11NO5/c8-2-1-7-3(6(11)12)5(10)4(2)9/h2-5,7-10H,1H2,(H,11,12)
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View in JSmol
Synonyms
ValueSource
3,4,5-Trihydroxypiperidine-2-carboxylateGenerator
Chemical FormulaC6H11NO5
Average Mass177.1560 Da
Monoisotopic Mass177.06372 Da
IUPAC Name3,4,5-trihydroxypiperidine-2-carboxylic acid
Traditional Name3,4,5-trihydroxypiperidine-2-carboxylic acid
CAS Registry NumberNot Available
SMILES
OC1CNC(C(O)C1O)C(O)=O
InChI Identifier
InChI=1S/C6H11NO5/c8-2-1-7-3(6(11)12)5(10)4(2)9/h2-5,7-10H,1H2,(H,11,12)
InChI KeyZHFMVVUVCALAMY-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
Baphia racemosaLOTUS Database
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
    • 

  • Piperidinecarboxylic acid
    • 

  • Beta-hydroxy acid
    • 

  • Hydroxy acid
    • 

  • Piperidine
    • 

  • 1,2-aminoalcohol
    • 

  • 1,2-diol
    • 

  • Amino acid
    • 

  • Secondary alcohol
    • 

  • Carboxylic acid
    • 

  • Secondary aliphatic amine
    • 

  • Azacycle
    • 

  • Monocarboxylic acid or derivatives
    • 

  • Organoheterocyclic compound
    • 

  • Secondary amine
    • 

  • Polyol
    • 

  • Organic oxygen compound
    • 

  • Organic nitrogen compound
    • 

  • Carbonyl group
    • 

  • Alcohol
    • 

  • Organonitrogen compound
    • 

  • Organooxygen compound
    • 

  • Organic oxide
    • 

  • Amine
    • 

  • Hydrocarbon derivative
    • 

  • Aliphatic heteromonocyclic compound
Molecular FrameworkAliphatic heteromonocyclic compounds
External DescriptorsNot Available
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-3.2ALOGPS
logP-5ChemAxon
logS0.16ALOGPS
pKa (Strongest Acidic)1.36ChemAxon
pKa (Strongest Basic)8.63ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count6ChemAxon
Hydrogen Donor Count5ChemAxon
Polar Surface Area110.02 ŲChemAxon
Rotatable Bond Count1ChemAxon
Refractivity36.44 m³·mol⁻¹ChemAxon
Polarizability15.82 ųChemAxon
Number of Rings1ChemAxon
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 IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound15599232  
PDB IDNot Available
ChEBI IDNot Available
Good Scents IDNot Available
References
General References
  1. LOTUS database [Link]