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Showing NP-Card for (2s,4r,5r)-4,5-dihydroxypiperidine-2-carboxylic acid (NP0248699)

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Record Information
Version2.0
Created at2022-09-07 11:02:53 UTC
Updated at2022-09-07 11:02:53 UTC
NP-MRD IDNP0248699
Secondary Accession NumbersNone
Natural Product Identification
Common Name(2s,4r,5r)-4,5-dihydroxypiperidine-2-carboxylic acid
DescriptionSCHEMBL17964197 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,4r,5r)-4,5-dihydroxypiperidine-2-carboxylic acid is found in Calliandra angustifolia. Based on a literature review very few articles have been published on SCHEMBL17964197.
Structure
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MOL3D MOLSDFPDBSMILESInChI

MOL for NP0248699 ((2s,4r,5r)-4,5-dihydroxypiperidine-2-carboxylic acid)


  Mrv1652309072213022D          

 11 11  0  0  1  0            999 V2000
    0.0000    2.4750    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    2.0625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    2.4750    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    1.2375    0.0000 C   0  0  2  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 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.1434   -0.4125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -0.4125    0.0000 C   0  0  2  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
    0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.8250    0.0000 N   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
  4  2  1  6  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  1  1  0  0  0
  6  8  1  0  0  0  0
  8  9  1  6  0  0  0
  8 10  1  0  0  0  0
 10 11  1  0  0  0  0
  4 11  1  0  0  0  0
M  END
Download

3D MOL for NP0248699 ((2s,4r,5r)-4,5-dihydroxypiperidine-2-carboxylic acid)

     RDKit          3D

 22 22  0  0  0  0  0  0  0  0999 V2000
    3.3124    1.2522   -0.0831 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.5035    0.3077   -0.3193 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9424   -1.0163   -0.2985 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.0644    0.6401   -0.5600 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.3437    0.6505    0.7568 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1491    0.6780    0.5935 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.5176    2.0025    0.3214 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6260   -0.2501   -0.4907 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.6689   -1.0602   -0.0821 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4700   -1.1514   -0.8946 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5219   -0.2942   -1.5097 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.4429   -1.6721    0.3012 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9963    1.6533   -1.0290 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6423    1.5813    1.2872 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7003   -0.2018    1.3723 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6603    0.4021    1.5273 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4566    2.1419    0.6097 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9582    0.2844   -1.4086 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3925   -1.4495    0.7969 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7771   -1.9509   -1.5812 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0799   -1.6636    0.0198 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2860   -0.8842   -1.9176 H   0  0  0  0  0  0  0  0  0  0  0  0
  9  8  1  0
  8 10  1  0
 10 11  1  0
 11  4  1  0
  4  5  1  0
  5  6  1  0
  6  7  1  0
  4  2  1  0
  2  3  1  0
  2  1  2  0
  6  8  1  0
  9 19  1  0
  8 18  1  6
 10 20  1  0
 10 21  1  0
 11 22  1  0
  4 13  1  6
  5 14  1  0
  5 15  1  0
  6 16  1  1
  7 17  1  0
  3 12  1  0
M  END
Download

3D SDF for NP0248699 ((2s,4r,5r)-4,5-dihydroxypiperidine-2-carboxylic acid)


  Mrv1652309072213022D          

 11 11  0  0  1  0            999 V2000
    0.0000    2.4750    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    2.0625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    2.4750    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    1.2375    0.0000 C   0  0  2  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 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.1434   -0.4125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -0.4125    0.0000 C   0  0  2  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
    0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.8250    0.0000 N   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
  4  2  1  6  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  1  1  0  0  0
  6  8  1  0  0  0  0
  8  9  1  6  0  0  0
  8 10  1  0  0  0  0
 10 11  1  0  0  0  0
  4 11  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0248699

> <DATABASE_NAME>
NP-MRD

> <SMILES>
O[C@@H]1CN[C@@H](C[C@H]1O)C(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C6H11NO4/c8-4-1-3(6(10)11)7-2-5(4)9/h3-5,7-9H,1-2H2,(H,10,11)/t3-,4+,5+/m0/s1

> <INCHI_KEY>
FGRNDHZIHWHWJL-VPENINKCSA-N

> <FORMULA>
C6H11NO4

> <MOLECULAR_WEIGHT>
161.157

> <EXACT_MASS>
161.068807838

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_ATOM_COUNT>
22

> <JCHEM_AVERAGE_POLARIZABILITY>
14.943274230405908

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2S,4R,5R)-4,5-dihydroxypiperidine-2-carboxylic acid

> <JCHEM_LOGP>
-4.346085431946321

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
13.665842347002176

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.5642405634817518

> <JCHEM_PKA_STRONGEST_BASIC>
9.194096579269237

> <JCHEM_POLAR_SURFACE_AREA>
89.79

> <JCHEM_REFRACTIVITY>
35.344699999999996

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
(2S,4R,5R)-4,5-dihydroxypiperidine-2-carboxylic acid

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for NP0248699 ((2s,4r,5r)-4,5-dihydroxypiperidine-2-carboxylic acid)

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PDB for NP0248699 ((2s,4r,5r)-4,5-dihydroxypiperidine-2-carboxylic acid)
HEADER    PROTEIN                                 07-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   07-SEP-22         0                                  
HETATM    1  O   UNK     0       0.000   4.620   0.000  0.00  0.00           O+0
HETATM    2  C   UNK     0       1.334   3.850   0.000  0.00  0.00           C+0
HETATM    3  O   UNK     0       2.667   4.620   0.000  0.00  0.00           O+0
HETATM    4  C   UNK     0       1.334   2.310   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       2.667   1.540   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       2.667  -0.000   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0       4.001  -0.770   0.000  0.00  0.00           O+0
HETATM    8  C   UNK     0       1.334  -0.770   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       0.000   0.000   0.000  0.00  0.00           C+0
HETATM   11  N   UNK     0       0.000   1.540   0.000  0.00  0.00           N+0
CONECT    1    2                                                            
CONECT    2    1    3    4                                                  
CONECT    3    2                                                            
CONECT    4    2    5   11                                                  
CONECT    5    4    6                                                       
CONECT    6    5    7    8                                                  
CONECT    7    6                                                            
CONECT    8    6    9   10                                                  
CONECT    9    8                                                            
CONECT   10    8   11                                                       
CONECT   11   10    4                                                       
MASTER        0    0    0    0    0    0    0    0   11    0   22    0
END

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3D PDB for NP0248699 ((2s,4r,5r)-4,5-dihydroxypiperidine-2-carboxylic acid)
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SMILES for NP0248699 ((2s,4r,5r)-4,5-dihydroxypiperidine-2-carboxylic acid)
O[C@@H]1CN[C@@H](C[C@H]1O)C(O)=O
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INCHI for NP0248699 ((2s,4r,5r)-4,5-dihydroxypiperidine-2-carboxylic acid)
InChI=1S/C6H11NO4/c8-4-1-3(6(10)11)7-2-5(4)9/h3-5,7-9H,1-2H2,(H,10,11)/t3-,4+,5+/m0/s1
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View in JSmol
SynonymsNot Available
Chemical FormulaC6H11NO4
Average Mass161.1570 Da
Monoisotopic Mass161.06881 Da
IUPAC Name(2S,4R,5R)-4,5-dihydroxypiperidine-2-carboxylic acid
Traditional Name(2S,4R,5R)-4,5-dihydroxypiperidine-2-carboxylic acid
CAS Registry NumberNot Available
SMILES
O[C@@H]1CN[C@@H](C[C@H]1O)C(O)=O
InChI Identifier
InChI=1S/C6H11NO4/c8-4-1-3(6(10)11)7-2-5(4)9/h3-5,7-9H,1-2H2,(H,10,11)/t3-,4+,5+/m0/s1
InChI KeyFGRNDHZIHWHWJL-VPENINKCSA-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
Calliandra angustifoliaLOTUS 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
    • 

  • Piperidinecarboxylic acid
    • 

  • Piperidine
    • 

  • 1,2-aminoalcohol
    • 

  • 1,2-diol
    • 

  • Amino acid
    • 

  • Secondary alcohol
    • 

  • Carboxylic acid
    • 

  • Secondary aliphatic amine
    • 

  • Monocarboxylic acid or derivatives
    • 

  • Azacycle
    • 

  • Secondary amine
    • 

  • Organoheterocyclic compound
    • 

  • Organonitrogen compound
    • 

  • Alcohol
    • 

  • Organic oxygen compound
    • 

  • Organic nitrogen compound
    • 

  • Organooxygen compound
    • 

  • Organic oxide
    • 

  • Hydrocarbon derivative
    • 

  • Amine
    • 

  • Carbonyl group
    • 

  • 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-4.3ChemAxon
pKa (Strongest Acidic)1.56ChemAxon
pKa (Strongest Basic)9.19ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count5ChemAxon
Hydrogen Donor Count4ChemAxon
Polar Surface Area89.79 ŲChemAxon
Rotatable Bond Count1ChemAxon
Refractivity35.34 m³·mol⁻¹ChemAxon
Polarizability14.94 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 ID61662160  
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound13989548  
PDB IDNot Available
ChEBI IDNot Available
Good Scents IDNot Available
References
General References
  1. LOTUS database [Link]