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Showing NP-Card for R-(+)-2-Pyrrolidinone-5-carboxylate (NP0002755)

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Record Information
Version2.0
Created at2020-11-23 19:39:36 UTC
Updated at2021-08-12 19:52:03 UTC
NP-MRD IDNP0002755
Secondary Accession NumbersNone
Natural Product Identification
Common NameR-(+)-2-Pyrrolidinone-5-carboxylate
Provided ByBMRBBMRB logo
Description5-Oxo-D-proline is also known as D-pyroglutamate. R-(+)-2-Pyrrolidinone-5-carboxylate is found in Rehmannia glutinosa. R-(+)-2-Pyrrolidinone-5-carboxylate was first documented in 2010 (PMID: 20932022). Based on a literature review very few articles have been published on 5-oxo-D-proline (PMID: 30611573) (PMID: 27477667).
Structure
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MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for NP0002755 (R-(+)-2-Pyrrolidinone-5-carboxylate)


     RDKit          2D

 16 16  0  0  0  0  0  0  0  0999 V2000
    3.3967   -1.3056    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.0053   -0.7453    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6407    0.7097    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1443    0.8126    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4160   -0.5788    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7413    0.1239    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9327    1.3237    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0124   -0.6725    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7342   -1.5417    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.5867    2.2087    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.1259    0.9202    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9747    1.2861    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4030    2.2901    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2534   -1.8233    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3376    0.0302    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6313   -3.0381    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  3  4  1  0
  4  5  1  0
  5  6  1  0
  6  7  2  0
  6  8  1  0
  5  9  1  0
  9  2  1  0
  3 10  1  6
  3 11  1  0
  4 12  1  6
  4 13  1  0
  5 14  1  6
  8 15  1  0
  9 16  1  0
M  END
Download

3D MOL for NP0002755 (R-(+)-2-Pyrrolidinone-5-carboxylate)

NP0002755
     RDKit          3D

 16 16  0  0  0  0  0  0  0  0999 V2000
   -1.7959    1.7342    1.4333 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3279    0.9690    0.5264 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6701   -0.4558    0.2784 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3346   -1.0268   -0.0980 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4246    0.1148   -0.7377 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.7337    0.3017   -0.0262 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9991    1.3193    0.6486 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.7320   -0.6802   -0.0925 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3656    1.2976   -0.4655 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1235   -0.9399    1.1593 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3224   -0.4788   -0.6130 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2152   -1.4682    0.7640 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5120   -1.8078   -0.8663 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5805   -0.0575   -1.8163 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.0143   -1.0526    0.8238 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2475    2.2310   -0.9183 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  3  4  1  0
  4  5  1  0
  5  6  1  0
  6  7  2  0
  6  8  1  0
  5  9  1  0
  9  2  1  0
  3 10  1  0
  3 11  1  0
  4 12  1  0
  4 13  1  0
  5 14  1  6
  8 15  1  0
  9 16  1  0
M  END
Download

3D SDF for NP0002755 (R-(+)-2-Pyrrolidinone-5-carboxylate)


     RDKit          2D

 16 16  0  0  0  0  0  0  0  0999 V2000
    3.3967   -1.3056    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.0053   -0.7453    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6407    0.7097    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1443    0.8126    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4160   -0.5788    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7413    0.1239    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9327    1.3237    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0124   -0.6725    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7342   -1.5417    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.5867    2.2087    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.1259    0.9202    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9747    1.2861    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4030    2.2901    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2534   -1.8233    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3376    0.0302    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6313   -3.0381    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  3  4  1  0
  4  5  1  0
  5  6  1  0
  6  7  2  0
  6  8  1  0
  5  9  1  0
  9  2  1  0
  3 10  1  6
  3 11  1  0
  4 12  1  6
  4 13  1  0
  5 14  1  6
  8 15  1  0
  9 16  1  0
M  END
> <DATABASE_ID>
NP0002755

> <DATABASE_NAME>
NP-MRD

> <SMILES>
OC(=O)[C@H]1CCC(=O)N1

> <INCHI_IDENTIFIER>
InChI=1S/C5H7NO3/c7-4-2-1-3(6-4)5(8)9/h3H,1-2H2,(H,6,7)(H,8,9)/t3-/m1/s1

> <INCHI_KEY>
ODHCTXKNWHHXJC-GSVOUGTGSA-N

> <FORMULA>
C5H7NO3

> <MOLECULAR_WEIGHT>
129.114

> <EXACT_MASS>
129.042593095

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_AVERAGE_POLARIZABILITY>
11.41580763523854

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2R)-5-oxopyrrolidine-2-carboxylic acid

> <ALOGPS_LOGP>
-1.01

> <JCHEM_LOGP>
-0.8896697023333333

> <ALOGPS_LOGS>
0.07

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
12.760445138872768

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.6133555504913617

> <JCHEM_PKA_STRONGEST_BASIC>
-1.7569547770416478

> <JCHEM_POLAR_SURFACE_AREA>
66.39999999999999

> <JCHEM_REFRACTIVITY>
28.0878

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.51e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
5-oxo-D-proline

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for NP0002755 (R-(+)-2-Pyrrolidinone-5-carboxylate)

NP0002755
     RDKit          3D

 16 16  0  0  0  0  0  0  0  0999 V2000
   -1.7959    1.7342    1.4333 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3279    0.9690    0.5264 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6701   -0.4558    0.2784 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3346   -1.0268   -0.0980 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4246    0.1148   -0.7377 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.7337    0.3017   -0.0262 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9991    1.3193    0.6486 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.7320   -0.6802   -0.0925 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3656    1.2976   -0.4655 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1235   -0.9399    1.1593 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3224   -0.4788   -0.6130 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2152   -1.4682    0.7640 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5120   -1.8078   -0.8663 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5805   -0.0575   -1.8163 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.0143   -1.0526    0.8238 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2475    2.2310   -0.9183 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  3  4  1  0
  4  5  1  0
  5  6  1  0
  6  7  2  0
  6  8  1  0
  5  9  1  0
  9  2  1  0
  3 10  1  0
  3 11  1  0
  4 12  1  0
  4 13  1  0
  5 14  1  6
  8 15  1  0
  9 16  1  0
M  END
Download

PDB for NP0002755 (R-(+)-2-Pyrrolidinone-5-carboxylate)

HEADER    PROTEIN                                 23-FEB-12   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   23-FEB-12         0                                  
HETATM    1  O   UNK     0       2.109  -2.943   0.000  0.00  0.00           O+0
HETATM    2  C   UNK     0       2.735  -1.536   0.000  0.00  0.00           C+0
HETATM    3  O   UNK     0       4.267  -1.375   0.000  0.00  0.00           O+0
HETATM    4  C   UNK     0       1.830  -0.290   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       0.290  -0.290   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      -0.186   1.175   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       1.060   2.080   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0       1.060   3.620   0.000  0.00  0.00           O+0
HETATM    9  N   UNK     0       2.306   1.175   0.000  0.00  0.00           N+0
CONECT    1    2                                                            
CONECT    2    1    3    4                                                  
CONECT    3    2                                                            
CONECT    4    2    5    9                                                  
CONECT    5    4    6                                                       
CONECT    6    5    7                                                       
CONECT    7    6    8    9                                                  
CONECT    8    7                                                            
CONECT    9    7    4                                                       
MASTER        0    0    0    0    0    0    0    0    9    0   18    0
END
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3D PDB for NP0002755 (R-(+)-2-Pyrrolidinone-5-carboxylate)

COMPND    NP0002755
HETATM    1  O1  UNL     1      -1.796   1.734   1.433  1.00  0.00           O  
HETATM    2  C1  UNL     1      -1.328   0.969   0.526  1.00  0.00           C  
HETATM    3  C2  UNL     1      -1.670  -0.456   0.278  1.00  0.00           C  
HETATM    4  C3  UNL     1      -0.335  -1.027  -0.098  1.00  0.00           C  
HETATM    5  C4  UNL     1       0.425   0.115  -0.738  1.00  0.00           C  
HETATM    6  C5  UNL     1       1.734   0.302  -0.026  1.00  0.00           C  
HETATM    7  O2  UNL     1       1.999   1.319   0.649  1.00  0.00           O  
HETATM    8  O3  UNL     1       2.732  -0.680  -0.092  1.00  0.00           O  
HETATM    9  N1  UNL     1      -0.366   1.298  -0.465  1.00  0.00           N  
HETATM   10  H1  UNL     1      -2.123  -0.940   1.159  1.00  0.00           H  
HETATM   11  H2  UNL     1      -2.322  -0.479  -0.613  1.00  0.00           H  
HETATM   12  H3  UNL     1       0.215  -1.468   0.764  1.00  0.00           H  
HETATM   13  H4  UNL     1      -0.512  -1.808  -0.866  1.00  0.00           H  
HETATM   14  H5  UNL     1       0.580  -0.058  -1.816  1.00  0.00           H  
HETATM   15  H6  UNL     1       3.014  -1.053   0.824  1.00  0.00           H  
HETATM   16  H7  UNL     1      -0.248   2.231  -0.918  1.00  0.00           H  
CONECT    1    2    2
CONECT    2    3    9
CONECT    3    4   10   11
CONECT    4    5   12   13
CONECT    5    6    9   14
CONECT    6    7    7    8
CONECT    8   15
CONECT    9   16
END
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SMILES for NP0002755 (R-(+)-2-Pyrrolidinone-5-carboxylate)

OC(=O)[C@H]1CCC(=O)N1
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INCHI for NP0002755 (R-(+)-2-Pyrrolidinone-5-carboxylate)

InChI=1S/C5H7NO3/c7-4-2-1-3(6-4)5(8)9/h3H,1-2H2,(H,6,7)(H,8,9)/t3-/m1/s1
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View in JSmol
Synonyms
ValueSource
D-5-Pyrrolidone-2-carboxylic acidChEBI
D-Pyroglutamic acidChEBI
D-5-Pyrrolidone-2-carboxylateGenerator
D-PyroglutamateGenerator
PyrrolidonecarboxylateGenerator
5-KetoprolineMeSH
5-OxoprolineMeSH
Pidolate, magnesiumMeSH
Pidolic acidMeSH
5-Oxopyrrolidine-2-carboxylic acidMeSH
Magnesium pidolateMeSH
Pyroglutamic acidMeSH
PyroglutamateMeSH
Chemical FormulaC5H7NO3
Average Mass129.1140 Da
Monoisotopic Mass129.04259 Da
IUPAC Name(2R)-5-oxopyrrolidine-2-carboxylic acid
Traditional Name5-oxo-D-proline
CAS Registry NumberNot Available
SMILES
OC(=O)[C@H]1CCC(=O)N1
InChI Identifier
InChI=1S/C5H7NO3/c7-4-2-1-3(6-4)5(8)9/h3H,1-2H2,(H,6,7)(H,8,9)/t3-/m1/s1
InChI KeyODHCTXKNWHHXJC-GSVOUGTGSA-N
Experimental Spectra
Spectrum TypeDescriptionDepositor EmailDepositor OrganizationDepositorDeposition DateView
1D NMR13C NMR Spectrum (1D, 500 MHz, D2O, simulated)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 500 MHz, D2O, simulated)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 500 MHz, D2O, simulated)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 500 MHz, D2O, experimental)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
Predicted Spectra
Not Available
Chemical Shift Submissions
Not Available
Species
Species of Origin
Species NameSourceReference
Rehmannia glutinosaLOTUS Database
Chemical Taxonomy
DescriptionThis compound belongs to the class of organic compounds known as proline and derivatives. These are compounds containing proline or a derivative thereof resulting from reaction of proline at the amino group or the carboxy group, or from the replacement of any hydrogen of glycine by a heteroatom.
KingdomOrganic compounds
Super ClassOrganic acids and derivatives
ClassCarboxylic acids and derivatives
Sub ClassAmino acids, peptides, and analogues
Direct ParentProline and derivatives
Alternative Parents
Substituents
  • Proline or derivatives
  • Oxoproline
  • Pyrrolidine carboxylic acid
  • Pyrrolidine carboxylic acid or derivatives
  • Pyrrolidone
  • 2-pyrrolidone
  • Pyrrolidine
  • Carboxamide group
  • Lactam
  • Secondary carboxylic acid amide
  • Carboxylic acid
  • Monocarboxylic acid or derivatives
  • Azacycle
  • Organoheterocyclic compound
  • Organopnictogen compound
  • Organooxygen compound
  • Organonitrogen compound
  • Carbonyl group
  • Organic oxygen compound
  • Organic oxide
  • Hydrocarbon derivative
  • Organic nitrogen compound
  • Aliphatic heteromonocyclic compound
Molecular FrameworkAliphatic heteromonocyclic 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-1ALOGPS
logP-0.89ChemAxon
logS0.07ALOGPS
pKa (Strongest Acidic)3.61ChemAxon
pKa (Strongest Basic)-1.8ChemAxon
Physiological Charge-1ChemAxon
Hydrogen Acceptor Count3ChemAxon
Hydrogen Donor Count2ChemAxon
Polar Surface Area66.4 ŲChemAxon
Rotatable Bond Count1ChemAxon
Refractivity28.09 m³·mol⁻¹ChemAxon
Polarizability11.42 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 ID388752
KEGG Compound IDC02237
BioCyc IDCPD-656
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem CompoundNot Available
PDB IDNot Available
ChEBI ID16924
Good Scents IDNot Available
References
General References
  1. Shim K, Gulhar R, Jialal I: Exploratory metabolomics of nascent metabolic syndrome. J Diabetes Complications. 2019 Mar;33(3):212-216. doi: 10.1016/j.jdiacomp.2018.12.002. Epub 2018 Dec 10. [PubMed:30611573 ]
  2. Amino Y: Concise Synthesis of (2R,4R)-Monatin. Chem Pharm Bull (Tokyo). 2016;64(8):1242-7. doi: 10.1248/cpb.c16-00358. [PubMed:27477667 ]
  3. Nilson MG, Funk RL: Total synthesis of (-)-nakadomarin A. Org Lett. 2010 Nov 5;12(21):4912-5. doi: 10.1021/ol102079z. [PubMed:20932022 ]