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Showing NP-Card for d-proline (NP0156847)

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Record Information
Version2.0
Created at2022-09-02 14:07:10 UTC
Updated at2025-07-18 00:04:12 UTC
NP-MRD IDNP0156847
Natural Product DOIhttps://doi.org/10.57994/4339
Secondary Accession NumbersNone
Natural Product Identification
Common Named-proline
DescriptionD-Proline, also known as D-prolin or DPR, belongs to the class of organic compounds known as proline and derivatives. Proline and derivatives 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. D-Proline is a very strong basic compound (based on its pKa). D-Proline exists in all living species, ranging from bacteria to humans. D-proline can be converted into 1-pyrroline-2-carboxylic acid through its interaction with the enzyme D-amino-acid oxidase. In humans, D-proline is involved in the metabolic disorder called hyperornithinemia with gyrate atrophy (hoga). D-Proline is a potentially toxic compound. d-proline is found in Antirrhinum majus, Astragalus falcatus, Claviceps purpurea, Colchicum trigynum, Homo sapiens and Mus musculus. d-proline was first documented in 2000 (PMID: 11090086). The D-enantiomer of proline (PMID: 11510941) (PMID: 11244003) (PMID: 11489939) (PMID: 11849233).
Structure
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MOL3D MOLSDFPDBSMILESInChI

MOL for NP0156847 (d-proline)


  Mrv1652303021817302D          

  8  8  0  0  0  0            999 V2000
10000.682310000.1792    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10001.3973 9999.7677    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
10000.682310001.0035    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9999.297510000.2623    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
 9998.6301 9999.7773    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9998.8850 9998.9927    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9999.7100 9998.9927    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9999.9649 9999.7773    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  1  3  2  0  0  0  0
  5  6  1  0  0  0  0
  6  7  1  0  0  0  0
  7  8  1  0  0  0  0
  4  5  1  0  0  0  0
  4  8  1  0  0  0  0
  8  1  1  1  0  0  0
M  END
Download

3D MOL for NP0156847 (d-proline)

     RDKit          3D

 17 17  0  0  0  0  0  0  0  0999 V2000
    1.9899   -0.0408    1.8240 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.8789    0.1630    0.5326 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0455    0.2187   -0.1763 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.5527    0.3218   -0.0390 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.0030   -1.0257   -0.5173 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4949   -0.7995   -0.5193 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7075    0.4549    0.2839 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4378    0.7302    0.9530 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.7386    0.9828   -0.1051 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5359    1.0339   -0.8478 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2962   -1.7699    0.2165 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3392   -1.2924   -1.5178 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9262   -0.6958   -1.5221 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9766   -1.6599    0.0270 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5056    0.2893    1.0209 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9407    1.3084   -0.3426 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3846    1.7812    1.1046 H   0  0  0  0  0  0  0  0  0  0  0  0
  3  2  1  0
  2  1  2  0
  2  4  1  0
  4  5  1  0
  5  6  1  0
  6  7  1  0
  7  8  1  0
  8  4  1  0
  3  9  1  0
  4 10  1  6
  5 11  1  0
  5 12  1  0
  6 13  1  0
  6 14  1  0
  7 15  1  0
  7 16  1  0
  8 17  1  0
M  END
Download

3D SDF for NP0156847 (d-proline)


  Mrv1652303021817302D          

  8  8  0  0  0  0            999 V2000
10000.682310000.1792    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10001.3973 9999.7677    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
10000.682310001.0035    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9999.297510000.2623    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
 9998.6301 9999.7773    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9998.8850 9998.9927    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9999.7100 9998.9927    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9999.9649 9999.7773    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  1  3  2  0  0  0  0
  5  6  1  0  0  0  0
  6  7  1  0  0  0  0
  7  8  1  0  0  0  0
  4  5  1  0  0  0  0
  4  8  1  0  0  0  0
  8  1  1  1  0  0  0
M  END
> <DATABASE_ID>
NP0156847

> <DATABASE_NAME>
NP-MRD

> <SMILES>
OC(=O)[C@H]1CCCN1

> <INCHI_IDENTIFIER>
InChI=1S/C5H9NO2/c7-5(8)4-2-1-3-6-4/h4,6H,1-3H2,(H,7,8)/t4-/m1/s1

> <INCHI_KEY>
ONIBWKKTOPOVIA-SCSAIBSYSA-N

> <FORMULA>
C5H9NO2

> <MOLECULAR_WEIGHT>
115.1305

> <EXACT_MASS>
115.063328537

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_ATOM_COUNT>
17

> <JCHEM_AVERAGE_POLARIZABILITY>
11.387789363574521

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2R)-pyrrolidine-2-carboxylic acid

> <ALOGPS_LOGP>
-2.71

> <JCHEM_LOGP>
-2.568638276039985

> <ALOGPS_LOGS>
0.50

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.9406707712827913

> <JCHEM_PKA_STRONGEST_BASIC>
11.332026115136207

> <JCHEM_POLAR_SURFACE_AREA>
49.33

> <JCHEM_REFRACTIVITY>
28.064299999999996

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
3.65e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
D-proline

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for NP0156847 (d-proline)

Download
PDB for NP0156847 (d-proline)
HEADER    PROTEIN                                 02-MAR-18   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   02-MAR-18         0                                  
HETATM    1  C   UNK     0    8667.9408667.001   0.000  0.00  0.00           C+0
HETATM    2  O   UNK     0    8669.2758666.233   0.000  0.00  0.00           O+0
HETATM    3  O   UNK     0    8667.9408668.540   0.000  0.00  0.00           O+0
HETATM    4  N   UNK     0    8665.3558667.156   0.000  0.00  0.00           N+0
HETATM    5  C   UNK     0    8664.1108666.251   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0    8664.5858664.786   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0    8666.1258664.786   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0    8666.6018666.251   0.000  0.00  0.00           C+0
CONECT    1    2    3    8                                                  
CONECT    2    1                                                            
CONECT    3    1                                                            
CONECT    4    5    8                                                       
CONECT    5    6    4                                                       
CONECT    6    5    7                                                       
CONECT    7    6    8                                                       
CONECT    8    7    4    1                                                  
MASTER        0    0    0    0    0    0    0    0    8    0   16    0
END

Download
3D PDB for NP0156847 (d-proline)
Download
SMILES for NP0156847 (d-proline)
OC(=O)[C@H]1CCCN1
Download
INCHI for NP0156847 (d-proline)
InChI=1S/C5H9NO2/c7-5(8)4-2-1-3-6-4/h4,6H,1-3H2,(H,7,8)/t4-/m1/s1
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View in JSmol
Synonyms
ValueSource
(2R)-Pyrrolidine-2-carboxylic acidChEBI
(R)-2-CarboxypyrrolidineChEBI
(R)-Pyrrolidine-2-carboxylic acidChEBI
D-ProlinChEBI
DPRChEBI
(2R)-Pyrrolidine-2-carboxylateGenerator
(R)-Pyrrolidine-2-carboxylateGenerator
R)-2-CarboxypyrrolidineHMDB
R-ProlineHMDB
ProlineHMDB
Chemical FormulaC5H9NO2
Average Mass115.1305 Da
Monoisotopic Mass115.06333 Da
IUPAC Name(2R)-pyrrolidine-2-carboxylic acid
Traditional NameD-proline
CAS Registry NumberNot Available
SMILES
OC(=O)[C@H]1CCCN1
InChI Identifier
InChI=1S/C5H9NO2/c7-5(8)4-2-1-3-6-4/h4,6H,1-3H2,(H,7,8)/t4-/m1/s1
InChI KeyONIBWKKTOPOVIA-SCSAIBSYSA-N
Experimental Spectra
Spectrum TypeDescriptionDepositor EmailDepositor OrganizationDepositorDeposition DateView
HMBC NMR[1H, 13C] NMR Spectrum (2D, 600 MHz, C2D6OS, experimental)Not AvailableSumner lab, University of MissouriRonald Myers2025-07-16View Spectrum
COSY NMR[1H, 1H] NMR Spectrum (2D, 600 MHz, C2D6OS, experimental)Not AvailableSumner lab, University of MissouriRonald Myers2025-07-16View Spectrum
HSQC NMR[1H, 13C] NMR Spectrum (2D, 600 MHz, C2D6OS, experimental)Not AvailableSumner lab, University of MissouriRonald Myers2025-07-16View Spectrum
1D NMR1H NMR Spectrum (1D, 600 MHz, C2D6OS, experimental)Not AvailableSumner lab, University of MissouriRonald Myers2025-07-16View Spectrum
1D NMR1H NMR Spectrum (1D, 600.0 MHz, C2D6OS, experimental)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
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
Spectrum TypeDescriptionDepositor EmailDepositor OrganizationDepositorDeposition DateView
1D NMR1H NMR Spectrum (1D, 600.0, C2D6OS, simulated)rjm4kd@umsystem.eduSumner lab, University of MissouriRonald Myers2025-07-16View Spectrum
Species
Species of Origin
Species NameSourceReference
Antirrhinum majusLOTUS Database
Astragalus falcatusLOTUS Database
Claviceps purpureaLOTUS Database
Colchicum trigynumLOTUS Database
Homo sapiensLOTUS Database
Mus musculusLOTUS Database
Chemical Taxonomy
Description Belongs to the class of organic compounds known as proline and derivatives. Proline and derivatives 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
    • 

  • Alpha-amino acid
    • 

  • D-alpha-amino acid
    • 

  • Pyrrolidine carboxylic acid
    • 

  • Pyrrolidine carboxylic acid or derivatives
    • 

  • Pyrrolidine
    • 

  • Amino acid
    • 

  • Carboxylic acid
    • 

  • Secondary aliphatic amine
    • 

  • Monocarboxylic acid or derivatives
    • 

  • Secondary amine
    • 

  • Organoheterocyclic compound
    • 

  • Azacycle
    • 

  • Organic oxygen compound
    • 

  • Organooxygen compound
    • 

  • Organonitrogen compound
    • 

  • Amine
    • 

  • Organopnictogen compound
    • 

  • Organic oxide
    • 

  • Carbonyl group
    • 

  • Organic nitrogen compound
    • 

  • Hydrocarbon derivative
    • 

  • 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-2.7ALOGPS
logP-2.6ChemAxon
logS0.5ALOGPS
pKa (Strongest Acidic)1.94ChemAxon
pKa (Strongest Basic)11.33ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count3ChemAxon
Hydrogen Donor Count2ChemAxon
Polar Surface Area49.33 ŲChemAxon
Rotatable Bond Count1ChemAxon
Refractivity28.06 m³·mol⁻¹ChemAxon
Polarizability11.39 ųChemAxon
Number of Rings1ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
HMDB IDHMDB0003411  
DrugBank IDDB02853  
Phenol Explorer Compound IDNot Available
FoodDB IDFDB023166  
KNApSAcK IDNot Available
Chemspider ID8640  
KEGG Compound IDC00763  
BioCyc IDD-PROLINE  
BiGG ID35916  
Wikipedia LinkD-proline  
METLIN IDNot Available
PubChem Compound8988  
PDB IDNot Available
ChEBI ID16313  
Good Scents IDNot Available
References
General References
  1. Humbertclaude V, Rivier F, Roubertie A, Echenne B, Bellet H, Vallat C, Morin D: Is hyperprolinemia type I actually a benign trait? Report of a case with severe neurologic involvement and vigabatrin intolerance. J Child Neurol. 2001 Aug;16(8):622-3. [PubMed:11510941  ] 
  2. Goan SR, Junghahn I, Wissler M, Becker M, Aumann J, Just U, Martiny-Baron G, Fichtner I, Henschler R: Donor stromal cells from human blood engraft in NOD/SCID mice. Blood. 2000 Dec 1;96(12):3971-8. [PubMed:11090086  ] 
  3. Rhaleb NE, Peng H, Harding P, Tayeh M, LaPointe MC, Carretero OA: Effect of N-acetyl-seryl-aspartyl-lysyl-proline on DNA and collagen synthesis in rat cardiac fibroblasts. Hypertension. 2001 Mar;37(3):827-32. doi: 10.1161/01.hyp.37.3.827. [PubMed:11244003  ] 
  4. Clayton PT, Eaton S, Aynsley-Green A, Edginton M, Hussain K, Krywawych S, Datta V, Malingre HE, Berger R, van den Berg IE: Hyperinsulinism in short-chain L-3-hydroxyacyl-CoA dehydrogenase deficiency reveals the importance of beta-oxidation in insulin secretion. J Clin Invest. 2001 Aug;108(3):457-65. doi: 10.1172/JCI11294. [PubMed:11489939  ] 
  5. Watkins NA, Smethurst PA, Allen D, Smith GA, Ouwehand WH: Platelet alphaIIbbeta3 recombinant autoantibodies from the B-cell repertoire of a post-transfusion purpura patient. Br J Haematol. 2002 Mar;116(3):677-85. doi: 10.1046/j.0007-1048.2001.03301.x. [PubMed:11849233  ] 
  6. LOTUS database [Link]