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Showing NP-Card for 3,4-Dehydro-d/L-proline (NP0002612)

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Record Information
Version1.0
Created at2020-11-23 18:25:15 UTC
Updated at2021-08-12 19:51:39 UTC
NP-MRD IDNP0002612
Secondary Accession NumbersNone
Natural Product Identification
Common Name3,4-Dehydro-d/L-proline
Provided ByBMRBBMRB logo
Description(2S)-2,5-dihydro-1H-pyrrole-2-carboxylic acid 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. 3,4-Dehydro-d/L-proline is found in Santalum album . It was first documented in 2008 (PMID: 17984079). Based on a literature review very few articles have been published on (2S)-2,5-dihydro-1H-pyrrole-2-carboxylic acid (PMID: 34299166) (PMID: 29922306) (PMID: 28194412) (PMID: 26682613) (PMID: 25130741) (PMID: 24974330).
Structure
Thumb
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for NP0002612 (3,4-Dehydro-d/L-proline)


     RDKit          2D

 15 15  0  0  0  0  0  0  0  0999 V2000
   -2.6745   -1.7312    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7395   -0.5583    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2878    0.8379    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2562   -0.7815    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1483   -1.3083    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0832   -0.1354    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2566    1.1163    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1892    0.7170    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7711    1.0612    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6333   -2.2334    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5476   -2.7542    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.5818   -0.2023    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7083    2.5125    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5879    1.8076    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3622    1.6520    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  2  4  1  0
  4  5  1  0
  5  6  2  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
  6 12  1  0
  7 13  1  1
  7 14  1  0
  8 15  1  0
M  END
Download

3D MOL for NP0002612 (3,4-Dehydro-d/L-proline)

NP0002612
     RDKit          3D

 15 15  0  0  0  0  0  0  0  0999 V2000
    2.5427   -1.2456   -0.7893 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.8357   -0.3860   -0.1032 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4395    0.3775    0.8098 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.4224   -0.3837   -0.3479 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.2400    0.8737   -0.6501 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5105    0.7603   -0.2584 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6505   -0.6303    0.3020 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3306   -0.8095    0.8824 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.6262    1.3422    0.7067 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0925   -1.1566   -1.1006 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2434    1.7177   -1.1550 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2158    1.5687   -0.2848 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6810   -1.3230   -0.5578 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4618   -0.7284    1.0025 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1122    0.0229    1.5438 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  2  4  1  0
  4  5  1  0
  5  6  2  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
  6 12  1  0
  7 13  1  0
  7 14  1  0
  8 15  1  0
M  END
Download

3D SDF for NP0002612 (3,4-Dehydro-d/L-proline)


     RDKit          2D

 15 15  0  0  0  0  0  0  0  0999 V2000
   -2.6745   -1.7312    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7395   -0.5583    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2878    0.8379    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2562   -0.7815    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1483   -1.3083    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0832   -0.1354    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2566    1.1163    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1892    0.7170    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7711    1.0612    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6333   -2.2334    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5476   -2.7542    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.5818   -0.2023    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7083    2.5125    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5879    1.8076    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3622    1.6520    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  2  4  1  0
  4  5  1  0
  5  6  2  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
  6 12  1  0
  7 13  1  1
  7 14  1  0
  8 15  1  0
M  END
> <DATABASE_ID>
NP0002612

> <DATABASE_NAME>
NP-MRD

> <SMILES>
[H]OC(=O)[C@@]1([H])N([H])C([H])([H])C([H])=C1[H]

> <INCHI_IDENTIFIER>
InChI=1S/C5H7NO2/c7-5(8)4-2-1-3-6-4/h1-2,4,6H,3H2,(H,7,8)/t4-/m0/s1

> <INCHI_KEY>
OMGHIGVFLOPEHJ-BYPYZUCNSA-N

> <FORMULA>
C5H7NO2

> <MOLECULAR_WEIGHT>
113.116

> <EXACT_MASS>
113.047678469

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_ATOM_COUNT>
15

> <JCHEM_AVERAGE_POLARIZABILITY>
10.604424506941669

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2S)-2,5-dihydro-1H-pyrrole-2-carboxylic acid

> <ALOGPS_LOGP>
-2.50

> <JCHEM_LOGP>
-2.6187226565644472

> <ALOGPS_LOGS>
0.27

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.7623978918173915

> <JCHEM_PKA_STRONGEST_BASIC>
10.660674534478495

> <JCHEM_POLAR_SURFACE_AREA>
49.33

> <JCHEM_REFRACTIVITY>
28.8729

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
2.10e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(2S)-2,5-dihydro-1H-pyrrole-2-carboxylic acid

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for NP0002612 (3,4-Dehydro-d/L-proline)

NP0002612
     RDKit          3D

 15 15  0  0  0  0  0  0  0  0999 V2000
    2.5427   -1.2456   -0.7893 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.8357   -0.3860   -0.1032 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4395    0.3775    0.8098 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.4224   -0.3837   -0.3479 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.2400    0.8737   -0.6501 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5105    0.7603   -0.2584 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6505   -0.6303    0.3020 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3306   -0.8095    0.8824 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.6262    1.3422    0.7067 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0925   -1.1566   -1.1006 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2434    1.7177   -1.1550 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2158    1.5687   -0.2848 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6810   -1.3230   -0.5578 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4618   -0.7284    1.0025 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1122    0.0229    1.5438 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  2  4  1  0
  4  5  1  0
  5  6  2  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
  6 12  1  0
  7 13  1  0
  7 14  1  0
  8 15  1  0
M  END
Download

PDB for NP0002612 (3,4-Dehydro-d/L-proline)

HEADER    PROTEIN                                 12-NOV-20   NONE
TITLE     NULL                                                        
COMPND    MOLECULE: 97858                                             
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   12-NOV-20         0                                  
HETATM    1  C   UNK     0      -0.424  -1.533  -0.416  0.00  0.00           C+0
HETATM    2  C   UNK     0      -1.092  -0.385  -0.419  0.00  0.00           C+0
HETATM    3  C   UNK     0       0.989  -1.315  -0.395  0.00  0.00           C+0
HETATM    4  C   UNK     0      -0.202   0.743  -0.371  0.00  0.00           C+0
HETATM    5  C   UNK     0      -0.379   1.539   0.827  0.00  0.00           C+0
HETATM    6  N   UNK     0       1.149   0.149  -0.403  0.00  0.00           N+0
HETATM    7  O   UNK     0      -0.702   2.716   0.763  0.00  0.00           O+0
HETATM    8  O   UNK     0      -0.211   1.049   1.942  0.00  0.00           O+0
HETATM    9  H   UNK     0      -0.853  -2.429  -0.426  0.00  0.00           H+0
HETATM   10  H   UNK     0      -2.083  -0.317  -0.441  0.00  0.00           H+0
HETATM   11  H   UNK     0       1.431  -1.732   0.512  0.00  0.00           H+0
HETATM   12  H   UNK     0       1.462  -1.759  -1.274  0.00  0.00           H+0
HETATM   13  H   UNK     0      -0.346   1.340  -1.278  0.00  0.00           H+0
HETATM   14  H   UNK     0       1.584   0.409  -1.292  0.00  0.00           H+0
HETATM   15  H   UNK     0      -0.325   1.524   2.673  0.00  0.00           H+0
CONECT    1    2    9    3                                                  
CONECT    2    1    4   10                                                  
CONECT    3    1    6   11   12                                             
CONECT    4    2    5    6   13                                             
CONECT    5    4    7    8                                                  
CONECT    6    3    4   14                                                  
CONECT    7    5                                                            
CONECT    8    5   15                                                       
CONECT    9    1                                                            
CONECT   10    2                                                            
CONECT   11    3                                                            
CONECT   12    3                                                            
CONECT   13    4                                                            
CONECT   14    6                                                            
CONECT   15    8                                                            
MASTER        0    0    0    0    0    0    0    0   15    0   30    0
END
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3D PDB for NP0002612 (3,4-Dehydro-d/L-proline)

COMPND    NP0002612
HETATM    1  O1  UNL     1       2.543  -1.246  -0.789  1.00  0.00           O  
HETATM    2  C1  UNL     1       1.836  -0.386  -0.103  1.00  0.00           C  
HETATM    3  O2  UNL     1       2.440   0.377   0.810  1.00  0.00           O  
HETATM    4  C2  UNL     1       0.422  -0.384  -0.348  1.00  0.00           C  
HETATM    5  C3  UNL     1      -0.240   0.874  -0.650  1.00  0.00           C  
HETATM    6  C4  UNL     1      -1.510   0.760  -0.258  1.00  0.00           C  
HETATM    7  C5  UNL     1      -1.651  -0.630   0.302  1.00  0.00           C  
HETATM    8  N1  UNL     1      -0.331  -0.809   0.882  1.00  0.00           N  
HETATM    9  H1  UNL     1       2.626   1.342   0.707  1.00  0.00           H  
HETATM   10  H2  UNL     1       0.093  -1.157  -1.101  1.00  0.00           H  
HETATM   11  H3  UNL     1       0.243   1.718  -1.155  1.00  0.00           H  
HETATM   12  H4  UNL     1      -2.216   1.569  -0.285  1.00  0.00           H  
HETATM   13  H5  UNL     1      -1.681  -1.323  -0.558  1.00  0.00           H  
HETATM   14  H6  UNL     1      -2.462  -0.728   1.003  1.00  0.00           H  
HETATM   15  H7  UNL     1      -0.112   0.023   1.544  1.00  0.00           H  
CONECT    1    2    2
CONECT    2    3    4
CONECT    3    9
CONECT    4    5    8   10
CONECT    5    6    6   11
CONECT    6    7   12
CONECT    7    8   13   14
CONECT    8   15
END
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SMILES for NP0002612 (3,4-Dehydro-d/L-proline)

[H]OC(=O)[C@@]1([H])N([H])C([H])([H])C([H])=C1[H]
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INCHI for NP0002612 (3,4-Dehydro-d/L-proline)

InChI=1S/C5H7NO2/c7-5(8)4-2-1-3-6-4/h1-2,4,6H,3H2,(H,7,8)/t4-/m0/s1
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View in JSmol
Synonyms
ValueSource
(2S)-2,5-Dihydro-1H-pyrrole-2-carboxylateGenerator
Chemical FormulaC5H7NO2
Average Mass113.1160 Da
Monoisotopic Mass113.04768 Da
IUPAC Name(2S)-2,5-dihydro-1H-pyrrole-2-carboxylic acid
Traditional Name(2S)-2,5-dihydro-1H-pyrrole-2-carboxylic acid
CAS Registry NumberNot Available
SMILES
[H]OC(=O)[C@@]1([H])N([H])C([H])([H])C([H])=C1[H]
InChI Identifier
InChI=1S/C5H7NO2/c7-5(8)4-2-1-3-6-4/h1-2,4,6H,3H2,(H,7,8)/t4-/m0/s1
InChI KeyOMGHIGVFLOPEHJ-BYPYZUCNSA-N
Experimental Spectra
Spectrum TypeDescriptionDepositor EmailDepositor OrganizationDepositorDeposition DateView
1D NMR13C NMR Spectrum (1D, 400 MHz, D2O, simulated)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 400 MHz, D2O, simulated)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 400 MHz, D2O, simulated)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 400 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
Santalum albumPlant
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
  • Pyrroline carboxylic acid
  • Pyrroline carboxylic acid or derivatives
  • Pyrroline
  • Amino acid
  • Carboxylic acid
  • Secondary aliphatic amine
  • Monocarboxylic acid or derivatives
  • Secondary amine
  • Organoheterocyclic compound
  • Azacycle
  • Organic oxygen compound
  • Organic nitrogen compound
  • Organooxygen compound
  • Organonitrogen compound
  • Organopnictogen compound
  • Amine
  • Carbonyl group
  • Organic oxide
  • 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-2.5ALOGPS
logP-2.6ChemAxon
logS0.27ALOGPS
pKa (Strongest Acidic)1.76ChemAxon
pKa (Strongest Basic)10.66ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count3ChemAxon
Hydrogen Donor Count2ChemAxon
Polar Surface Area49.33 ŲChemAxon
Rotatable Bond Count1ChemAxon
Refractivity28.87 m³·mol⁻¹ChemAxon
Polarizability10.6 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 ID85089
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem CompoundNot Available
PDB IDNot Available
ChEBI IDNot Available
Good Scents IDNot Available
References
General References
  1. Ulrich EL, Akutsu H, Doreleijers JF, Harano Y, Ioannidis YE, Lin J, Livny M, Mading S, Maziuk D, Miller Z, Nakatani E, Schulte CF, Tolmie DE, Kent Wenger R, Yao H, Markley JL: BioMagResBank. Nucleic Acids Res. 2008 Jan;36(Database issue):D402-8. doi: 10.1093/nar/gkm957. Epub 2007 Nov 4. [PubMed:17984079 ]
  2. Pinski A, Betekhtin A, Kwasniewska J, Chajec L, Wolny E, Hasterok R: 3,4-Dehydro-L-proline Induces Programmed Cell Death in the Roots of Brachypodium distachyon. Int J Mol Sci. 2021 Jul 14;22(14). pii: ijms22147548. doi: 10.3390/ijms22147548. [PubMed:34299166 ]
  3. Li YY, Chen XM, Zhang Y, Cho YH, Wang AR, Yeung EC, Zeng X, Guo SX, Lee YI: Immunolocalization and Changes of Hydroxyproline-Rich Glycoproteins During Symbiotic Germination of Dendrobium officinale. Front Plant Sci. 2018 Apr 25;9:552. doi: 10.3389/fpls.2018.00552. eCollection 2018. [PubMed:29922306 ]
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  5. Rizzo A, Rikken GL, Mathevet R: Ab initio study of the enantio-selective magnetic-field-induced second harmonic generation in chiral molecules. Phys Chem Chem Phys. 2016 Jan 21;18(3):1846-58. doi: 10.1039/c5cp07127e. Epub 2015 Dec 18. [PubMed:26682613 ]
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