NP-MRD: Showing NP-Card for (2r)-1-{[(4s)-4-amino-4-carboxy-1-hydroxybutylidene]amino}pyrrolidine-2-carboxylic acid (NP0183544)

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Record Information

Version

2.0

Created at

2022-09-03 22:28:31 UTC

Updated at

2022-09-03 22:28:32 UTC

NP-MRD ID

NP0183544

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(2r)-1-{[(4s)-4-amino-4-carboxy-1-hydroxybutylidene]amino}pyrrolidine-2-carboxylic acid

Description

(2r)-1-{[(4s)-4-amino-4-carboxy-1-hydroxybutylidene]amino}pyrrolidine-2-carboxylic acid is found in Linum usitatissimum.

Structure

MOL 3D MOL SDF PDB SMILES InChI

     RDKit          3D

 35 35  0  0  0  0  0  0  0  0999 V2000
    2.8829   -1.2585    0.9593 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.1846   -0.3427   -0.1064 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.9925    0.4212   -0.5373 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8954   -0.4401   -1.0686 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3242   -1.4363   -0.1793 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9142   -2.6366    0.1570 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8494   -1.2124    0.3697 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5702   -0.0474    0.1284 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3293    1.2382    0.7618 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6865    1.9090    0.8344 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5005    1.2762   -0.2523 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6778    0.1023   -0.7840 C   0  0  2  0  0  0  0  0  0  0  0  0
   -3.5378   -1.0888   -0.7956 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5571   -1.1544   -1.5268 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2479   -2.1830    0.0054 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.3411    0.5304    0.2412 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.8974    0.3974    1.3380 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.7912    1.4761   -0.6421 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.8671   -0.8264    1.8942 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.5049   -2.0849    0.9429 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.5107   -0.9681   -0.9850 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2902    1.2081   -1.2913 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5802    1.0532    0.3139 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2222   -0.9411   -2.0419 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0859    0.2683   -1.4357 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4126   -3.5011    0.0382 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9279    1.0939    1.7767 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6668    1.8841    0.1726 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1483    1.7400    1.8482 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6102    2.9941    0.6319 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7131    1.9593   -1.0974 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4671    0.9464    0.1577 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2840    0.3530   -1.8051 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2371   -2.0153    1.0159 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.3136    1.2859   -1.4776 H   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  0
  2  3  1  0
  3  4  1  0
  4  5  1  0
  5  6  1  0
  5  7  2  0
  7  8  1  0
  8  9  1  0
  9 10  1  0
 10 11  1  0
 11 12  1  0
 12 13  1  0
 13 15  1  0
 13 14  2  0
  2 16  1  0
 16 18  1  0
 16 17  2  0
 12  8  1  0
  2 21  1  6
  1 19  1  0
  1 20  1  0
  3 22  1  0
  3 23  1  0
  4 24  1  0
  4 25  1  0
  6 26  1  0
  9 27  1  0
  9 28  1  0
 10 29  1  0
 10 30  1  0
 11 31  1  0
 11 32  1  0
 12 33  1  6
 15 34  1  0
 18 35  1  0
M  END


  Mrv1652305221920352D          

 20 20  0  0  1  0            999 V2000
   -3.5607    4.8674    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9732    4.1529    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1904    3.8754    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5240    3.4629    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7537    4.6959    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9049    3.4629    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -3.4211    3.5398    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.2385    3.8754    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6194    3.8754    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5927    2.7328    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9049    2.6379    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9530    3.4629    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6674    3.8754    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2385    4.7004    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.3338    3.4629    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.6194    4.7004    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3773    2.4779    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9796    2.1808    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.9049    4.2879    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2180    3.3263    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  0  0  0  0
  4  3  1  0  0  0  0
  5  1  1  0  0  0  0
  6  3  1  0  0  0  0
  7  2  1  0  0  0  0
  8  4  1  0  0  0  0
  9  6  1  0  0  0  0
  7 10  1  1  0  0  0
  6 11  1  6  0  0  0
 12  8  2  0  0  0  0
 13  5  1  0  0  0  0
 13  7  1  0  0  0  0
 12 13  1  4  0  0  0
 14  8  1  0  0  0  0
 15  9  2  0  0  0  0
 16  9  1  0  0  0  0
 17 10  2  0  0  0  0
 18 10  1  0  0  0  0
  6 19  1  6  0  0  0
  7 20  1  6  0  0  0
M  END
> <DATABASE_ID>
NP0183544

> <DATABASE_NAME>
NP-MRD

> <SMILES>
[H][C@](N)(CCC(O)=NN1CCC[C@]1([H])C(O)=O)C(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C10H17N3O5/c11-6(9(15)16)3-4-8(14)12-13-5-1-2-7(13)10(17)18/h6-7H,1-5,11H2,(H,12,14)(H,15,16)(H,17,18)/t6-,7+/m0/s1

> <INCHI_KEY>
KWWHDNLMGLRNRN-NKWVEPMBSA-N

> <FORMULA>
C10H17N3O5

> <MOLECULAR_WEIGHT>
259.2591

> <EXACT_MASS>
259.116820669

> <JCHEM_ACCEPTOR_COUNT>
8

> <JCHEM_ATOM_COUNT>
35

> <JCHEM_AVERAGE_POLARIZABILITY>
25.313255738240407

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2R)-1-{[(4S)-4-amino-4-carboxy-1-hydroxybutylidene]amino}pyrrolidine-2-carboxylic acid

> <ALOGPS_LOGP>
-3.24

> <JCHEM_LOGP>
-3.2999328574686375

> <ALOGPS_LOGS>
-1.71

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
3.984842937075189

> <JCHEM_PKA_STRONGEST_ACIDIC>
2.0550933107466776

> <JCHEM_PKA_STRONGEST_BASIC>
9.536100975909461

> <JCHEM_POLAR_SURFACE_AREA>
136.45

> <JCHEM_REFRACTIVITY>
60.09590000000001

> <JCHEM_ROTATABLE_BOND_COUNT>
6

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
5.02e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(2R)-1-{[(4S)-4-amino-4-carboxy-1-hydroxybutylidene]amino}pyrrolidine-2-carboxylic acid

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 22-MAY-19   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   22-MAY-19         0                                  
HETATM    1  C   UNK     0      -6.647   9.086   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -7.417   7.752   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       0.355   7.234   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -0.978   6.464   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      -5.140   8.766   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       1.689   6.464   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      -6.386   6.608   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      -2.312   7.234   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       3.023   7.234   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      -6.706   5.101   0.000  0.00  0.00           C+0
HETATM   11  N   UNK     0       1.689   4.924   0.000  0.00  0.00           N+0
HETATM   12  N   UNK     0      -3.646   6.464   0.000  0.00  0.00           N+0
HETATM   13  N   UNK     0      -4.979   7.234   0.000  0.00  0.00           N+0
HETATM   14  O   UNK     0      -2.312   8.774   0.000  0.00  0.00           O+0
HETATM   15  O   UNK     0       4.357   6.464   0.000  0.00  0.00           O+0
HETATM   16  O   UNK     0       3.023   8.774   0.000  0.00  0.00           O+0
HETATM   17  O   UNK     0      -8.171   4.625   0.000  0.00  0.00           O+0
HETATM   18  O   UNK     0      -5.562   4.071   0.000  0.00  0.00           O+0
HETATM   19  H   UNK     0       1.689   8.004   0.000  0.00  0.00           H+0
HETATM   20  H   UNK     0      -7.874   6.209   0.000  0.00  0.00           H+0
CONECT    1    2    5                                                       
CONECT    2    1    7                                                       
CONECT    3    4    6                                                       
CONECT    4    3    8                                                       
CONECT    5    1   13                                                       
CONECT    6    3    9   11   19                                             
CONECT    7    2   10   13   20                                             
CONECT    8    4   12   14                                                  
CONECT    9    6   15   16                                                  
CONECT   10    7   17   18                                                  
CONECT   11    6                                                            
CONECT   12    8   13                                                       
CONECT   13    5    7   12                                                  
CONECT   14    8                                                            
CONECT   15    9                                                            
CONECT   16    9                                                            
CONECT   17   10                                                            
CONECT   18   10                                                            
CONECT   19    6                                                            
CONECT   20    7                                                            
MASTER        0    0    0    0    0    0    0    0   20    0   40    0
END

View in JSmol

Synonyms

Value	Source
N-(D-2-Carboxy-1-pyrrolidinyl)-L-glutamine	ChEBI
N-(gamma-L-Glutamyl)amino-D-proline	ChEBI
N-(g-L-Glutamyl)amino-D-proline	Generator
N-(Γ-L-glutamyl)amino-D-proline	Generator
1-((N-gamma-Glu)-amino)-pro	MeSH
1-((N-gamma-L-Glutamyl)-amino)-D-proline	MeSH

Chemical Formula

C₁₀H₁₇N₃O₅

Average Mass

259.2591 Da

Monoisotopic Mass

259.11682 Da

IUPAC Name

(2R)-1-{[(4S)-4-amino-4-carboxy-1-hydroxybutylidene]amino}pyrrolidine-2-carboxylic acid

Traditional Name

(2R)-1-{[(4S)-4-amino-4-carboxy-1-hydroxybutylidene]amino}pyrrolidine-2-carboxylic acid

CAS Registry Number

Not Available

SMILES

[H][C@](N)(CCC(O)=NN1CCC[C@]1([H])C(O)=O)C(O)=O

InChI Identifier

InChI=1S/C10H17N3O5/c11-6(9(15)16)3-4-8(14)12-13-5-1-2-7(13)10(17)18/h6-7H,1-5,11H2,(H,12,14)(H,15,16)(H,17,18)/t6-,7+/m0/s1

InChI Key

KWWHDNLMGLRNRN-NKWVEPMBSA-N

Experimental Spectra

Not Available

Predicted Spectra

Spectrum Type	Description	Depositor ID	Depositor Organization	Depositor	Deposition Date	View
1D NMR	¹³C NMR Spectrum (1D, 25 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 252 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 50 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 75 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 101 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 126 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 151 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 176 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 201 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 226 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum

Chemical Shift Submissions

Not Available

Species

Species of Origin

Species Name	Source	Reference
Linum usitatissimum	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as glutamine and derivatives. Glutamine and derivatives are compounds containing glutamine or a derivative thereof resulting from reaction of glutamine at the amino group or the carboxy group, or from the replacement of any hydrogen of glycine by a heteroatom.

Kingdom

Organic compounds

Super Class

Organic acids and derivatives

Class

Carboxylic acids and derivatives

Sub Class

Amino acids, peptides, and analogues

Direct Parent

Glutamine and derivatives

Alternative Parents

Substituents

Glutamine or derivatives
Proline or derivatives
Alpha-amino acid
L-alpha-amino acid
Pyrrolidine carboxylic acid
Pyrrolidine carboxylic acid or derivatives
Heterocyclic fatty acid
Dicarboxylic acid or derivatives
Fatty acid
Fatty acyl
Pyrrolidine
Carboxylic acid hydrazide
Amino acid
Azacycle
Organoheterocyclic compound
Carboxylic acid
Hydrocarbon derivative
Primary amine
Organooxygen compound
Organonitrogen compound
Primary aliphatic amine
Organopnictogen compound
Organic oxygen compound
Organic oxide
Carbonyl group
Amine
Organic nitrogen compound
Aliphatic heteromonocyclic compound

Molecular Framework

Aliphatic heteromonocyclic compounds

External Descriptors

carbohydrazide (CHEBI:28004 )
pyrrolidinemonocarboxylic acid (CHEBI:28004 )
D-proline derivative (CHEBI:28004 )

Physical Properties

State

Not Available

Experimental Properties

Property	Value	Reference
Melting Point	Not Available	Not Available
Boiling Point	Not Available	Not Available
Water Solubility	Not Available	Not Available
LogP	Not Available	Not Available

Predicted Properties

Property	Value	Source
logP	-3.2	ALOGPS
logP	-3.3	ChemAxon
logS	-1.7	ALOGPS
pKa (Strongest Acidic)	2.06	ChemAxon
pKa (Strongest Basic)	9.54	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	8	ChemAxon
Hydrogen Donor Count	4	ChemAxon
Polar Surface Area	136.45 Å²	ChemAxon
Rotatable Bond Count	6	ChemAxon
Refractivity	60.1 m³·mol⁻¹	ChemAxon
Polarizability	25.31 Å³	ChemAxon
Number of Rings	1	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

External Links

HMDB ID

Not Available

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

FDB017896

KNApSAcK ID

Not Available

Chemspider ID

Not Available

KEGG Compound ID

C05939

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

160920

PDB ID

Not Available

ChEBI ID

28004

Good Scents ID

Not Available

References

General References

LOTUS database [Link]

Showing NP-Card for (2r)-1-{[(4s)-4-amino-4-carboxy-1-hydroxybutylidene]amino}pyrrolidine-2-carboxylic acid (NP0183544)

MOL for NP0183544 ((2r)-1-{[(4s)-4-amino-4-carboxy-1-hydroxybutylidene]amino}pyrrolidine-2-carboxylic acid)

3D MOL for NP0183544 ((2r)-1-{[(4s)-4-amino-4-carboxy-1-hydroxybutylidene]amino}pyrrolidine-2-carboxylic acid)

3D SDF for NP0183544 ((2r)-1-{[(4s)-4-amino-4-carboxy-1-hydroxybutylidene]amino}pyrrolidine-2-carboxylic acid)

3D-SDF for NP0183544 ((2r)-1-{[(4s)-4-amino-4-carboxy-1-hydroxybutylidene]amino}pyrrolidine-2-carboxylic acid)

PDB for NP0183544 ((2r)-1-{[(4s)-4-amino-4-carboxy-1-hydroxybutylidene]amino}pyrrolidine-2-carboxylic acid)

3D PDB for NP0183544 ((2r)-1-{[(4s)-4-amino-4-carboxy-1-hydroxybutylidene]amino}pyrrolidine-2-carboxylic acid)

SMILES for NP0183544 ((2r)-1-{[(4s)-4-amino-4-carboxy-1-hydroxybutylidene]amino}pyrrolidine-2-carboxylic acid)

INCHI for NP0183544 ((2r)-1-{[(4s)-4-amino-4-carboxy-1-hydroxybutylidene]amino}pyrrolidine-2-carboxylic acid)

Structure for NP0183544 ((2r)-1-{[(4s)-4-amino-4-carboxy-1-hydroxybutylidene]amino}pyrrolidine-2-carboxylic acid)

3D Structure for NP0183544 ((2r)-1-{[(4s)-4-amino-4-carboxy-1-hydroxybutylidene]amino}pyrrolidine-2-carboxylic acid)