NP-MRD: Showing NP-Card for (2r)-2-[(4r)-1-(2-hydroxy-4-{[(2s,3r,4s,5r)-3,4,5-trihydroxyoxan-2-yl]oxy}butyl)-2-iminoimidazolidin-4-yl]-3-[(2r)-4-methyl-5-oxo-2h-furan-2-yl]propanoic acid (NP0197103)

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Record Information

Version

2.0

Created at

2022-09-04 15:18:19 UTC

Updated at

2022-09-04 15:18:19 UTC

NP-MRD ID

NP0197103

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(2r)-2-[(4r)-1-(2-hydroxy-4-{[(2s,3r,4s,5r)-3,4,5-trihydroxyoxan-2-yl]oxy}butyl)-2-iminoimidazolidin-4-yl]-3-[(2r)-4-methyl-5-oxo-2h-furan-2-yl]propanoic acid

Description

CHEMBL2407423 belongs to the class of organic compounds known as o-glycosyl compounds. These are glycoside in which a sugar group is bonded through one carbon to another group via a O-glycosidic bond. (2r)-2-[(4r)-1-(2-hydroxy-4-{[(2s,3r,4s,5r)-3,4,5-trihydroxyoxan-2-yl]oxy}butyl)-2-iminoimidazolidin-4-yl]-3-[(2r)-4-methyl-5-oxo-2h-furan-2-yl]propanoic acid is found in Plumbago zeylanica. Based on a literature review very few articles have been published on CHEMBL2407423.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652309042217182D          

 33 35  0  0  1  0            999 V2000
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   -3.2221   -4.3546    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4151   -4.1830    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0026   -4.8975    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.1822   -4.9837    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6972   -4.3163    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.0328   -3.5626    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5479   -2.8952    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8533   -3.4764    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
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M  END

     RDKit          3D

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M  END


  Mrv1652309042217182D          

 33 35  0  0  1  0            999 V2000
   -3.8352   -3.8025    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2221   -4.3546    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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M  END
> <DATABASE_ID>
NP0197103

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CC1=C[C@@H](C[C@H]([C@@H]2CN(CC(O)CCO[C@H]3OC[C@@H](O)[C@H](O)[C@H]3O)C(=N)N2)C(O)=O)OC1=O

> <INCHI_IDENTIFIER>
InChI=1S/C20H31N3O10/c1-9-4-11(33-18(9)30)5-12(17(28)29)13-7-23(20(21)22-13)6-10(24)2-3-31-19-16(27)15(26)14(25)8-32-19/h4,10-16,19,24-27H,2-3,5-8H2,1H3,(H2,21,22)(H,28,29)/t10?,11-,12+,13-,14+,15-,16+,19-/m0/s1

> <INCHI_KEY>
GSQGGVXWVLMSPQ-MDYKANHUSA-N

> <FORMULA>
C20H31N3O10

> <MOLECULAR_WEIGHT>
473.479

> <EXACT_MASS>
473.20094421

> <JCHEM_ACCEPTOR_COUNT>
12

> <JCHEM_ATOM_COUNT>
64

> <JCHEM_AVERAGE_POLARIZABILITY>
46.87910324790807

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
7

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2R)-2-[(4R)-1-(2-hydroxy-4-{[(2S,3R,4S,5R)-3,4,5-trihydroxyoxan-2-yl]oxy}butyl)-2-iminoimidazolidin-4-yl]-3-[(2R)-4-methyl-5-oxo-2,5-dihydrofuran-2-yl]propanoic acid

> <JCHEM_LOGP>
-3.8011325564906877

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
12.23618032938875

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.6876257958767016

> <JCHEM_PKA_STRONGEST_BASIC>
11.09937886063365

> <JCHEM_POLAR_SURFACE_AREA>
202.1

> <JCHEM_REFRACTIVITY>
120.87650000000002

> <JCHEM_ROTATABLE_BOND_COUNT>
10

> <JCHEM_RULE_OF_FIVE>
0

> <JCHEM_TRADITIONAL_IUPAC>
(2R)-2-[(4R)-1-(2-hydroxy-4-{[(2S,3R,4S,5R)-3,4,5-trihydroxyoxan-2-yl]oxy}butyl)-2-iminoimidazolidin-4-yl]-3-[(2R)-4-methyl-5-oxo-2H-furan-2-yl]propanoic acid

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 04-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   04-SEP-22         0                                  
HETATM    1  C   UNK     0      -7.159  -7.098   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -6.015  -8.129   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -4.508  -7.808   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -3.738  -9.142   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      -2.207  -9.303   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      -1.302  -8.057   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      -1.928  -6.650   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0      -1.023  -5.404   0.000  0.00  0.00           O+0
HETATM    9  O   UNK     0      -3.459  -6.489   0.000  0.00  0.00           O+0
HETATM   10  C   UNK     0       0.230  -8.218   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       1.260  -7.074   0.000  0.00  0.00           C+0
HETATM   12  N   UNK     0       2.667  -7.700   0.000  0.00  0.00           N+0
HETATM   13  C   UNK     0       4.001  -6.930   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       5.335  -7.700   0.000  0.00  0.00           C+0
HETATM   15  O   UNK     0       5.335  -9.240   0.000  0.00  0.00           O+0
HETATM   16  C   UNK     0       6.668  -6.930   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       8.002  -7.700   0.000  0.00  0.00           C+0
HETATM   18  O   UNK     0       9.336  -6.930   0.000  0.00  0.00           O+0
HETATM   19  C   UNK     0      10.669  -7.700   0.000  0.00  0.00           C+0
HETATM   20  O   UNK     0      12.003  -6.930   0.000  0.00  0.00           O+0
HETATM   21  C   UNK     0      13.337  -7.700   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0      13.337  -9.240   0.000  0.00  0.00           C+0
HETATM   23  O   UNK     0      14.670 -10.010   0.000  0.00  0.00           O+0
HETATM   24  C   UNK     0      12.003 -10.010   0.000  0.00  0.00           C+0
HETATM   25  O   UNK     0      12.003 -11.550   0.000  0.00  0.00           O+0
HETATM   26  C   UNK     0      10.669  -9.240   0.000  0.00  0.00           C+0
HETATM   27  O   UNK     0       9.336 -10.010   0.000  0.00  0.00           O+0
HETATM   28  C   UNK     0       2.506  -9.232   0.000  0.00  0.00           C+0
HETATM   29  N   UNK     0       3.651 -10.262   0.000  0.00  0.00           N+0
HETATM   30  N   UNK     0       1.000  -9.552   0.000  0.00  0.00           N+0
HETATM   31  O   UNK     0      -4.769 -10.286   0.000  0.00  0.00           O+0
HETATM   32  C   UNK     0      -6.176  -9.660   0.000  0.00  0.00           C+0
HETATM   33  O   UNK     0      -7.509 -10.430   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3   32                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5   31                                                  
CONECT    5    4    6                                                       
CONECT    6    5    7   10                                                  
CONECT    7    6    8    9                                                  
CONECT    8    7                                                            
CONECT    9    7                                                            
CONECT   10    6   11   30                                                  
CONECT   11   10   12                                                       
CONECT   12   11   13   28                                                  
CONECT   13   12   14                                                       
CONECT   14   13   15   16                                                  
CONECT   15   14                                                            
CONECT   16   14   17                                                       
CONECT   17   16   18                                                       
CONECT   18   17   19                                                       
CONECT   19   18   20   26                                                  
CONECT   20   19   21                                                       
CONECT   21   20   22                                                       
CONECT   22   21   23   24                                                  
CONECT   23   22                                                            
CONECT   24   22   25   26                                                  
CONECT   25   24                                                            
CONECT   26   24   19   27                                                  
CONECT   27   26                                                            
CONECT   28   12   29   30                                                  
CONECT   29   28                                                            
CONECT   30   28   10                                                       
CONECT   31    4   32                                                       
CONECT   32   31    2   33                                                  
CONECT   33   32                                                            
MASTER        0    0    0    0    0    0    0    0   33    0   70    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₂₀H₃₁N₃O₁₀

Average Mass

473.4790 Da

Monoisotopic Mass

473.20094 Da

IUPAC Name

(2R)-2-[(4R)-1-(2-hydroxy-4-{[(2S,3R,4S,5R)-3,4,5-trihydroxyoxan-2-yl]oxy}butyl)-2-iminoimidazolidin-4-yl]-3-[(2R)-4-methyl-5-oxo-2,5-dihydrofuran-2-yl]propanoic acid

Traditional Name

(2R)-2-[(4R)-1-(2-hydroxy-4-{[(2S,3R,4S,5R)-3,4,5-trihydroxyoxan-2-yl]oxy}butyl)-2-iminoimidazolidin-4-yl]-3-[(2R)-4-methyl-5-oxo-2H-furan-2-yl]propanoic acid

CAS Registry Number

Not Available

SMILES

CC1=C[C@@H](C[C@H]([C@@H]2CN(CC(O)CCO[C@H]3OC[C@@H](O)[C@H](O)[C@H]3O)C(=N)N2)C(O)=O)OC1=O

InChI Identifier

InChI=1S/C20H31N3O10/c1-9-4-11(33-18(9)30)5-12(17(28)29)13-7-23(20(21)22-13)6-10(24)2-3-31-19-16(27)15(26)14(25)8-32-19/h4,10-16,19,24-27H,2-3,5-8H2,1H3,(H2,21,22)(H,28,29)/t10?,11-,12+,13-,14+,15-,16+,19-/m0/s1

InChI Key

GSQGGVXWVLMSPQ-MDYKANHUSA-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
Plumbago zeylanica	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as o-glycosyl compounds. These are glycoside in which a sugar group is bonded through one carbon to another group via a O-glycosidic bond.

Kingdom

Organic compounds

Super Class

Organic oxygen compounds

Class

Organooxygen compounds

Sub Class

Carbohydrates and carbohydrate conjugates

Direct Parent

O-glycosyl compounds

Alternative Parents

Substituents

O-glycosyl compound
Imidazolyl carboxylic acid derivative
2-furanone
Dicarboxylic acid or derivatives
Monosaccharide
Oxane
Dihydrofuran
2-imidazoline
Alpha,beta-unsaturated carboxylic ester
Enoate ester
Carboxylic acid ester
Guanidine
Lactone
Secondary alcohol
Acetal
Carboxylic acid derivative
Carboxylic acid
Oxacycle
Azacycle
Organoheterocyclic compound
Organic 1,3-dipolar compound
Propargyl-type 1,3-dipolar organic compound
Polyol
Carboximidamide
Organic nitrogen compound
Carbonyl group
Alcohol
Organopnictogen compound
Organic oxide
Organonitrogen compound
Hydrocarbon derivative
Aliphatic heteromonocyclic compound

Molecular Framework

Aliphatic heteromonocyclic compounds

External Descriptors

Not Available

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	-3.8	ChemAxon
pKa (Strongest Acidic)	3.69	ChemAxon
pKa (Strongest Basic)	11.1	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	12	ChemAxon
Hydrogen Donor Count	7	ChemAxon
Polar Surface Area	202.1 Å²	ChemAxon
Rotatable Bond Count	10	ChemAxon
Refractivity	120.88 m³·mol⁻¹	ChemAxon
Polarizability	46.88 Å³	ChemAxon
Number of Rings	3	ChemAxon
Bioavailability	No	ChemAxon
Rule of Five	No	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	Yes	ChemAxon

External Links

HMDB ID

Not Available

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

Not Available

KNApSAcK ID

Not Available

Chemspider ID

30821889

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

71746628

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

LOTUS database [Link]

Showing NP-Card for (2r)-2-[(4r)-1-(2-hydroxy-4-{[(2s,3r,4s,5r)-3,4,5-trihydroxyoxan-2-yl]oxy}butyl)-2-iminoimidazolidin-4-yl]-3-[(2r)-4-methyl-5-oxo-2h-furan-2-yl]propanoic acid (NP0197103)

MOL for NP0197103 ((2r)-2-[(4r)-1-(2-hydroxy-4-{[(2s,3r,4s,5r)-3,4,5-trihydroxyoxan-2-yl]oxy}butyl)-2-iminoimidazolidin-4-yl]-3-[(2r)-4-methyl-5-oxo-2h-furan-2-yl]propanoic acid)

3D MOL for NP0197103 ((2r)-2-[(4r)-1-(2-hydroxy-4-{[(2s,3r,4s,5r)-3,4,5-trihydroxyoxan-2-yl]oxy}butyl)-2-iminoimidazolidin-4-yl]-3-[(2r)-4-methyl-5-oxo-2h-furan-2-yl]propanoic acid)

3D SDF for NP0197103 ((2r)-2-[(4r)-1-(2-hydroxy-4-{[(2s,3r,4s,5r)-3,4,5-trihydroxyoxan-2-yl]oxy}butyl)-2-iminoimidazolidin-4-yl]-3-[(2r)-4-methyl-5-oxo-2h-furan-2-yl]propanoic acid)

3D-SDF for NP0197103 ((2r)-2-[(4r)-1-(2-hydroxy-4-{[(2s,3r,4s,5r)-3,4,5-trihydroxyoxan-2-yl]oxy}butyl)-2-iminoimidazolidin-4-yl]-3-[(2r)-4-methyl-5-oxo-2h-furan-2-yl]propanoic acid)

PDB for NP0197103 ((2r)-2-[(4r)-1-(2-hydroxy-4-{[(2s,3r,4s,5r)-3,4,5-trihydroxyoxan-2-yl]oxy}butyl)-2-iminoimidazolidin-4-yl]-3-[(2r)-4-methyl-5-oxo-2h-furan-2-yl]propanoic acid)

3D PDB for NP0197103 ((2r)-2-[(4r)-1-(2-hydroxy-4-{[(2s,3r,4s,5r)-3,4,5-trihydroxyoxan-2-yl]oxy}butyl)-2-iminoimidazolidin-4-yl]-3-[(2r)-4-methyl-5-oxo-2h-furan-2-yl]propanoic acid)

SMILES for NP0197103 ((2r)-2-[(4r)-1-(2-hydroxy-4-{[(2s,3r,4s,5r)-3,4,5-trihydroxyoxan-2-yl]oxy}butyl)-2-iminoimidazolidin-4-yl]-3-[(2r)-4-methyl-5-oxo-2h-furan-2-yl]propanoic acid)

INCHI for NP0197103 ((2r)-2-[(4r)-1-(2-hydroxy-4-{[(2s,3r,4s,5r)-3,4,5-trihydroxyoxan-2-yl]oxy}butyl)-2-iminoimidazolidin-4-yl]-3-[(2r)-4-methyl-5-oxo-2h-furan-2-yl]propanoic acid)

Structure for NP0197103 ((2r)-2-[(4r)-1-(2-hydroxy-4-{[(2s,3r,4s,5r)-3,4,5-trihydroxyoxan-2-yl]oxy}butyl)-2-iminoimidazolidin-4-yl]-3-[(2r)-4-methyl-5-oxo-2h-furan-2-yl]propanoic acid)

3D Structure for NP0197103 ((2r)-2-[(4r)-1-(2-hydroxy-4-{[(2s,3r,4s,5r)-3,4,5-trihydroxyoxan-2-yl]oxy}butyl)-2-iminoimidazolidin-4-yl]-3-[(2r)-4-methyl-5-oxo-2h-furan-2-yl]propanoic acid)