NP-MRD: Showing NP-Card for 1h-indol-3-yl (2s,3s,4s,5r)-3,4,5-trihydroxy-5-(hydroxymethyl)oxolane-2-carboxylate (NP0241586)

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Record Information

Version

2.0

Created at

2022-09-07 01:42:37 UTC

Updated at

2022-09-07 01:42:37 UTC

NP-MRD ID

NP0241586

Secondary Accession Numbers

None

Natural Product Identification

Common Name

1h-indol-3-yl (2s,3s,4s,5r)-3,4,5-trihydroxy-5-(hydroxymethyl)oxolane-2-carboxylate

Description

SCHEMBL13845658 belongs to the class of organic compounds known as c-glycosyl compounds. These are glycoside in which a sugar group is bonded through one carbon to another group via a C-glycosidic bond. 1h-indol-3-yl (2s,3s,4s,5r)-3,4,5-trihydroxy-5-(hydroxymethyl)oxolane-2-carboxylate is found in Isatis tinctoria and Persicaria tinctoria. Based on a literature review very few articles have been published on SCHEMBL13845658.

Structure

MOL 3D MOL SDF PDB SMILES InChI

     RDKit          3D

 37 39  0  0  0  0  0  0  0  0999 V2000
    0.7165    1.9042    0.3879 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0758    0.9151    0.0129 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6040   -0.3469    0.1994 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.8231   -0.5939    0.7873 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0822   -0.8006    2.1116 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3839   -1.0035    2.2658 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.0327   -0.9416    1.0746 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.3592   -1.0814    0.7112 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.6935   -0.9571   -0.6206 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.6954   -0.6982   -1.5426 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3832   -0.5579   -1.1989 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0447   -0.6825    0.1402 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2547    1.0101   -0.6390 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.7819   -0.2067   -0.9712 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1104   -0.2401   -0.6471 C   0  0  2  0  0  0  0  0  0  0  0  0
   -3.2334   -0.9850    0.5431 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9856   -0.9072   -1.6708 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.2945   -0.8813   -1.1719 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5512    1.1649   -0.3292 C   0  0  1  0  0  0  0  0  0  0  0  0
   -4.5884    1.2183    0.5686 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2570    1.7314    0.2386 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.1645    3.0971    0.0658 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.3220   -0.7930    2.8837 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.8735   -1.1872    3.1591 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.1030   -1.2831    1.4668 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.7150   -1.0564   -0.9655 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.9874   -0.6048   -2.5883 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5812   -0.3545   -1.9037 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1673    1.6103   -1.5821 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4340   -1.5630    0.6753 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6935   -1.9767   -1.7092 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9077   -0.4867   -2.6767 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.2178   -1.0064   -0.1780 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7472    1.7533   -1.2693 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0380    2.1128    0.4658 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1221    1.4330    1.3134 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9272    3.2449   -0.9034 H   0  0  0  0  0  0  0  0  0  0  0  0
 18 17  1  0
 17 15  1  0
 15 16  1  1
 15 14  1  0
 14 13  1  0
 13 21  1  0
 21 22  1  0
 21 19  1  0
 19 20  1  0
 13  2  1  0
  2  1  2  0
  2  3  1  0
  3  4  1  0
  4  5  2  0
  5  6  1  0
  6  7  1  0
  7  8  2  0
  8  9  1  0
  9 10  2  0
 10 11  1  0
 11 12  2  0
 19 15  1  0
 12  4  1  0
 12  7  1  0
 18 33  1  0
 17 31  1  0
 17 32  1  0
 16 30  1  0
 13 29  1  6
 21 36  1  1
 22 37  1  0
 19 34  1  6
 20 35  1  0
  5 23  1  0
  6 24  1  0
  8 25  1  0
  9 26  1  0
 10 27  1  0
 11 28  1  0
M  END


  Mrv1652309072203422D          

 22 24  0  0  1  0            999 V2000
    2.2428   -2.5916    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4358   -2.7631    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8838   -2.1500    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.1387   -1.3654    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6538   -0.6979    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1387   -0.0305    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.9233   -0.2854    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6378    0.1271    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3523   -0.2854    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3523   -1.1104    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6378   -1.5229    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9233   -1.1104    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1809   -3.5477    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.6658   -4.2152    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.1809   -4.8826    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.8953   -5.2951    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.8453   -5.6363    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3302   -6.3037    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.3963   -4.6277    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.2712   -5.1126    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.3963   -3.8027    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.2712   -3.3177    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  2  0  0  0  0
  5  6  1  0  0  0  0
  6  7  1  0  0  0  0
  7  8  2  0  0  0  0
  8  9  1  0  0  0  0
  9 10  2  0  0  0  0
 10 11  1  0  0  0  0
 11 12  2  0  0  0  0
  4 12  1  0  0  0  0
  7 12  1  0  0  0  0
 13  2  1  1  0  0  0
 13 14  1  0  0  0  0
 14 15  1  0  0  0  0
 15 16  1  1  0  0  0
 15 17  1  6  0  0  0
 17 18  1  0  0  0  0
 15 19  1  0  0  0  0
 19 20  1  1  0  0  0
 19 21  1  0  0  0  0
 13 21  1  0  0  0  0
 21 22  1  6  0  0  0
M  END
> <DATABASE_ID>
NP0241586

> <DATABASE_NAME>
NP-MRD

> <SMILES>
OC[C@@]1(O)O[C@@H]([C@@H](O)[C@@H]1O)C(=O)OC1=CNC2=CC=CC=C12

> <INCHI_IDENTIFIER>
InChI=1S/C14H15NO7/c16-6-14(20)12(18)10(17)11(22-14)13(19)21-9-5-15-8-4-2-1-3-7(8)9/h1-5,10-12,15-18,20H,6H2/t10-,11+,12+,14-/m1/s1

> <INCHI_KEY>
KGXOHVOUKNLUNP-OWTLIXCDSA-N

> <FORMULA>
C14H15NO7

> <MOLECULAR_WEIGHT>
309.274

> <EXACT_MASS>
309.084851827

> <JCHEM_ACCEPTOR_COUNT>
6

> <JCHEM_ATOM_COUNT>
37

> <JCHEM_AVERAGE_POLARIZABILITY>
29.543026671785544

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
5

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
1H-indol-3-yl (2S,3S,4S,5R)-3,4,5-trihydroxy-5-(hydroxymethyl)oxolane-2-carboxylate

> <JCHEM_LOGP>
-0.5351102823333334

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
12.628656812121154

> <JCHEM_PKA_STRONGEST_ACIDIC>
10.274102848038757

> <JCHEM_PKA_STRONGEST_BASIC>
-3.4512936448794225

> <JCHEM_POLAR_SURFACE_AREA>
132.24

> <JCHEM_REFRACTIVITY>
71.86140000000002

> <JCHEM_ROTATABLE_BOND_COUNT>
4

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
1H-indol-3-yl (2S,3S,4S,5R)-3,4,5-trihydroxy-5-(hydroxymethyl)oxolane-2-carboxylate

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 07-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   07-SEP-22         0                                  
HETATM    1  O   UNK     0       4.187  -4.838   0.000  0.00  0.00           O+0
HETATM    2  C   UNK     0       2.680  -5.158   0.000  0.00  0.00           C+0
HETATM    3  O   UNK     0       1.650  -4.013   0.000  0.00  0.00           O+0
HETATM    4  C   UNK     0       2.126  -2.549   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       1.220  -1.303   0.000  0.00  0.00           C+0
HETATM    6  N   UNK     0       2.126  -0.057   0.000  0.00  0.00           N+0
HETATM    7  C   UNK     0       3.590  -0.533   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       4.924   0.237   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       6.258  -0.533   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       6.258  -2.073   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       4.924  -2.843   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       3.590  -2.073   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       2.204  -6.622   0.000  0.00  0.00           C+0
HETATM   14  O   UNK     0       3.109  -7.868   0.000  0.00  0.00           O+0
HETATM   15  C   UNK     0       2.204  -9.114   0.000  0.00  0.00           C+0
HETATM   16  O   UNK     0       3.538  -9.884   0.000  0.00  0.00           O+0
HETATM   17  C   UNK     0       1.578 -10.521   0.000  0.00  0.00           C+0
HETATM   18  O   UNK     0       2.483 -11.767   0.000  0.00  0.00           O+0
HETATM   19  C   UNK     0       0.740  -8.638   0.000  0.00  0.00           C+0
HETATM   20  O   UNK     0      -0.506  -9.543   0.000  0.00  0.00           O+0
HETATM   21  C   UNK     0       0.740  -7.098   0.000  0.00  0.00           C+0
HETATM   22  O   UNK     0      -0.506  -6.193   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3   13                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5   12                                                  
CONECT    5    4    6                                                       
CONECT    6    5    7                                                       
CONECT    7    6    8   12                                                  
CONECT    8    7    9                                                       
CONECT    9    8   10                                                       
CONECT   10    9   11                                                       
CONECT   11   10   12                                                       
CONECT   12   11    4    7                                                  
CONECT   13    2   14   21                                                  
CONECT   14   13   15                                                       
CONECT   15   14   16   17   19                                             
CONECT   16   15                                                            
CONECT   17   15   18                                                       
CONECT   18   17                                                            
CONECT   19   15   20   21                                                  
CONECT   20   19                                                            
CONECT   21   19   13   22                                                  
CONECT   22   21                                                            
MASTER        0    0    0    0    0    0    0    0   22    0   48    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₁₄H₁₅NO₇

Average Mass

309.2740 Da

Monoisotopic Mass

309.08485 Da

IUPAC Name

Not Available

Traditional Name

Not Available

CAS Registry Number

Not Available

SMILES

OC[C@@]1(O)O[C@@H]([C@@H](O)[C@@H]1O)C(=O)OC1=CNC2=CC=CC=C12

InChI Identifier

InChI=1S/C14H15NO7/c16-6-14(20)12(18)10(17)11(22-14)13(19)21-9-5-15-8-4-2-1-3-7(8)9/h1-5,10-12,15-18,20H,6H2/t10-,11+,12+,14-/m1/s1

InChI Key

KGXOHVOUKNLUNP-OWTLIXCDSA-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
Isatis tinctoria	LOTUS Database	35616633
Persicaria tinctoria	LOTUS Database	35616633

Chemical Taxonomy

Description

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

Kingdom

Organic compounds

Super Class

Organic oxygen compounds

Class

Organooxygen compounds

Sub Class

Carbohydrates and carbohydrate conjugates

Direct Parent

C-glycosyl compounds

Alternative Parents

Substituents

C-glycosyl compound
Pentose monosaccharide
Indole
Indole or derivatives
Beta-hydroxy acid
Sugar acid
Hydroxy acid
Monosaccharide
Substituted pyrrole
Benzenoid
Pyrrole
Heteroaromatic compound
Oxolane
Secondary alcohol
Carboxylic acid ester
Hemiacetal
Organoheterocyclic compound
Azacycle
Carboxylic acid derivative
Polyol
Oxacycle
Monocarboxylic acid or derivatives
Organic nitrogen compound
Primary alcohol
Alcohol
Hydrocarbon derivative
Carbonyl group
Organic oxide
Organonitrogen compound
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic heteropolycyclic 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

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

Not Available

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

6325414

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

LOTUS database [Link]

Showing NP-Card for 1h-indol-3-yl (2s,3s,4s,5r)-3,4,5-trihydroxy-5-(hydroxymethyl)oxolane-2-carboxylate (NP0241586)

MOL for NP0241586 (1h-indol-3-yl (2s,3s,4s,5r)-3,4,5-trihydroxy-5-(hydroxymethyl)oxolane-2-carboxylate)

3D MOL for NP0241586 (1h-indol-3-yl (2s,3s,4s,5r)-3,4,5-trihydroxy-5-(hydroxymethyl)oxolane-2-carboxylate)

3D SDF for NP0241586 (1h-indol-3-yl (2s,3s,4s,5r)-3,4,5-trihydroxy-5-(hydroxymethyl)oxolane-2-carboxylate)

3D-SDF for NP0241586 (1h-indol-3-yl (2s,3s,4s,5r)-3,4,5-trihydroxy-5-(hydroxymethyl)oxolane-2-carboxylate)

PDB for NP0241586 (1h-indol-3-yl (2s,3s,4s,5r)-3,4,5-trihydroxy-5-(hydroxymethyl)oxolane-2-carboxylate)

3D PDB for NP0241586 (1h-indol-3-yl (2s,3s,4s,5r)-3,4,5-trihydroxy-5-(hydroxymethyl)oxolane-2-carboxylate)

SMILES for NP0241586 (1h-indol-3-yl (2s,3s,4s,5r)-3,4,5-trihydroxy-5-(hydroxymethyl)oxolane-2-carboxylate)

INCHI for NP0241586 (1h-indol-3-yl (2s,3s,4s,5r)-3,4,5-trihydroxy-5-(hydroxymethyl)oxolane-2-carboxylate)

Structure for NP0241586 (1h-indol-3-yl (2s,3s,4s,5r)-3,4,5-trihydroxy-5-(hydroxymethyl)oxolane-2-carboxylate)

3D Structure for NP0241586 (1h-indol-3-yl (2s,3s,4s,5r)-3,4,5-trihydroxy-5-(hydroxymethyl)oxolane-2-carboxylate)