NP-MRD: Showing NP-Card for 1h-indol-3-yl 3,4,5-trihydroxy-5-(hydroxymethyl)oxolane-2-carboxylate (NP0242654)

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Record Information

Version

2.0

Created at

2022-09-07 03:01:21 UTC

Updated at

2022-09-07 03:01:21 UTC

NP-MRD ID

NP0242654

Secondary Accession Numbers

None

Natural Product Identification

Common Name

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

Description

AC1NAP75 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 3,4,5-trihydroxy-5-(hydroxymethyl)oxolane-2-carboxylate is found in Isatis tinctoria. AC1NAP75 is an extremely weak basic (essentially neutral) compound (based on its pKa).

Structure

MOL 3D MOL SDF PDB SMILES InChI

     RDKit          3D

 37 39  0  0  0  0  0  0  0  0999 V2000
    0.1237    0.4713    0.9783 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2457   -0.2220    0.0040 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6377   -0.3655   -1.0486 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.9008    0.2381   -1.0347 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2058    1.4925   -1.5082 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5120    1.6766   -1.3044 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.0758    0.5831   -0.7119 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.3523    0.2939   -0.3110 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.6404   -0.9102    0.2694 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.6574   -1.8582    0.4642 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3823   -1.5364    0.0496 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0458   -0.3401   -0.5379 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5913   -0.8308    0.0536 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.2035   -0.4984    1.2200 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3993    0.1083    0.9874 C   0  0  1  0  0  0  0  0  0  0  0  0
   -4.3754   -0.4881    1.7856 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3891    1.5876    1.3956 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4359    2.2776    0.6467 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7456   -0.0440   -0.4675 C   0  0  2  0  0  0  0  0  0  0  0  0
   -4.5154   -1.2123   -0.5884 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3928   -0.2704   -1.0947 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.5568   -1.1745   -2.1336 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.5477    2.2318   -1.9688 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.0504    2.5392   -1.5589 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.1318    1.0117   -0.4509 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.6510   -1.1065    0.5728 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.9314   -2.7963    0.9271 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.6137   -2.2698    0.1986 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5456   -1.9511    0.0015 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8532   -1.2135    1.3576 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1780    1.6471    2.4727 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3868    2.0151    1.1676 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7510    3.2045    0.5513 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2601    0.8321   -0.8736 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3766   -1.6732   -1.4399 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9436    0.6416   -1.4962 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3142   -2.0906   -1.9214 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  6
 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


  Mrv1533004151519082D          

 22 24  0  0  0  0            999 V2000
   -2.1188   -3.3462    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7832   -4.0999    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9628   -4.1861    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1343   -4.9931    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9628   -3.3611    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1781   -3.1062    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3068   -3.7736    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1318   -3.7736    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1781   -4.4410    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0768   -5.2257    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0768   -2.3215    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4752   -1.7084    0.0000 O   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  2  1  0  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  3  5  1  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
  7  9  1  0  0  0  0
  3  9  1  0  0  0  0
  9 10  1  0  0  0  0
  6 11  1  0  0  0  0
 11 12  2  0  0  0  0
 11 13  1  0  0  0  0
 13 14  1  0  0  0  0
 14 15  2  0  0  0  0
 15 16  1  0  0  0  0
 16 17  1  0  0  0  0
 17 18  2  0  0  0  0
 18 19  1  0  0  0  0
 19 20  2  0  0  0  0
 20 21  1  0  0  0  0
 21 22  2  0  0  0  0
 14 22  1  0  0  0  0
 17 22  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0242654

> <DATABASE_NAME>
NP-MRD

> <SMILES>
OCC1(O)OC(C(O)C1O)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

> <INCHI_KEY>
KGXOHVOUKNLUNP-UHFFFAOYSA-N

> <FORMULA>
C14H15NO7

> <MOLECULAR_WEIGHT>
309.274

> <EXACT_MASS>
309.084851827

> <JCHEM_ACCEPTOR_COUNT>
6

> <JCHEM_ATOM_COUNT>
37

> <JCHEM_AVERAGE_POLARIZABILITY>
29.152278198878356

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
5

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

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

> <ALOGPS_LOGP>
0.10

> <JCHEM_LOGP>
-0.5351102823333334

> <ALOGPS_LOGS>
-1.40

> <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>
71.8614

> <JCHEM_ROTATABLE_BOND_COUNT>
4

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.24e+01 g/l

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

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 15-APR-15   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   15-APR-15         0                                  
HETATM    1  O   UNK     0      -3.955  -6.246   0.000  0.00  0.00           O+0
HETATM    2  C   UNK     0      -3.329  -7.653   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -1.797  -7.814   0.000  0.00  0.00           C+0
HETATM    4  O   UNK     0      -2.117  -9.320   0.000  0.00  0.00           O+0
HETATM    5  O   UNK     0      -1.797  -6.274   0.000  0.00  0.00           O+0
HETATM    6  C   UNK     0      -0.333  -5.798   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       0.573  -7.044   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0       2.113  -7.044   0.000  0.00  0.00           O+0
HETATM    9  C   UNK     0      -0.333  -8.290   0.000  0.00  0.00           C+0
HETATM   10  O   UNK     0       0.143  -9.755   0.000  0.00  0.00           O+0
HETATM   11  C   UNK     0       0.143  -4.334   0.000  0.00  0.00           C+0
HETATM   12  O   UNK     0      -0.887  -3.189   0.000  0.00  0.00           O+0
HETATM   13  O   UNK     0       1.650  -4.013   0.000  0.00  0.00           O+0
HETATM   14  C   UNK     0       2.126  -2.549   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       1.220  -1.303   0.000  0.00  0.00           C+0
HETATM   16  N   UNK     0       2.126  -0.057   0.000  0.00  0.00           N+0
HETATM   17  C   UNK     0       3.590  -0.533   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       4.924   0.237   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       6.258  -0.533   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       6.258  -2.073   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0       4.924  -2.843   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0       3.590  -2.073   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4    5    9                                             
CONECT    4    3                                                            
CONECT    5    3    6                                                       
CONECT    6    5    7   11                                                  
CONECT    7    6    8    9                                                  
CONECT    8    7                                                            
CONECT    9    7    3   10                                                  
CONECT   10    9                                                            
CONECT   11    6   12   13                                                  
CONECT   12   11                                                            
CONECT   13   11   14                                                       
CONECT   14   13   15   22                                                  
CONECT   15   14   16                                                       
CONECT   16   15   17                                                       
CONECT   17   16   18   22                                                  
CONECT   18   17   19                                                       
CONECT   19   18   20                                                       
CONECT   20   19   21                                                       
CONECT   21   20   22                                                       
CONECT   22   21   14   17                                                  
MASTER        0    0    0    0    0    0    0    0   22    0   48    0
END

View in JSmol

Synonyms

Value	Source
1H-indol-3-yl 3,4,5-Trihydroxy-5-(hydroxymethyl)oxolane-2-carboxylic acid	Generator

Chemical Formula

C₁₄H₁₅NO₇

Average Mass

309.2740 Da

Monoisotopic Mass

309.08485 Da

IUPAC Name

1H-indol-3-yl 3,4,5-trihydroxy-5-(hydroxymethyl)oxolane-2-carboxylate

Traditional Name

1H-indol-3-yl 3,4,5-trihydroxy-5-(hydroxymethyl)oxolane-2-carboxylate

CAS Registry Number

Not Available

SMILES

OCC1(O)OC(C(O)C1O)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

InChI Key

KGXOHVOUKNLUNP-UHFFFAOYSA-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

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
logP	0.1	ALOGPS
logP	-0.54	ChemAxon
logS	-1.4	ALOGPS
pKa (Strongest Acidic)	10.27	ChemAxon
pKa (Strongest Basic)	-3.5	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	6	ChemAxon
Hydrogen Donor Count	5	ChemAxon
Polar Surface Area	132.24 Å²	ChemAxon
Rotatable Bond Count	4	ChemAxon
Refractivity	71.86 m³·mol⁻¹	ChemAxon
Polarizability	29.15 Å³	ChemAxon
Number of Rings	3	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

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

4480503

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 3,4,5-trihydroxy-5-(hydroxymethyl)oxolane-2-carboxylate (NP0242654)

MOL for NP0242654 (1h-indol-3-yl 3,4,5-trihydroxy-5-(hydroxymethyl)oxolane-2-carboxylate)

3D MOL for NP0242654 (1h-indol-3-yl 3,4,5-trihydroxy-5-(hydroxymethyl)oxolane-2-carboxylate)

3D SDF for NP0242654 (1h-indol-3-yl 3,4,5-trihydroxy-5-(hydroxymethyl)oxolane-2-carboxylate)

3D-SDF for NP0242654 (1h-indol-3-yl 3,4,5-trihydroxy-5-(hydroxymethyl)oxolane-2-carboxylate)

PDB for NP0242654 (1h-indol-3-yl 3,4,5-trihydroxy-5-(hydroxymethyl)oxolane-2-carboxylate)

3D PDB for NP0242654 (1h-indol-3-yl 3,4,5-trihydroxy-5-(hydroxymethyl)oxolane-2-carboxylate)

SMILES for NP0242654 (1h-indol-3-yl 3,4,5-trihydroxy-5-(hydroxymethyl)oxolane-2-carboxylate)

INCHI for NP0242654 (1h-indol-3-yl 3,4,5-trihydroxy-5-(hydroxymethyl)oxolane-2-carboxylate)

Structure for NP0242654 (1h-indol-3-yl 3,4,5-trihydroxy-5-(hydroxymethyl)oxolane-2-carboxylate)

3D Structure for NP0242654 (1h-indol-3-yl 3,4,5-trihydroxy-5-(hydroxymethyl)oxolane-2-carboxylate)