NP-MRD: Showing NP-Card for RA-XI (NP0139140)

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Record Information

Version

1.0

Created at

2022-06-29 19:40:59 UTC

Updated at

2022-06-29 19:40:59 UTC

NP-MRD ID

NP0139140

Secondary Accession Numbers

None

Natural Product Identification

Common Name

RA-XI

Description

RA-XI belongs to the class of organic compounds known as tetralins. These are polycyclic aromatic compounds containing a tetralin moiety, which consists of a benzene fused to a cyclohexane. RA-XI is found in Rubia cordifolia. RA-XI is an extremely weak basic (essentially neutral) compound (based on its pKa).

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1533004241502452D          

 59 63  0  0  0  0            999 V2000
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   -0.3916    5.6548    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
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    0.3863    4.4561    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4292    3.6322    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2628    3.1831    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2199    2.3592    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5150    1.9844    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5188    1.1564    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.2691    0.8132    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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   -0.8750    0.9286    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
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  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  3  4  2  0  0  0  0
  4  5  1  0  0  0  0
  5  6  2  0  0  0  0
  6  7  1  0  0  0  0
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  8  9  1  0  0  0  0
  9 10  1  0  0  0  0
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 13 14  1  0  0  0  0
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 16 17  2  0  0  0  0
 16 18  1  0  0  0  0
 13 19  1  0  0  0  0
 19 20  1  0  0  0  0
 20 21  2  0  0  0  0
 20 22  1  0  0  0  0
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 22 24  1  0  0  0  0
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 27 28  1  0  0  0  0
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 29 30  2  0  0  0  0
 30 31  1  0  0  0  0
 31 32  2  0  0  0  0
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  6 58  1  0  0  0  0
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  3 59  1  0  0  0  0
M  END

     RDKit          3D

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M  END


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M  END
> <DATABASE_ID>
NP0139140

> <DATABASE_NAME>
NP-MRD

> <SMILES>
COC1=CC=C(CC2N(C)C(=O)C(CCC(O)=O)NC(=O)C(C)NC(=O)C3CC4=CC=C(O)C(OC5=CC=C(CC(N(C)C(=O)C(C)NC2=O)C(=O)N3C)C=C5)=C4)C=C1

> <INCHI_IDENTIFIER>
InChI=1S/C42H50N6O11/c1-23-37(52)45-30(16-18-36(50)51)41(56)46(3)31(19-25-7-12-28(58-6)13-8-25)39(54)44-24(2)40(55)48(5)33-20-26-9-14-29(15-10-26)59-35-22-27(11-17-34(35)49)21-32(38(53)43-23)47(4)42(33)57/h7-15,17,22-24,30-33,49H,16,18-21H2,1-6H3,(H,43,53)(H,44,54)(H,45,52)(H,50,51)

> <INCHI_KEY>
JYSZOVOBXGDGIQ-UHFFFAOYSA-N

> <FORMULA>
C42H50N6O11

> <MOLECULAR_WEIGHT>
814.893

> <EXACT_MASS>
814.353756454

> <JCHEM_ACCEPTOR_COUNT>
10

> <JCHEM_ATOM_COUNT>
109

> <JCHEM_AVERAGE_POLARIZABILITY>
81.69308221486403

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
5

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
3-{24-hydroxy-10-[(4-methoxyphenyl)methyl]-4,9,13,15,29-pentamethyl-2,5,8,11,14,30-hexaoxo-22-oxa-3,6,9,12,15,29-hexaazatetracyclo[14.12.2.2¹⁸,²¹.1²³,²⁷]tritriaconta-18,20,23(31),24,26,32-hexaen-7-yl}propanoic acid

> <ALOGPS_LOGP>
2.59

> <JCHEM_LOGP>
1.133547390666666

> <ALOGPS_LOGS>
-4.57

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
5

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
8.423015029168484

> <JCHEM_PKA_STRONGEST_ACIDIC>
4.014929552447184

> <JCHEM_PKA_STRONGEST_BASIC>
-3.424516758659561

> <JCHEM_POLAR_SURFACE_AREA>
224.21999999999997

> <JCHEM_REFRACTIVITY>
211.7488

> <JCHEM_ROTATABLE_BOND_COUNT>
6

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
2.19e-02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
3-{24-hydroxy-10-[(4-methoxyphenyl)methyl]-4,9,13,15,29-pentamethyl-2,5,8,11,14,30-hexaoxo-22-oxa-3,6,9,12,15,29-hexaazatetracyclo[14.12.2.2¹⁸,²¹.1²³,²⁷]tritriaconta-18,20,23(31),24,26,32-hexaen-7-yl}propanoic acid

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 24-APR-15   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   24-APR-15         0                                  
HETATM    1  C   UNK     0      -2.103  11.255   0.000  0.00  0.00           C+0
HETATM    2  O   UNK     0      -0.731  10.556   0.000  0.00  0.00           O+0
HETATM    3  C   UNK     0      -0.651   9.018   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       0.721   8.318   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       0.801   6.780   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      -0.491   5.942   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      -0.411   4.404   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       0.961   3.704   0.000  0.00  0.00           C+0
HETATM    9  N   UNK     0       0.968   2.159   0.000  0.00  0.00           N+0
HETATM   10  C   UNK     0       2.369   1.518   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      -0.208   1.151   0.000  0.00  0.00           C+0
HETATM   12  O   UNK     0      -1.633   1.733   0.000  0.00  0.00           O+0
HETATM   13  C   UNK     0      -0.074  -0.392   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      -1.370  -1.222   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0      -2.738  -0.515   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0      -4.035  -1.346   0.000  0.00  0.00           C+0
HETATM   17  O   UNK     0      -3.964  -2.884   0.000  0.00  0.00           O+0
HETATM   18  O   UNK     0      -5.403  -0.639   0.000  0.00  0.00           O+0
HETATM   19  N   UNK     0       1.270  -1.157   0.000  0.00  0.00           N+0
HETATM   20  C   UNK     0       1.541  -2.681   0.000  0.00  0.00           C+0
HETATM   21  O   UNK     0       0.308  -3.603   0.000  0.00  0.00           O+0
HETATM   22  C   UNK     0       2.924  -3.371   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0       3.094  -4.901   0.000  0.00  0.00           C+0
HETATM   24  N   UNK     0       4.119  -2.395   0.000  0.00  0.00           N+0
HETATM   25  C   UNK     0       5.514  -3.035   0.000  0.00  0.00           C+0
HETATM   26  O   UNK     0       5.558  -4.575   0.000  0.00  0.00           O+0
HETATM   27  C   UNK     0       6.882  -2.308   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0       7.765  -3.670   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0       9.318  -4.030   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0       9.004  -2.518   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0      10.050  -1.432   0.000  0.00  0.00           C+0
HETATM   32  C   UNK     0      11.487  -1.934   0.000  0.00  0.00           C+0
HETATM   33  O   UNK     0      12.551  -0.820   0.000  0.00  0.00           O+0
HETATM   34  C   UNK     0      12.052  -3.343   0.000  0.00  0.00           C+0
HETATM   35  O   UNK     0      13.241  -2.188   0.000  0.00  0.00           O+0
HETATM   36  C   UNK     0      13.484  -0.577   0.000  0.00  0.00           C+0
HETATM   37  C   UNK     0      14.078   0.887   0.000  0.00  0.00           C+0
HETATM   38  C   UNK     0      13.149   2.187   0.000  0.00  0.00           C+0
HETATM   39  C   UNK     0      11.571   2.094   0.000  0.00  0.00           C+0
HETATM   40  C   UNK     0       9.961   2.542   0.000  0.00  0.00           C+0
HETATM   41  C   UNK     0       8.414   2.076   0.000  0.00  0.00           C+0
HETATM   42  N   UNK     0       6.992   2.768   0.000  0.00  0.00           N+0
HETATM   43  C   UNK     0       5.865   1.719   0.000  0.00  0.00           C+0
HETATM   44  C   UNK     0       6.413   4.210   0.000  0.00  0.00           C+0
HETATM   45  O   UNK     0       7.534   5.266   0.000  0.00  0.00           O+0
HETATM   46  C   UNK     0       5.007   4.873   0.000  0.00  0.00           C+0
HETATM   47  C   UNK     0       4.930   6.411   0.000  0.00  0.00           C+0
HETATM   48  N   UNK     0       3.674   4.075   0.000  0.00  0.00           N+0
HETATM   49  C   UNK     0       2.215   4.605   0.000  0.00  0.00           C+0
HETATM   50  O   UNK     0       2.004   6.130   0.000  0.00  0.00           O+0
HETATM   51  C   UNK     0       7.607   0.677   0.000  0.00  0.00           C+0
HETATM   52  O   UNK     0       6.098   0.980   0.000  0.00  0.00           O+0
HETATM   53  N   UNK     0       6.855  -0.695   0.000  0.00  0.00           N+0
HETATM   54  C   UNK     0       5.360  -0.326   0.000  0.00  0.00           C+0
HETATM   55  C   UNK     0      10.999   0.678   0.000  0.00  0.00           C+0
HETATM   56  C   UNK     0      11.949  -0.515   0.000  0.00  0.00           C+0
HETATM   57  C   UNK     0      10.871  -4.433   0.000  0.00  0.00           C+0
HETATM   58  C   UNK     0      -1.863   6.641   0.000  0.00  0.00           C+0
HETATM   59  C   UNK     0      -1.943   8.179   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4   59                                                  
CONECT    4    3    5                                                       
CONECT    5    4    6                                                       
CONECT    6    5    7   58                                                  
CONECT    7    6    8                                                       
CONECT    8    7    9   49                                                  
CONECT    9    8   10   11                                                  
CONECT   10    9                                                            
CONECT   11    9   12   13                                                  
CONECT   12   11                                                            
CONECT   13   11   14   19                                                  
CONECT   14   13   15                                                       
CONECT   15   14   16                                                       
CONECT   16   15   17   18                                                  
CONECT   17   16                                                            
CONECT   18   16                                                            
CONECT   19   13   20                                                       
CONECT   20   19   21   22                                                  
CONECT   21   20                                                            
CONECT   22   20   23   24                                                  
CONECT   23   22                                                            
CONECT   24   22   25                                                       
CONECT   25   24   26   27                                                  
CONECT   26   25                                                            
CONECT   27   25   28   53                                                  
CONECT   28   27   29                                                       
CONECT   29   28   30   57                                                  
CONECT   30   29   31                                                       
CONECT   31   30   32                                                       
CONECT   32   31   33   34                                                  
CONECT   33   32                                                            
CONECT   34   32   35   57                                                  
CONECT   35   34   36                                                       
CONECT   36   35   37   56                                                  
CONECT   37   36   38                                                       
CONECT   38   37   39                                                       
CONECT   39   38   40   55                                                  
CONECT   40   39   41                                                       
CONECT   41   40   42   51                                                  
CONECT   42   41   43   44                                                  
CONECT   43   42                                                            
CONECT   44   42   45   46                                                  
CONECT   45   44                                                            
CONECT   46   44   47   48                                                  
CONECT   47   46                                                            
CONECT   48   46   49                                                       
CONECT   49   48    8   50                                                  
CONECT   50   49                                                            
CONECT   51   41   52   53                                                  
CONECT   52   51                                                            
CONECT   53   51   27   54                                                  
CONECT   54   53                                                            
CONECT   55   39   56                                                       
CONECT   56   55   36                                                       
CONECT   57   34   29                                                       
CONECT   58    6   59                                                       
CONECT   59   58    3                                                       
MASTER        0    0    0    0    0    0    0    0   59    0  126    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₄₂H₅₀N₆O₁₁

Average Mass

814.8930 Da

Monoisotopic Mass

814.35376 Da

IUPAC Name

3-{24-hydroxy-10-[(4-methoxyphenyl)methyl]-4,9,13,15,29-pentamethyl-2,5,8,11,14,30-hexaoxo-22-oxa-3,6,9,12,15,29-hexaazatetracyclo[14.12.2.2¹⁸,²¹.1²³,²⁷]tritriaconta-18,20,23(31),24,26,32-hexaen-7-yl}propanoic acid

Traditional Name

CAS Registry Number

Not Available

SMILES

COC1=CC=C(CC2N(C)C(=O)C(CCC(O)=O)NC(=O)C(C)NC(=O)C3CC4=CC=C(O)C(OC5=CC=C(CC(N(C)C(=O)C(C)NC2=O)C(=O)N3C)C=C5)=C4)C=C1

InChI Identifier

InChI=1S/C42H50N6O11/c1-23-37(52)45-30(16-18-36(50)51)41(56)46(3)31(19-25-7-12-28(58-6)13-8-25)39(54)44-24(2)40(55)48(5)33-20-26-9-14-29(15-10-26)59-35-22-27(11-17-34(35)49)21-32(38(53)43-23)47(4)42(33)57/h7-15,17,22-24,30-33,49H,16,18-21H2,1-6H3,(H,43,53)(H,44,54)(H,45,52)(H,50,51)

InChI Key

JYSZOVOBXGDGIQ-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
Rubia cordifolia	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as tetralins. These are polycyclic aromatic compounds containing a tetralin moiety, which consists of a benzene fused to a cyclohexane.

Kingdom

Organic compounds

Super Class

Benzenoids

Class

Tetralins

Sub Class

Not Available

Direct Parent

Tetralins

Alternative Parents

Substituents

Naphthalene
Tetralin
1-hydroxy-4-unsubstituted benzenoid
1-hydroxy-2-unsubstituted benzenoid
Ketal
Secondary alcohol
Acetal
Dialkyl ether
Oxirane
Ether
Oxacycle
Organoheterocyclic compound
Organic oxygen compound
Organooxygen compound
Hydrocarbon derivative
Alcohol
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	2.59	ALOGPS
logP	1.13	ChemAxon
logS	-4.6	ALOGPS
pKa (Strongest Acidic)	4.01	ChemAxon
pKa (Strongest Basic)	-3.4	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	10	ChemAxon
Hydrogen Donor Count	5	ChemAxon
Polar Surface Area	224.22 Å²	ChemAxon
Rotatable Bond Count	6	ChemAxon
Refractivity	211.75 m³·mol⁻¹	ChemAxon
Polarizability	81.69 Å³	ChemAxon
Number of Rings	5	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

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

131676023

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Not Available

Showing NP-Card for RA-XI (NP0139140)

MOL for NP0139140 (RA-XI)

3D MOL for NP0139140 (RA-XI)

3D SDF for NP0139140 (RA-XI)

3D-SDF for NP0139140 (RA-XI)

PDB for NP0139140 (RA-XI)

3D PDB for NP0139140 (RA-XI)

SMILES for NP0139140 (RA-XI)

INCHI for NP0139140 (RA-XI)

Structure for NP0139140 (RA-XI)

3D Structure for NP0139140 (RA-XI)