NP-MRD: Showing NP-Card for Cnidimol A (NP0139239)

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Record Information

Version

1.0

Created at

2022-06-29 19:45:26 UTC

Updated at

2022-06-29 19:45:26 UTC

NP-MRD ID

NP0139239

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Cnidimol A

Description

Cnidimol A is found in Cnidium japonicum and Cnidium monnieri.

Structure

MOL 3D MOL SDF PDB SMILES InChI

     RDKit          3D

 36 37  0  0  0  0  0  0  0  0999 V2000
    4.3404    0.5610    1.5655 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5773   -0.0449    0.4237 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4401   -0.6322    0.6736 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6159   -1.2504   -0.3558 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2385   -0.6552   -0.4384 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0495    0.2370   -1.4352 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9659    0.5594   -2.3508 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3097    0.7781   -1.5016 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3112    0.4459   -0.5820 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5116    0.9942   -0.6906 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5011    0.7333    0.1334 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.8522    1.3725   -0.0182 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2525   -0.1542    1.1461 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0107   -0.7666    1.3158 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8146   -1.5679    2.2444 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0088   -0.4569    0.4233 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7524   -1.0106    0.5079 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3829   -1.9007    1.4649 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.1496    0.0496   -0.8950 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.4146   -0.5920   -0.8970 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.7682    1.4157    2.0132 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.5158   -0.1989    2.3410 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.3163    0.9855    1.2387 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0805   -0.6675    1.6979 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9899   -1.3668   -1.3506 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4176   -2.3126   -0.0021 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7976    1.2189   -3.1031 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5326    1.4816   -2.2912 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.0573    1.9929    0.8821 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.8549    2.0576   -0.8975 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.6630    0.6374   -0.0983 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0218   -0.4061    1.8464 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8292   -2.3123    2.2127 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.6344   -0.3010   -1.7607 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.4036    1.1381   -1.0909 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.0500   -0.0620   -0.3734 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2 19  1  0
 19 20  1  0
  2  3  2  0
  3  4  1  0
  4  5  1  0
  5 17  2  0
 17 18  1  0
 17 16  1  0
 16  9  2  0
  9 10  1  0
 10 11  1  0
 11 12  1  0
 11 13  2  0
 13 14  1  0
 14 15  2  0
  9  8  1  0
  8  6  2  0
  6  7  1  0
  6  5  1  0
 14 16  1  0
  1 21  1  0
  1 22  1  0
  1 23  1  0
 19 34  1  0
 19 35  1  0
 20 36  1  0
  3 24  1  0
  4 25  1  0
  4 26  1  0
 18 33  1  0
 12 29  1  0
 12 30  1  0
 12 31  1  0
 13 32  1  0
  8 28  1  0
  7 27  1  0
M  END


  Mrv1652306292221452D          

 20 21  0  0  0  0            999 V2000
   -1.4289    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145   -1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000   -1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000   -2.4750    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000   -0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -2.4750    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579   -1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579   -2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724   -2.8875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724   -3.7125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2868   -2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2868   -1.6500    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579   -0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  2  0  0  0  0
  3  4  1  0  0  0  0
  4  5  2  0  0  0  0
  4  6  1  0  0  0  0
  6  7  2  0  0  0  0
  7  8  1  0  0  0  0
  2  8  1  0  0  0  0
  7  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
  6 12  1  0  0  0  0
 12 13  1  0  0  0  0
 11 14  1  0  0  0  0
 14 15  1  0  0  0  0
 15 16  2  0  0  0  0
 16 17  1  0  0  0  0
 16 18  1  0  0  0  0
 18 19  1  0  0  0  0
 10 20  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0139239

> <DATABASE_NAME>
NP-MRD

> <SMILES>
C\C(CO)=C\CC1=C(O)C2=C(OC(C)=CC2=O)C=C1O

> <INCHI_IDENTIFIER>
InChI=1S/C15H16O5/c1-8(7-16)3-4-10-11(17)6-13-14(15(10)19)12(18)5-9(2)20-13/h3,5-6,16-17,19H,4,7H2,1-2H3/b8-3-

> <INCHI_KEY>
UXNWJSOMYWKDPT-BAQGIRSFSA-N

> <FORMULA>
C15H16O5

> <MOLECULAR_WEIGHT>
276.288

> <EXACT_MASS>
276.099773615

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_ATOM_COUNT>
36

> <JCHEM_AVERAGE_POLARIZABILITY>
28.242106666064508

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
5,7-dihydroxy-6-[(2Z)-4-hydroxy-3-methylbut-2-en-1-yl]-2-methyl-4H-chromen-4-one

> <ALOGPS_LOGP>
1.91

> <JCHEM_LOGP>
2.3622184686666663

> <ALOGPS_LOGS>
-3.12

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
8.016635729048078

> <JCHEM_PKA_STRONGEST_ACIDIC>
6.408640573098163

> <JCHEM_PKA_STRONGEST_BASIC>
-2.7258164959241276

> <JCHEM_POLAR_SURFACE_AREA>
86.99000000000001

> <JCHEM_REFRACTIVITY>
77.0865

> <JCHEM_ROTATABLE_BOND_COUNT>
3

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
2.11e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
5,7-dihydroxy-6-[(2Z)-4-hydroxy-3-methylbut-2-en-1-yl]-2-methylchromen-4-one

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 29-JUN-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   29-JUN-22         0                                  
HETATM    1  C   UNK     0      -2.667   0.000   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -1.334  -0.770   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -1.334  -2.310   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       0.000  -3.080   0.000  0.00  0.00           C+0
HETATM    5  O   UNK     0       0.000  -4.620   0.000  0.00  0.00           O+0
HETATM    6  C   UNK     0       1.334  -2.310   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0       0.000  -0.000   0.000  0.00  0.00           O+0
HETATM    9  C   UNK     0       2.667  -0.000   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       4.001  -0.770   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       4.001  -2.310   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       2.667  -3.080   0.000  0.00  0.00           C+0
HETATM   13  O   UNK     0       2.667  -4.620   0.000  0.00  0.00           O+0
HETATM   14  C   UNK     0       5.335  -3.080   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       5.335  -4.620   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       6.668  -5.390   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       6.668  -6.930   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       8.002  -4.620   0.000  0.00  0.00           C+0
HETATM   19  O   UNK     0       8.002  -3.080   0.000  0.00  0.00           O+0
HETATM   20  O   UNK     0       5.335  -0.000   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3    8                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5    6                                                  
CONECT    5    4                                                            
CONECT    6    4    7   12                                                  
CONECT    7    6    8    9                                                  
CONECT    8    7    2                                                       
CONECT    9    7   10                                                       
CONECT   10    9   11   20                                                  
CONECT   11   10   12   14                                                  
CONECT   12   11    6   13                                                  
CONECT   13   12                                                            
CONECT   14   11   15                                                       
CONECT   15   14   16                                                       
CONECT   16   15   17   18                                                  
CONECT   17   16                                                            
CONECT   18   16   19                                                       
CONECT   19   18                                                            
CONECT   20   10                                                            
MASTER        0    0    0    0    0    0    0    0   20    0   42    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₁₅H₁₆O₅

Average Mass

276.2880 Da

Monoisotopic Mass

276.09977 Da

IUPAC Name

5,7-dihydroxy-6-[(2Z)-4-hydroxy-3-methylbut-2-en-1-yl]-2-methyl-4H-chromen-4-one

Traditional Name

5,7-dihydroxy-6-[(2Z)-4-hydroxy-3-methylbut-2-en-1-yl]-2-methylchromen-4-one

CAS Registry Number

Not Available

SMILES

C\C(CO)=C\CC1=C(O)C2=C(OC(C)=CC2=O)C=C1O

InChI Identifier

InChI=1S/C15H16O5/c1-8(7-16)3-4-10-11(17)6-13-14(15(10)19)12(18)5-9(2)20-13/h3,5-6,16-17,19H,4,7H2,1-2H3/b8-3-

InChI Key

UXNWJSOMYWKDPT-BAQGIRSFSA-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
Cnidium japonicum	LOTUS Database	35616633
Cnidium monnieri	LOTUS Database	35616633

Chemical Taxonomy

Classification

Not classified

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	1.91	ALOGPS
logP	2.36	ChemAxon
logS	-3.1	ALOGPS
pKa (Strongest Acidic)	6.41	ChemAxon
pKa (Strongest Basic)	-2.7	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	5	ChemAxon
Hydrogen Donor Count	3	ChemAxon
Polar Surface Area	86.99 Å²	ChemAxon
Rotatable Bond Count	3	ChemAxon
Refractivity	77.09 m³·mol⁻¹	ChemAxon
Polarizability	28.24 Å³	ChemAxon
Number of Rings	2	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

External Links

Not Available

References

General References

Not Available

Showing NP-Card for Cnidimol A (NP0139239)

MOL for NP0139239 (Cnidimol A)

3D MOL for NP0139239 (Cnidimol A)

3D SDF for NP0139239 (Cnidimol A)

3D-SDF for NP0139239 (Cnidimol A)

PDB for NP0139239 (Cnidimol A)

3D PDB for NP0139239 (Cnidimol A)

SMILES for NP0139239 (Cnidimol A)

INCHI for NP0139239 (Cnidimol A)

Structure for NP0139239 (Cnidimol A)

3D Structure for NP0139239 (Cnidimol A)