NP-MRD: Showing NP-Card for Dalnigrin (NP0044060)

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Record Information

Version

2.0

Created at

2021-11-12 23:47:52 UTC

Updated at

2026-02-13 04:02:12 UTC

NP-MRD ID

NP0044060

Natural Product DOI

https://doi.org/10.57994/6587

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Dalnigrin

Description

Dalnigrin belongs to the class of organic compounds known as neoflavones. These are neoflavonoids with a structure based on the 4-phenylcoumarin skeleton. Dalnigrin is found in Dalbergia nigra. Dalnigrin was first documented in 2010 (PMID: 20457458). Based on a literature review very few articles have been published on Dalnigrin.

Structure

MOL 3D MOL SDF PDB SMILES InChI

     RDKit          3D

 36 38  0  0  0  0  0  0  0  0999 V2000
    5.8081    1.3536   -1.3314 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.2183    1.1565   -0.0673 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.9606    0.6239    0.1212 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4870    0.4775    1.4005 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2369   -0.0508    1.6065 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3947   -0.4597    0.5635 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1288   -1.0144    0.9346 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0736   -2.1041    1.7933 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1597   -2.6105    2.0827 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2141   -3.6088    2.8687 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2811   -2.1442    1.6118 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2660   -1.1150    0.7985 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4404   -0.6085    0.2940 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4482    0.4736   -0.5589 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6430    0.9593   -1.0493 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.8671    0.3522   -0.6817 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2710    1.0742   -0.9256 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2135    2.1766   -1.7878 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0746    0.5662   -0.4186 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0493   -0.5135    0.4324 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8878   -0.3051   -0.7070 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1430    0.2256   -0.9152 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.7374    1.9390   -1.1743 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.1369    1.8981   -2.0228 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.0453    0.3254   -1.7316 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.1298    0.7908    2.2256 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9124   -0.1441    2.6401 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.0174   -2.4661    2.1659 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3647   -1.1158    0.6104 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.7991   -0.7471   -0.7940 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.7033    0.7283   -1.2938 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.0579    0.6170    0.3714 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1003    2.5173   -2.1354 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1417    1.0358   -0.6879 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2688   -0.6212   -1.5412 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.5082    0.3381   -1.9104 H   0  0  0  0  0  0  0  0  0  0  0  0
 10  9  2  0
  9 11  1  0
 11 12  1  0
 12 13  2  0
 13 14  1  0
 14 15  1  0
 15 16  1  0
 14 17  2  0
 17 18  1  0
 17 19  1  0
 19 20  2  0
 20  7  1  0
  7  8  2  0
  7  6  1  0
  6  5  2  0
  5  4  1  0
  4  3  2  0
  3  2  1  0
  2  1  1  0
  3 22  1  0
 22 21  2  0
  8  9  1  0
 12 20  1  0
  6 21  1  0
 13 29  1  0
 16 30  1  0
 16 31  1  0
 16 32  1  0
 18 33  1  0
 19 34  1  0
  8 28  1  0
  5 27  1  0
  4 26  1  0
  1 23  1  0
  1 24  1  0
  1 25  1  0
 22 36  1  0
 21 35  1  0
M  END


  Mrv1652311132100472D          

 22 24  0  0  0  0            999 V2000
    0.0000    0.0000    0.0000 O   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
    1.4289    0.0000    0.0000 O   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
    2.8579    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2868   -0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.0013   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724   -1.2375    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   -1.6500    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
    0.7145   -1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -2.8875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -3.7125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -4.1250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -4.9500    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -5.3625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -3.7125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -2.8875    0.0000 C   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  1  0  0  0  0
  5  6  2  0  0  0  0
  6  7  1  0  0  0  0
  7  8  1  0  0  0  0
  6  9  1  0  0  0  0
  9 10  1  0  0  0  0
  9 11  2  0  0  0  0
 11 12  1  0  0  0  0
  4 12  2  0  0  0  0
 12 13  1  0  0  0  0
 13 14  2  0  0  0  0
  2 14  1  0  0  0  0
 13 15  1  0  0  0  0
 15 16  1  0  0  0  0
 16 17  2  0  0  0  0
 17 18  1  0  0  0  0
 18 19  1  0  0  0  0
 19 20  1  0  0  0  0
 18 21  2  0  0  0  0
 21 22  1  0  0  0  0
 15 22  2  0  0  0  0
M  END
> <DATABASE_ID>
NP0044060

> <DATABASE_NAME>
NP-MRD

> <SMILES>
COC1=CC=C(C=C1)C1=CC(=O)OC2=C1C=C(O)C(OC)=C2

> <INCHI_IDENTIFIER>
InChI=1S/C17H14O5/c1-20-11-5-3-10(4-6-11)12-8-17(19)22-15-9-16(21-2)14(18)7-13(12)15/h3-9,18H,1-2H3

> <INCHI_KEY>
VGFANVFKVOTCIW-UHFFFAOYSA-N

> <FORMULA>
C17H14O5

> <MOLECULAR_WEIGHT>
298.294

> <EXACT_MASS>
298.084123551

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_ATOM_COUNT>
36

> <JCHEM_AVERAGE_POLARIZABILITY>
30.669403963012233

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
6-hydroxy-7-methoxy-4-(4-methoxyphenyl)-2H-chromen-2-one

> <ALOGPS_LOGP>
3.54

> <JCHEM_LOGP>
2.5976503399999995

> <ALOGPS_LOGS>
-4.05

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_ACIDIC>
9.765059931376395

> <JCHEM_PKA_STRONGEST_BASIC>
-4.5615028618679005

> <JCHEM_POLAR_SURFACE_AREA>
64.99000000000001

> <JCHEM_REFRACTIVITY>
90.00859999999999

> <JCHEM_ROTATABLE_BOND_COUNT>
3

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
2.66e-02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
6-hydroxy-7-methoxy-4-(4-methoxyphenyl)chromen-2-one

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 13-NOV-21   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   13-NOV-21         0                                  
HETATM    1  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM    2  C   UNK     0       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM    3  O   UNK     0       2.667   0.000   0.000  0.00  0.00           O+0
HETATM    4  C   UNK     0       4.001  -0.770   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       5.335   0.000   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       6.668  -0.770   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0       8.002  -0.000   0.000  0.00  0.00           O+0
HETATM    8  C   UNK     0       9.336  -0.770   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       6.668  -2.310   0.000  0.00  0.00           C+0
HETATM   10  O   UNK     0       8.002  -3.080   0.000  0.00  0.00           O+0
HETATM   11  C   UNK     0       5.335  -3.080   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       4.001  -2.310   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       2.667  -3.080   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       1.334  -2.310   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       2.667  -4.620   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       4.001  -5.390   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       4.001  -6.930   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       2.667  -7.700   0.000  0.00  0.00           C+0
HETATM   19  O   UNK     0       2.667  -9.240   0.000  0.00  0.00           O+0
HETATM   20  C   UNK     0       4.001 -10.010   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0       1.334  -6.930   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0       1.334  -5.390   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3   14                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5   12                                                  
CONECT    5    4    6                                                       
CONECT    6    5    7    9                                                  
CONECT    7    6    8                                                       
CONECT    8    7                                                            
CONECT    9    6   10   11                                                  
CONECT   10    9                                                            
CONECT   11    9   12                                                       
CONECT   12   11    4   13                                                  
CONECT   13   12   14   15                                                  
CONECT   14   13    2                                                       
CONECT   15   13   16   22                                                  
CONECT   16   15   17                                                       
CONECT   17   16   18                                                       
CONECT   18   17   19   21                                                  
CONECT   19   18   20                                                       
CONECT   20   19                                                            
CONECT   21   18   22                                                       
CONECT   22   21   15                                                       
MASTER        0    0    0    0    0    0    0    0   22    0   48    0
END

View in JSmol

Synonyms

Value	Source
4'-O-Methylmelanettin	MeSH
6-Hydroxy-7-methoxy-4-(4-methoxyphenyl)-2H-1-benzopyran-2-one	MeSH

Chemical Formula

C₁₇H₁₄O₅

Average Mass

298.2940 Da

Monoisotopic Mass

298.08412 Da

IUPAC Name

6-hydroxy-7-methoxy-4-(4-methoxyphenyl)-2H-chromen-2-one

Traditional Name

6-hydroxy-7-methoxy-4-(4-methoxyphenyl)chromen-2-one

CAS Registry Number

Not Available

SMILES

COC1=CC=C(C=C1)C1=CC(=O)OC2=C1C=C(O)C(OC)=C2

InChI Identifier

InChI=1S/C17H14O5/c1-20-11-5-3-10(4-6-11)12-8-17(19)22-15-9-16(21-2)14(18)7-13(12)15/h3-9,18H,1-2H3

InChI Key

VGFANVFKVOTCIW-UHFFFAOYSA-N

Experimental Spectra

Spectrum Type	Description	Depositor Email	Depositor Organization	Depositor	Deposition Date	View
1D NMR	¹³C NMR Spectrum (1D, 50 MHz, Methanol-d4, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 150 MHz, Methanol-d4, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 250 MHz, Methanol-d4, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 175 MHz, Methanol-d4, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 75 MHz, Methanol-d4, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 100 MHz, Methanol-d4, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 225 MHz, Methanol-d4, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 200 MHz, Methanol-d4, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 125 MHz, Methanol-d4, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 25 MHz, Methanol-d4, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, Methanol-d4, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, Methanol-d4, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, Methanol-d4, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, Methanol-d4, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, Methanol-d4, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, Methanol-d4, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, Methanol-d4, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, Methanol-d4, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, Methanol-d4, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, Methanol-d4, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum

Predicted Spectra

Not Available

Chemical Shift Submissions

Spectrum Type	Description	Depositor Email	Depositor Organization	Depositor	Deposition Date	View
1D NMR	¹H NMR Spectrum (1D, 400.0, Methanol-d4, simulated)	[email protected]	Not Available	Not Available	2026-02-13	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 100.0, Methanol-d4, simulated)	[email protected]	Not Available	Not Available	2026-02-13	View Spectrum

Species

Species of Origin

Species Name	Source	Reference
Dalbergia nigra	LOTUS Database	35616633
Dalbergia spruceana		Not Available

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as neoflavones. These are neoflavonoids with a structure based on the 4-phenylcoumarin skeleton.

Kingdom

Organic compounds

Super Class

Phenylpropanoids and polyketides

Class

Neoflavonoids

Sub Class

Neoflavones

Direct Parent

Neoflavones

Alternative Parents

Substituents

4-phenylcoumarin
Hydroxycoumarin
Coumarin
1-benzopyran
Benzopyran
Phenoxy compound
Anisole
Phenol ether
Methoxybenzene
1-hydroxy-2-unsubstituted benzenoid
Alkyl aryl ether
Phenol
Pyranone
Monocyclic benzene moiety
Pyran
Benzenoid
Heteroaromatic compound
Lactone
Oxacycle
Organoheterocyclic compound
Ether
Organic oxygen compound
Hydrocarbon derivative
Organic oxide
Organooxygen 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	3.54	ALOGPS
logP	2.6	ChemAxon
logS	-4	ALOGPS
pKa (Strongest Acidic)	9.77	ChemAxon
pKa (Strongest Basic)	-4.6	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	4	ChemAxon
Hydrogen Donor Count	1	ChemAxon
Polar Surface Area	64.99 Å²	ChemAxon
Rotatable Bond Count	3	ChemAxon
Refractivity	90.01 m³·mol⁻¹	ChemAxon
Polarizability	30.67 Å³	ChemAxon
Number of Rings	3	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

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

91279357

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Kite GC, Green PW, Veitch NC, Groves MC, Gasson PE, Simmonds MS: Dalnigrin, a neoflavonoid marker for the identification of Brazilian rosewood (Dalbergia nigra) in CITES enforcement. Phytochemistry. 2010 Jul;71(10):1122-31. doi: 10.1016/j.phytochem.2010.04.011. Epub 2010 May 8. [PubMed:20457458 ]
DOI: 10.1016/j.phytochem.2010.04.011
PMID: 20457458

Showing NP-Card for Dalnigrin (NP0044060)

MOL for NP0044060 (Dalnigrin)

3D MOL for NP0044060 (Dalnigrin)

3D SDF for NP0044060 (Dalnigrin)

3D-SDF for NP0044060 (Dalnigrin)

PDB for NP0044060 (Dalnigrin)

3D PDB for NP0044060 (Dalnigrin)

SMILES for NP0044060 (Dalnigrin)

INCHI for NP0044060 (Dalnigrin)

Structure for NP0044060 (Dalnigrin)

3D Structure for NP0044060 (Dalnigrin)