NP-MRD: Showing NP-Card for (s)-dnpa (NP0312031)

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Record Information

Version

2.0

Created at

2022-09-11 08:27:37 UTC

Updated at

2022-09-11 08:27:38 UTC

NP-MRD ID

NP0312031

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(s)-dnpa

Description

(s)-dnpa is found in Streptomyces coelicolor and Streptomyces violaceoruber.

Structure

MOL 3D MOL SDF PDB SMILES InChI

     RDKit          3D

 35 37  0  0  0  0  0  0  0  0999 V2000
   -0.3308    3.1670   -0.1929 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6922    1.7289   -0.0649 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2178    0.7903   -0.1128 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6209    1.1263   -0.2934 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9497    2.3179   -0.4029 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.6039    0.0657   -0.3419 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9533    0.3576   -0.5137 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.4649    1.6157   -0.6480 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.8452   -0.7151   -0.5510 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.3860   -1.9876   -0.4218 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0456   -2.2596   -0.2522 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1332   -1.2437   -0.2092 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6946   -1.5236   -0.0279 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2285   -0.6008    0.0220 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6526   -0.9790    0.2076 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5746    0.1318   -0.2461 C   0  0  1  0  0  0  0  0  0  0  0  0
   -3.9269    0.0465    0.4032 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6246   -1.2262    0.1017 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1597   -2.1372   -0.6087 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.8851   -1.4026    0.6567 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0116    1.3766    0.1077 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.2876    3.5362    0.6556 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2684    3.7988   -0.1192 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0724    3.4223   -1.1922 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.0761    2.4993   -0.6568 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.8835   -0.5176   -0.6816 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.0837   -2.8455   -0.4499 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.7201   -3.2897   -0.1529 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4454   -2.5898    0.0649 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8380   -1.8502   -0.4839 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8754   -1.3283    1.2235 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6829    0.1084   -1.3430 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8101    0.2377    1.4824 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5468    0.8636   -0.0224 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.3759   -0.6943    1.1858 H   0  0  0  0  0  0  0  0  0  0  0  0
 16 17  1  0
 17 18  1  0
 18 20  1  0
 18 19  2  0
 16 15  1  0
 15 14  1  0
 14 13  2  0
 13 12  1  0
 12  6  2  0
  6  7  1  0
  7  8  1  0
  7  9  2  0
  9 10  1  0
 10 11  2  0
  6  4  1  0
  4  5  2  0
  4  3  1  0
  3  2  2  0
  2  1  1  0
  2 21  1  0
 21 16  1  0
  3 14  1  0
 11 12  1  0
 16 32  1  6
 17 33  1  0
 17 34  1  0
 20 35  1  0
 15 30  1  0
 15 31  1  0
 13 29  1  0
  8 25  1  0
  9 26  1  0
 10 27  1  0
 11 28  1  0
  1 22  1  0
  1 23  1  0
  1 24  1  0
M  END

SDN
  Mrv0541 02241214102D          

 22 24  0  0  0  0            999 V2000
    2.0309   -1.6668    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.0309   -0.8418    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3164   -0.4293    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6020   -0.8418    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6020   -1.6668    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1125   -0.4293    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8270   -0.8418    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5414   -0.4293    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8270   -1.6668    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7454   -0.4293    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7454    0.3957    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0309    0.8082    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3164    0.3957    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6020    0.8082    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1125    0.3957    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8270    0.8082    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5414    0.3957    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.2559    0.8082    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2559    1.6332    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9704    2.0457    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5414    2.0457    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5414    0.9797    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  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
  4  6  1  0  0  0  0
  6  7  2  0  0  0  0
  7  9  1  0  0  0  0
  7  8  1  0  0  0  0
 10  2  2  0  0  0  0
 11 10  1  0  0  0  0
 11 12  2  0  0  0  0
 12 13  1  0  0  0  0
 13  3  2  0  0  0  0
 13 14  1  0  0  0  0
 14 15  2  0  0  0  0
 15  6  1  0  0  0  0
 15 16  1  0  0  0  0
 16 17  1  0  0  0  0
 17  8  1  0  0  0  0
 17 18  1  6  0  0  0
 17 22  1  1  0  0  0
 18 19  1  0  0  0  0
 19 20  2  0  0  0  0
 19 21  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0312031

> <DATABASE_NAME>
NP-MRD

> <SMILES>
[H][C@@]1(CC(O)=O)CC2=CC3=C(C(O)=CC=C3)C(=O)C2=C(C)O1

> <INCHI_IDENTIFIER>
InChI=1S/C16H14O5/c1-8-14-10(6-11(21-8)7-13(18)19)5-9-3-2-4-12(17)15(9)16(14)20/h2-5,11,17H,6-7H2,1H3,(H,18,19)/t11-/m0/s1

> <INCHI_KEY>
HHXSOTFPYPQSBU-NSHDSACASA-N

> <FORMULA>
C16H14O5

> <MOLECULAR_WEIGHT>
286.2794

> <EXACT_MASS>
286.084123558

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_AVERAGE_POLARIZABILITY>
29.214717058340668

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
2-[(3S)-9-hydroxy-1-methyl-10-oxo-3H,4H,10H-naphtho[2,3-c]pyran-3-yl]acetic acid

> <ALOGPS_LOGP>
2.01

> <JCHEM_LOGP>
1.9389911376666669

> <ALOGPS_LOGS>
-3.34

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
9.846649317614387

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.7347210027870665

> <JCHEM_PKA_STRONGEST_BASIC>
-4.424720128062732

> <JCHEM_POLAR_SURFACE_AREA>
83.83

> <JCHEM_REFRACTIVITY>
77.35470000000001

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.30e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(S)-dnpa

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 24-FEB-12   NONE
TITLE     NULL                                                        
COMPND    MOLECULE: SDN                                               
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   24-FEB-12         0                                  
HETATM    1  O   UNK     0       3.791  -3.111   0.000  0.00  0.00           O+0
HETATM    2  C   UNK     0       3.791  -1.571   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       2.457  -0.801   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       1.124  -1.571   0.000  0.00  0.00           C+0
HETATM    5  O   UNK     0       1.124  -3.111   0.000  0.00  0.00           O+0
HETATM    6  C   UNK     0      -0.210  -0.801   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      -1.544  -1.571   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0      -2.877  -0.801   0.000  0.00  0.00           O+0
HETATM    9  C   UNK     0      -1.544  -3.111   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       5.125  -0.801   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       5.125   0.739   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       3.791   1.509   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       2.457   0.739   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       1.124   1.509   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0      -0.210   0.739   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0      -1.544   1.509   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0      -2.877   0.739   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0      -4.211   1.509   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0      -4.211   3.049   0.000  0.00  0.00           C+0
HETATM   20  O   UNK     0      -5.545   3.819   0.000  0.00  0.00           O+0
HETATM   21  O   UNK     0      -2.877   3.819   0.000  0.00  0.00           O+0
HETATM   22  H   UNK     0      -2.877   1.829   0.000  0.00  0.00           H+0
CONECT    1    2                                                            
CONECT    2    1    3   10                                                  
CONECT    3    2    4   13                                                  
CONECT    4    3    5    6                                                  
CONECT    5    4                                                            
CONECT    6    4    7   15                                                  
CONECT    7    6    9    8                                                  
CONECT    8    7   17                                                       
CONECT    9    7                                                            
CONECT   10    2   11                                                       
CONECT   11   10   12                                                       
CONECT   12   11   13                                                       
CONECT   13   12    3   14                                                  
CONECT   14   13   15                                                       
CONECT   15   14    6   16                                                  
CONECT   16   15   17                                                       
CONECT   17   16    8   18   22                                             
CONECT   18   17   19                                                       
CONECT   19   18   20   21                                                  
CONECT   20   19                                                            
CONECT   21   19                                                            
CONECT   22   17                                                            
MASTER        0    0    0    0    0    0    0    0   22    0   48    0
END

View in JSmol

Synonyms

Value	Source
4-Dihydro-9-hydroxy-1-methyl-10-oxo-3-H-naphtho[2,3-c]pyran-3-acetic acid	ChEBI
4-Dihydro-9-hydroxy-1-methyl-10-oxo-3-H-naphtho[2,3-c]pyran-3-acetate	Generator
[(3S)-9-Hydroxy-1-methyl-10-oxo-4,10-dihydro-3H-benzo[g]isochromen-3-yl]acetate	Generator
4-Dihydro-9-hydroxy-1-methyl-10-oxo-3-H-naphtho-(2,3-c)-pyran-3-acetic acid	MeSH
4-Dihydro-9-hydroxy-1-methyl-10-oxo-3-H-naphtho-(2,3-c)-pyran-3-(S)-acetic acid	MeSH

Chemical Formula

C₁₆H₁₄O₅

Average Mass

286.2794 Da

Monoisotopic Mass

286.08412 Da

IUPAC Name

2-[(3S)-9-hydroxy-1-methyl-10-oxo-3H,4H,10H-naphtho[2,3-c]pyran-3-yl]acetic acid

Traditional Name

(S)-dnpa

CAS Registry Number

Not Available

SMILES

[H][C@@]1(CC(O)=O)CC2=CC3=C(C(O)=CC=C3)C(=O)C2=C(C)O1

InChI Identifier

InChI=1S/C16H14O5/c1-8-14-10(6-11(21-8)7-13(18)19)5-9-3-2-4-12(17)15(9)16(14)20/h2-5,11,17H,6-7H2,1H3,(H,18,19)/t11-/m0/s1

InChI Key

HHXSOTFPYPQSBU-NSHDSACASA-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
Streptomyces coelicolor	LOTUS Database	35616633
Streptomyces violaceoruber	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as naphthopyranones. Naphthopyranones are compounds containing a naphthopyran skeleton where a ring carbon bears a carboxylic acid group. Naphthtopyran is made up of the pyran ring fused to a naphthalene ring system.

Kingdom

Organic compounds

Super Class

Organoheterocyclic compounds

Class

Naphthopyrans

Sub Class

Naphthopyranones

Direct Parent

Naphthopyranones

Alternative Parents

Substituents

Naphthopyranone
Naphthalene
Aryl ketone
1-hydroxy-4-unsubstituted benzenoid
1-hydroxy-2-unsubstituted benzenoid
Pyranone
Benzenoid
Pyran
Vinylogous ester
Vinylogous acid
Ketone
Carboxylic acid derivative
Carboxylic acid
Monocarboxylic acid or derivatives
Oxacycle
Organic oxygen compound
Organic oxide
Hydrocarbon derivative
Organooxygen compound
Carbonyl group
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic heteropolycyclic compounds

External Descriptors

cyclic ketone (CHEBI:31034 )
monocarboxylic acid (CHEBI:31034 )
phenols (CHEBI:31034 )
polyketide (CHEBI:31034 )
aromatic ketone (CHEBI:31034 )
naphthopyran (CHEBI:31034 )

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	2.01	ALOGPS
logP	1.94	ChemAxon
logS	-3.3	ALOGPS
pKa (Strongest Acidic)	3.73	ChemAxon
pKa (Strongest Basic)	-4.4	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	5	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	83.83 Å²	ChemAxon
Rotatable Bond Count	2	ChemAxon
Refractivity	77.35 m³·mol⁻¹	ChemAxon
Polarizability	29.21 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

DB08541

Phenol Explorer Compound ID

Not Available

FoodDB ID

Not Available

KNApSAcK ID

Not Available

Chemspider ID

Not Available

KEGG Compound ID

C12434

BioCyc ID

CPD1A0-6111

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

135440050

PDB ID

SDN

ChEBI ID

31034

Good Scents ID

Not Available

References

General References

LOTUS database [Link]

Showing NP-Card for (s)-dnpa (NP0312031)

MOL for NP0312031 ((s)-dnpa)

3D MOL for NP0312031 ((s)-dnpa)

3D SDF for NP0312031 ((s)-dnpa)

3D-SDF for NP0312031 ((s)-dnpa)

PDB for NP0312031 ((s)-dnpa)

3D PDB for NP0312031 ((s)-dnpa)

SMILES for NP0312031 ((s)-dnpa)

INCHI for NP0312031 ((s)-dnpa)

Structure for NP0312031 ((s)-dnpa)

3D Structure for NP0312031 ((s)-dnpa)