NP-MRD: Showing NP-Card for Nybomycin D (NP0353048)

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Record Information

Version

2.0

Created at

2026-02-17 01:57:18 UTC

Updated at

2026-02-17 04:01:32 UTC

NP-MRD ID

NP0353048

Natural Product DOI

https://doi.org/10.57994/7374

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Nybomycin D

Description

10-Hydroxy-1,4,6,9-tetramethyl-1H,2H,8H,9H-pyrido[3,2-g]quinoline-2,8-dione belongs to the class of organic compounds known as hydroquinolones. Hydroquinolones are compounds containing a hydrogenated quinoline bearing a ketone group. Nybomycin D was first documented in 2019 (PMID: 31833370). 10-Hydroxy-1,4,6,9-tetramethyl-1H,2H,8H,9H-pyrido[3,2-g]quinoline-2,8-dione is an extremely weak basic (essentially neutral) compound (based on its pKa).

Structure

MOL SDF PDB SMILES InChI


  Mrv1533004241512262D          

 21 23  0  0  0  0            999 V2000
    2.1434   -3.7125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -2.8875    0.0000 N   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
    0.7145   -2.8875    0.0000 O   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
    2.1434   -1.2375    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
    2.8579   -1.6500    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 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0013   -1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.7158   -1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.7158   -2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.4302   -2.8875    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.0013   -2.8875    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    5.0013   -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
    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 O   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
    5.0013   -0.4125    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  2  0  0  0  0
  3  5  1  0  0  0  0
  5  6  2  0  0  0  0
  6  7  1  0  0  0  0
  6  8  1  0  0  0  0
  8  9  2  0  0  0  0
  9 10  1  0  0  0  0
 10 11  1  0  0  0  0
 11 12  2  0  0  0  0
 12 13  1  0  0  0  0
 13 14  2  0  0  0  0
 13 15  1  0  0  0  0
 15 16  1  0  0  0  0
 15 17  1  0  0  0  0
 10 17  2  0  0  0  0
 17 18  1  0  0  0  0
 18 19  1  0  0  0  0
 18 20  2  0  0  0  0
  2 20  1  0  0  0  0
  8 20  1  0  0  0  0
 11 21  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0353048

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CN1C(=O)C=C(C)C2=CC3=C(N(C)C(=O)C=C3C)C(O)=C12

> <INCHI_IDENTIFIER>
InChI=1S/C16H16N2O3/c1-8-5-12(19)17(3)14-10(8)7-11-9(2)6-13(20)18(4)15(11)16(14)21/h5-7,21H,1-4H3

> <INCHI_KEY>
CKHJQWGAUDMNBP-UHFFFAOYSA-N

> <FORMULA>
C16H16N2O3

> <MOLECULAR_WEIGHT>
284.315

> <EXACT_MASS>
284.116092383

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_ATOM_COUNT>
37

> <JCHEM_AVERAGE_POLARIZABILITY>
30.16010581463485

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
10-hydroxy-1,4,6,9-tetramethyl-1H,2H,8H,9H-pyrido[3,2-g]quinoline-2,8-dione

> <ALOGPS_LOGP>
1.47

> <JCHEM_LOGP>
1.244394892999999

> <ALOGPS_LOGS>
-2.33

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_ACIDIC>
7.747735337407999

> <JCHEM_PKA_STRONGEST_BASIC>
-1.179577450959159

> <JCHEM_POLAR_SURFACE_AREA>
60.85000000000001

> <JCHEM_REFRACTIVITY>
81.2771

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.34e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
10-hydroxy-1,4,6,9-tetramethylpyrido[3,2-g]quinoline-2,8-dione

> <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       4.001  -6.930   0.000  0.00  0.00           C+0
HETATM    2  N   UNK     0       4.001  -5.390   0.000  0.00  0.00           N+0
HETATM    3  C   UNK     0       2.667  -4.620   0.000  0.00  0.00           C+0
HETATM    4  O   UNK     0       1.334  -5.390   0.000  0.00  0.00           O+0
HETATM    5  C   UNK     0       2.667  -3.080   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       4.001  -2.310   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       4.001  -0.770   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       5.335  -3.080   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  C   UNK     0       8.002  -3.080   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       9.336  -2.310   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      10.669  -3.080   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      10.669  -4.620   0.000  0.00  0.00           C+0
HETATM   14  O   UNK     0      12.003  -5.390   0.000  0.00  0.00           O+0
HETATM   15  N   UNK     0       9.336  -5.390   0.000  0.00  0.00           N+0
HETATM   16  C   UNK     0       9.336  -6.930   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       8.002  -4.620   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       6.668  -5.390   0.000  0.00  0.00           C+0
HETATM   19  O   UNK     0       6.668  -6.930   0.000  0.00  0.00           O+0
HETATM   20  C   UNK     0       5.335  -4.620   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0       9.336  -0.770   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3   20                                                  
CONECT    3    2    4    5                                                  
CONECT    4    3                                                            
CONECT    5    3    6                                                       
CONECT    6    5    7    8                                                  
CONECT    7    6                                                            
CONECT    8    6    9   20                                                  
CONECT    9    8   10                                                       
CONECT   10    9   11   17                                                  
CONECT   11   10   12   21                                                  
CONECT   12   11   13                                                       
CONECT   13   12   14   15                                                  
CONECT   14   13                                                            
CONECT   15   13   16   17                                                  
CONECT   16   15                                                            
CONECT   17   15   10   18                                                  
CONECT   18   17   19   20                                                  
CONECT   19   18                                                            
CONECT   20   18    2    8                                                  
CONECT   21   11                                                            
MASTER        0    0    0    0    0    0    0    0   21    0   46    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₁₆H₁₆N₂O₃

Average Mass

284.3150 Da

Monoisotopic Mass

284.11609 Da

IUPAC Name

10-hydroxy-1,4,6,9-tetramethyl-1H,2H,8H,9H-pyrido[3,2-g]quinoline-2,8-dione

Traditional Name

10-hydroxy-1,4,6,9-tetramethylpyrido[3,2-g]quinoline-2,8-dione

CAS Registry Number

Not Available

SMILES

CN1C(=O)C=C(C)C2=CC3=C(N(C)C(=O)C=C3C)C(O)=C12

InChI Identifier

InChI=1S/C16H16N2O3/c1-8-5-12(19)17(3)14-10(8)7-11-9(2)6-13(20)18(4)15(11)16(14)21/h5-7,21H,1-4H3

InChI Key

CKHJQWGAUDMNBP-UHFFFAOYSA-N

Experimental Spectra

Spectrum Type	Description	Depositor Email	Depositor Organization	Depositor	Deposition Date	View

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, Trifluoroacetic acid-d, simulated)	[email protected]	Not Available	Not Available	2026-02-17	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 100.0, Trifluoroacetic acid-d, simulated)	[email protected]	Not Available	Not Available	2026-02-17	View Spectrum

Species

Species of Origin

Species Name	Source	Reference
Streptomyces sp. AD-3-6		Not Available

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as hydroquinolones. Hydroquinolones are compounds containing a hydrogenated quinoline bearing a ketone group.

Kingdom

Organic compounds

Super Class

Organoheterocyclic compounds

Class

Quinolines and derivatives

Sub Class

Quinolones and derivatives

Direct Parent

Hydroquinolones

Alternative Parents

Substituents

Dihydroquinolone
8-hydroxyquinoline
Dihydroquinoline
1-hydroxy-4-unsubstituted benzenoid
Methylpyridine
Phenol
Pyridinone
Benzenoid
Pyridine
Heteroaromatic compound
Lactam
Azacycle
Organic nitrogen compound
Hydrocarbon derivative
Organooxygen compound
Organonitrogen compound
Organic oxide
Organic oxygen 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	1.47	ALOGPS
logP	1.24	ChemAxon
logS	-2.3	ALOGPS
pKa (Strongest Acidic)	7.75	ChemAxon
pKa (Strongest Basic)	-1.2	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	3	ChemAxon
Hydrogen Donor Count	1	ChemAxon
Polar Surface Area	60.85 Å²	ChemAxon
Rotatable Bond Count	0	ChemAxon
Refractivity	81.28 m³·mol⁻¹	ChemAxon
Polarizability	30.16 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

69004958

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Showing NP-Card for Nybomycin D (NP0353048)

MOL for NP0353048 (Nybomycin D)

3D MOL for NP0353048 (Nybomycin D)

3D SDF for NP0353048 (Nybomycin D)

3D-SDF for NP0353048 (Nybomycin D)

PDB for NP0353048 (Nybomycin D)

3D PDB for NP0353048 (Nybomycin D)

SMILES for NP0353048 (Nybomycin D)

INCHI for NP0353048 (Nybomycin D)

Structure for NP0353048 (Nybomycin D)

3D Structure for NP0353048 (Nybomycin D)