NP-MRD: Showing NP-Card for Antibiotic OS 3966B (NP0062009)

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Record Information

Version

1.0

Created at

2022-04-28 06:41:49 UTC

Updated at

2022-04-28 06:41:49 UTC

NP-MRD ID

NP0062009

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Antibiotic OS 3966B

Description

Nanaomycin B 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. Antibiotic OS 3966B is found in Streptomyces rasa var. notoensis. It was first documented in 2015 (PMID: 26100318). Based on a literature review very few articles have been published on Nanaomycin B.

Structure

MOL 3D MOL SDF PDB SMILES InChI

     RDKit          3D

 39 41  0  0  0  0  0  0  0  0999 V2000
    0.8086   -3.0351    0.5377 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1261   -1.6105    0.1305 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.9122   -1.0464    1.1133 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.4472    0.1737    0.8110 C   0  0  1  0  0  0  0  0  0  0  0  0
    3.8638    0.1722    0.3567 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2742    1.5615    0.0763 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.5294    2.3271    1.0254 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.3775    2.0182   -1.2173 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.6131    0.9401   -0.2284 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2058    0.6368    0.1020 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.8218    1.4433   -0.5338 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5732    2.4197   -1.2586 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2162    1.0464   -0.2779 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2624    1.9269   -0.4756 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5745    1.5635   -0.2384 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7726    0.2649    0.2087 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7487   -0.6325    0.4140 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0244   -1.9147    0.8626 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4329   -0.2409    0.1669 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3248   -1.1789    0.3774 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5023   -2.2006    1.0762 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0586   -0.8266   -0.2723 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.2621   -0.9437   -1.6520 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0483   -3.4875   -0.1042 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7592   -3.6151    0.4101 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5791   -3.1068    1.6282 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7925   -1.7037   -0.7786 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.3731    0.8080    1.7417 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.5605   -0.2592    1.1037 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.9048   -0.4181   -0.6037 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.4154    3.0300   -1.4048 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7972    2.0205   -0.1524 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9594    0.5581   -1.2127 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1106    0.6525    1.2278 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0595    2.9295   -0.8260 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.3802    2.2654   -0.3983 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.8221    0.0003    0.3898 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9886   -2.1591    1.0295 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3669   -0.3789   -2.1509 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  1  0
  4  5  1  0
  5  6  1  0
  6  8  1  0
  6  7  2  0
  4  9  1  0
  9 10  1  0
 10 11  1  0
 11 12  2  0
 11 13  1  0
 13 14  2  0
 14 15  1  0
 15 16  2  0
 16 17  1  0
 17 18  1  0
 17 19  2  0
 19 20  1  0
 20 21  2  0
 20 22  1  0
 22 23  1  6
 22  2  1  0
 22 10  1  0
 19 13  1  0
  1 24  1  0
  1 25  1  0
  1 26  1  0
  2 27  1  6
  4 28  1  1
  5 29  1  0
  5 30  1  0
  8 31  1  0
  9 32  1  0
  9 33  1  0
 10 34  1  1
 14 35  1  0
 15 36  1  0
 16 37  1  0
 18 38  1  0
 23 39  1  0
M  END


  Mrv1652304282208412D          

 23 25  0  0  1  0            999 V2000
    4.2868    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2868   -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
    2.8579   -0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579    0.8250    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
    2.1434    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434    2.0625    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.8250    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.4289    0.0000    0.0000 C   0  0  2  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 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -0.4125    0.0000 C   0  0  1  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
    0.0000    0.8250    0.0000 C   0  0  2  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    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145    2.0625    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
    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
    1.4289   -0.8250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724   -1.2375    0.0000 O   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  2  0  0  0  0
  4  5  1  0  0  0  0
  5  6  2  0  0  0  0
  1  6  1  0  0  0  0
  5  7  1  0  0  0  0
  7  8  2  0  0  0  0
  9  7  1  1  0  0  0
  9 10  1  0  0  0  0
 10 11  1  0  0  0  0
  4 11  1  0  0  0  0
 11 12  2  0  0  0  0
 10 13  1  0  0  0  0
 13 14  1  0  0  0  0
 14 15  1  0  0  0  0
 15 16  1  0  0  0  0
  9 16  1  0  0  0  0
 15 17  1  1  0  0  0
 17 18  1  0  0  0  0
 18 19  2  0  0  0  0
 18 20  1  0  0  0  0
 13 21  1  6  0  0  0
 10 22  1  1  0  0  0
  3 23  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0062009

> <DATABASE_NAME>
NP-MRD

> <SMILES>
C[C@@H]1O[C@@H](CC(O)=O)C[C@H]2C(=O)C3=CC=CC(O)=C3C(=O)[C@]12O

> <INCHI_IDENTIFIER>
InChI=1S/C16H16O7/c1-7-16(22)10(5-8(23-7)6-12(18)19)14(20)9-3-2-4-11(17)13(9)15(16)21/h2-4,7-8,10,17,22H,5-6H2,1H3,(H,18,19)/t7-,8+,10-,16-/m0/s1

> <INCHI_KEY>
IRFITFGOKXSNHV-DWOGJIGDSA-N

> <FORMULA>
C16H16O7

> <MOLECULAR_WEIGHT>
320.297

> <EXACT_MASS>
320.089602855

> <JCHEM_ACCEPTOR_COUNT>
7

> <JCHEM_ATOM_COUNT>
39

> <JCHEM_AVERAGE_POLARIZABILITY>
30.925160664566025

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
2-[(1S,3R,4aR,10aR)-9,10a-dihydroxy-1-methyl-5,10-dioxo-1H,3H,4H,4aH,5H,10H,10aH-naphtho[2,3-c]pyran-3-yl]acetic acid

> <ALOGPS_LOGP>
1.11

> <JCHEM_LOGP>
1.0577994899999994

> <ALOGPS_LOGS>
-1.52

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
8.068251399269352

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.4538264137214982

> <JCHEM_PKA_STRONGEST_BASIC>
-4.191728386876831

> <JCHEM_POLAR_SURFACE_AREA>
121.13000000000001

> <JCHEM_REFRACTIVITY>
77.15640000000002

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
9.64e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
[(1S,3R,4aR,10aR)-9,10a-dihydroxy-1-methyl-5,10-dioxo-1H,3H,4H,4aH-naphtho[2,3-c]pyran-3-yl]acetic acid

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 28-APR-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   28-APR-22         0                                  
HETATM    1  C   UNK     0       8.002   1.540   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       8.002  -0.000   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       6.668  -0.770   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       5.335  -0.000   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       5.335   1.540   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       6.668   2.310   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       4.001   2.310   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0       4.001   3.850   0.000  0.00  0.00           O+0
HETATM    9  C   UNK     0       2.667   1.540   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       2.667   0.000   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       4.001  -0.770   0.000  0.00  0.00           C+0
HETATM   12  O   UNK     0       4.001  -2.310   0.000  0.00  0.00           O+0
HETATM   13  C   UNK     0       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM   14  O   UNK     0       0.000  -0.000   0.000  0.00  0.00           O+0
HETATM   15  C   UNK     0       0.000   1.540   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       1.334   2.310   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0      -1.334   2.310   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0      -1.334   3.850   0.000  0.00  0.00           C+0
HETATM   19  O   UNK     0      -2.667   4.620   0.000  0.00  0.00           O+0
HETATM   20  O   UNK     0       0.000   4.620   0.000  0.00  0.00           O+0
HETATM   21  C   UNK     0       1.334  -2.310   0.000  0.00  0.00           C+0
HETATM   22  O   UNK     0       2.667  -1.540   0.000  0.00  0.00           O+0
HETATM   23  O   UNK     0       6.668  -2.310   0.000  0.00  0.00           O+0
CONECT    1    2    6                                                       
CONECT    2    1    3                                                       
CONECT    3    2    4   23                                                  
CONECT    4    3    5   11                                                  
CONECT    5    4    6    7                                                  
CONECT    6    5    1                                                       
CONECT    7    5    8    9                                                  
CONECT    8    7                                                            
CONECT    9    7   10   16                                                  
CONECT   10    9   11   13   22                                             
CONECT   11   10    4   12                                                  
CONECT   12   11                                                            
CONECT   13   10   14   21                                                  
CONECT   14   13   15                                                       
CONECT   15   14   16   17                                                  
CONECT   16   15    9                                                       
CONECT   17   15   18                                                       
CONECT   18   17   19   20                                                  
CONECT   19   18                                                            
CONECT   20   18                                                            
CONECT   21   13                                                            
CONECT   22   10                                                            
CONECT   23    3                                                            
MASTER        0    0    0    0    0    0    0    0   23    0   50    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₁₆H₁₆O₇

Average Mass

320.2970 Da

Monoisotopic Mass

320.08960 Da

IUPAC Name

2-[(1S,3R,4aR,10aR)-9,10a-dihydroxy-1-methyl-5,10-dioxo-1H,3H,4H,4aH,5H,10H,10aH-naphtho[2,3-c]pyran-3-yl]acetic acid

Traditional Name

[(1S,3R,4aR,10aR)-9,10a-dihydroxy-1-methyl-5,10-dioxo-1H,3H,4H,4aH-naphtho[2,3-c]pyran-3-yl]acetic acid

CAS Registry Number

Not Available

SMILES

C[C@@H]1O[C@@H](CC(O)=O)C[C@H]2C(=O)C3=CC=CC(O)=C3C(=O)[C@]12O

InChI Identifier

InChI=1S/C16H16O7/c1-7-16(22)10(5-8(23-7)6-12(18)19)14(20)9-3-2-4-11(17)13(9)15(16)21/h2-4,7-8,10,17,22H,5-6H2,1H3,(H,18,19)/t7-,8+,10-,16-/m0/s1

InChI Key

IRFITFGOKXSNHV-DWOGJIGDSA-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, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 252 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 50 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 75 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 101 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 126 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 151 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 176 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 201 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 226 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, 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 rasa var. notoensis	Bacteria	KNApSAcK

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
Naphthoquinone
Naphthalene
Tetralin
Quinone
Aryl ketone
Aryl alkyl ketone
1-hydroxy-4-unsubstituted benzenoid
1-hydroxy-2-unsubstituted benzenoid
Phenol
Pyranone
Pyran
Benzenoid
Oxane
Tertiary alcohol
Vinylogous acid
Ketone
Oxacycle
Carboxylic acid derivative
Carboxylic acid
Dialkyl ether
Ether
Monocarboxylic acid or derivatives
Organic oxide
Carbonyl group
Hydrocarbon derivative
Alcohol
Organic oxygen compound
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	1.11	ALOGPS
logP	1.06	ChemAxon
logS	-1.5	ALOGPS
pKa (Strongest Acidic)	3.45	ChemAxon
pKa (Strongest Basic)	-4.2	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	7	ChemAxon
Hydrogen Donor Count	3	ChemAxon
Polar Surface Area	121.13 Å²	ChemAxon
Rotatable Bond Count	2	ChemAxon
Refractivity	77.16 m³·mol⁻¹	ChemAxon
Polarizability	30.93 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

C00017990

Chemspider ID

57260705

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

12804716

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Nakashima T, Boonsnongcheep P, Kimura T, Iwatsuki M, Sato N, Nonaka K, Prathanturarug S, Takahashi Y, Omura S: New compounds, nanaomycin F and G, discovered by physicochemical screening from a culture broth of Streptomyces rosa subsp. notoensis OS-3966. J Biosci Bioeng. 2015 Nov;120(5):596-600. doi: 10.1016/j.jbiosc.2015.03.018. Epub 2015 Jun 20. [PubMed:26100318 ]

Showing NP-Card for Antibiotic OS 3966B (NP0062009)

MOL for NP0062009 (Antibiotic OS 3966B)

3D MOL for NP0062009 (Antibiotic OS 3966B)

3D SDF for NP0062009 (Antibiotic OS 3966B)

3D-SDF for NP0062009 (Antibiotic OS 3966B)

PDB for NP0062009 (Antibiotic OS 3966B)

3D PDB for NP0062009 (Antibiotic OS 3966B)

SMILES for NP0062009 (Antibiotic OS 3966B)

INCHI for NP0062009 (Antibiotic OS 3966B)

Structure for NP0062009 (Antibiotic OS 3966B)

3D Structure for NP0062009 (Antibiotic OS 3966B)