NP-MRD: Showing NP-Card for Xanthothricin (NP0012535)

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Record Information

Version

2.0

Created at

2021-01-05 21:53:56 UTC

Updated at

2021-07-15 17:12:02 UTC

NP-MRD ID

NP0012535

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Xanthothricin

Provided By

NPAtlas

Description

Toxoflavin is also known as xanthothricin or 1-methylreumycin. Toxoflavin is a secondary metabolite. Secondary metabolites are metabolically or physiologically non-essential metabolites that may serve a role as defense or signalling molecules. In some cases they are simply molecules that arise from the incomplete metabolism of other secondary metabolites. Xanthothricin is found in Burkholderia glumae, Streptomyces hiroshimensis and Unknown-fungus sp.. Xanthothricin was first documented in 1954 (PMID: 24542943). Based on a literature review a small amount of articles have been published on toxoflavin (PMID: 19662654) (PMID: 25806356) (PMID: 25845410).

Structure

MOL 3D MOL SDF 3D SDF PDB SMILES InChI


  Mrv1652306242117093D          

 21 22  0  0  0  0            999 V2000
   -2.9108    1.1917   -0.4976 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1208   -0.0413   -0.3838 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6578   -1.2290   -0.4271 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9124   -2.3501   -0.3204 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5738   -2.2996   -0.1634 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.0143   -1.1113   -0.1140 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3777   -0.9609    0.0442 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0969   -1.9821    0.1461 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.9064    0.2517    0.0861 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.3325    0.4641    0.2507 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1410    1.3472   -0.0225 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6661    2.5045    0.0199 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1949    1.2939   -0.1791 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8019    0.0790   -0.2303 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3581    1.8685   -1.2098 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9160    1.0063   -0.8904 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8921    1.6572    0.5021 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3424   -3.3498   -0.3542 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.5553    0.8765    1.2615 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.6641    1.2319   -0.4874 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.9266   -0.4486    0.0316 H   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
  4  5  1  0  0  0  0
  5  6  2  0  0  0  0
  6  7  1  0  0  0  0
  7  8  2  0  0  0  0
  7  9  1  0  0  0  0
  9 10  1  0  0  0  0
  9 11  1  0  0  0  0
 11 12  2  0  0  0  0
 11 13  1  0  0  0  0
 13 14  2  0  0  0  0
 14  2  1  0  0  0  0
 14  6  1  0  0  0  0
  1 15  1  0  0  0  0
  1 16  1  0  0  0  0
  1 17  1  0  0  0  0
  4 18  1  0  0  0  0
 10 19  1  0  0  0  0
 10 20  1  0  0  0  0
 10 21  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0012535

> <DATABASE_NAME>
NP-MRD

> <SMILES>
[H]C1=NN(C2=NC(=O)N(C(=O)C2=N1)C([H])([H])[H])C([H])([H])[H]

> <INCHI_IDENTIFIER>
InChI=1S/C7H7N5O2/c1-11-6(13)4-5(10-7(11)14)12(2)9-3-8-4/h3H,1-2H3

> <INCHI_KEY>
SLGRAIAQIAUZAQ-UHFFFAOYSA-N

> <FORMULA>
C7H7N5O2

> <MOLECULAR_WEIGHT>
193.1628

> <EXACT_MASS>
193.059974493

> <JCHEM_ACCEPTOR_COUNT>
6

> <JCHEM_ATOM_COUNT>
21

> <JCHEM_AVERAGE_POLARIZABILITY>
17.41237326840658

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
1,6-dimethyl-1H,5H,6H,7H-pyrimido[5,4-e][1,2,4]triazine-5,7-dione

> <ALOGPS_LOGP>
-0.57

> <JCHEM_LOGP>
-1.118445807

> <ALOGPS_LOGS>
-2.22

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_BASIC>
-4.427192415548857

> <JCHEM_POLAR_SURFACE_AREA>
77.7

> <JCHEM_REFRACTIVITY>
46.0117

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.16e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
toxoflavin

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 24-JUN-21   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   24-JUN-21         0                                  
HETATM    1  C   UNK     0      -2.911   1.192  -0.498  0.00  0.00           C+0
HETATM    2  N   UNK     0      -2.121  -0.041  -0.384  0.00  0.00           N+0
HETATM    3  N   UNK     0      -2.658  -1.229  -0.427  0.00  0.00           N+0
HETATM    4  C   UNK     0      -1.912  -2.350  -0.320  0.00  0.00           C+0
HETATM    5  N   UNK     0      -0.574  -2.300  -0.163  0.00  0.00           N+0
HETATM    6  C   UNK     0       0.014  -1.111  -0.114  0.00  0.00           C+0
HETATM    7  C   UNK     0       1.378  -0.961   0.044  0.00  0.00           C+0
HETATM    8  O   UNK     0       2.097  -1.982   0.146  0.00  0.00           O+0
HETATM    9  N   UNK     0       1.906   0.252   0.086  0.00  0.00           N+0
HETATM   10  C   UNK     0       3.333   0.464   0.251  0.00  0.00           C+0
HETATM   11  C   UNK     0       1.141   1.347  -0.023  0.00  0.00           C+0
HETATM   12  O   UNK     0       1.666   2.505   0.020  0.00  0.00           O+0
HETATM   13  N   UNK     0      -0.195   1.294  -0.179  0.00  0.00           N+0
HETATM   14  C   UNK     0      -0.802   0.079  -0.230  0.00  0.00           C+0
HETATM   15  H   UNK     0      -2.358   1.869  -1.210  0.00  0.00           H+0
HETATM   16  H   UNK     0      -3.916   1.006  -0.890  0.00  0.00           H+0
HETATM   17  H   UNK     0      -2.892   1.657   0.502  0.00  0.00           H+0
HETATM   18  H   UNK     0      -2.342  -3.350  -0.354  0.00  0.00           H+0
HETATM   19  H   UNK     0       3.555   0.877   1.262  0.00  0.00           H+0
HETATM   20  H   UNK     0       3.664   1.232  -0.487  0.00  0.00           H+0
HETATM   21  H   UNK     0       3.927  -0.449   0.032  0.00  0.00           H+0
CONECT    1    2   15   16   17                                             
CONECT    2    1    3   14                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5   18                                                  
CONECT    5    4    6                                                       
CONECT    6    5    7   14                                                  
CONECT    7    6    8    9                                                  
CONECT    8    7                                                            
CONECT    9    7   10   11                                                  
CONECT   10    9   19   20   21                                             
CONECT   11    9   12   13                                                  
CONECT   12   11                                                            
CONECT   13   11   14                                                       
CONECT   14   13    2    6                                                  
CONECT   15    1                                                            
CONECT   16    1                                                            
CONECT   17    1                                                            
CONECT   18    4                                                            
CONECT   19   10                                                            
CONECT   20   10                                                            
CONECT   21   10                                                            
MASTER        0    0    0    0    0    0    0    0   21    0   44    0
END

View in JSmol View NMR Assignments

Synonyms

Value	Source
1,6-Dimethylpyrimido(5,4-e)-as-triazine-5,7(1H,6H)-dione	ChEBI
1,6-Dimethylpyrimido[5,4-e][1,2,4]triazine-5,7-dione	ChEBI
1-Methylreumycin	ChEBI
NC72	ChEBI
NSC67078	ChEBI
PKF118-310	ChEBI
Toxoflavine	ChEBI
Xanthothricin	ChEBI
Xanthotricin	ChEBI
1,6-dimethylpyrimido(5,4-e)-As- triazine-5,7(1H,6H)-dione	MeSH

Chemical Formula

C₇H₇N₅O₂

Average Mass

193.1628 Da

Monoisotopic Mass

193.05997 Da

IUPAC Name

1,6-dimethyl-1H,5H,6H,7H-pyrimido[5,4-e][1,2,4]triazine-5,7-dione

Traditional Name

toxoflavin

CAS Registry Number

Not Available

SMILES

CN1N=CN=C2C(=O)N(C)C(=O)N=C12

InChI Identifier

InChI=1S/C7H7N5O2/c1-11-6(13)4-5(10-7(11)14)12(2)9-3-8-4/h3H,1-2H3

InChI Key

SLGRAIAQIAUZAQ-UHFFFAOYSA-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
Burkholderia glumae	LOTUS Database	35616633
Streptomyces hiroshimensis	LOTUS Database	35616633
Unknown-fungus sp.	NPAtlas	24542943

Chemical Taxonomy

Description

This compound belongs to the class of organic compounds known as pyrimidones. These are compounds that contain a pyrimidine ring, which bears a ketone. Pyrimidine is a 6-membered ring consisting of four carbon atoms and two nitrogen centers at the 1- and 3- ring positions.

Kingdom

Organic compounds

Super Class

Organoheterocyclic compounds

Class

Diazines

Sub Class

Pyrimidines and pyrimidine derivatives

Direct Parent

Pyrimidones

Alternative Parents

Substituents

Pyrimidone
1,2,4-triazine
Triazine
Heteroaromatic compound
Vinylogous amide
Lactam
Azacycle
Organic nitrogen compound
Organic oxygen compound
Organopnictogen compound
Organic oxide
Hydrocarbon derivative
Organooxygen compound
Organonitrogen compound
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic heteropolycyclic compounds

External Descriptors

9,11,15-octadecatrienoic acid (CHEBI:80729 )

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	-0.57	ALOGPS
logP	-1.1	ChemAxon
logS	-2.2	ALOGPS
pKa (Strongest Basic)	-4.4	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	6	ChemAxon
Hydrogen Donor Count	0	ChemAxon
Polar Surface Area	77.7 Å²	ChemAxon
Rotatable Bond Count	0	ChemAxon
Refractivity	46.01 m³·mol⁻¹	ChemAxon
Polarizability	17.41 Å³	ChemAxon
Number of Rings	2	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

External Links

NPAtlas ID

NPA004485

HMDB ID

Not Available

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

Not Available

KNApSAcK ID

Not Available

Chemspider ID

59912

KEGG Compound ID

C16789

BioCyc ID

CPD-21056

BiGG ID

Not Available

Wikipedia Link

Toxoflavin

METLIN ID

Not Available

PubChem Compound

66541

PDB ID

Not Available

ChEBI ID

80729

Good Scents ID

Not Available

References

General References

MACHLOWITZ RA, FISHER WP, McKAY BS, TYTELL AA, CHARNEY J: Xanthothricin, a new antibiotic. Antibiot Chemother (Northfield). 1954 Mar;4(3):259-61. [PubMed:24542943 ]
Wei W, Chua MS, Grepper S, So S: Small molecule antagonists of Tcf4/beta-catenin complex inhibit the growth of HCC cells in vitro and in vivo. Int J Cancer. 2010 May 15;126(10):2426-36. doi: 10.1002/ijc.24810. [PubMed:19662654 ]
Chen R, Barphagha IK, Ham JH: Identification of potential genetic components involved in the deviant quorum-sensing signaling pathways of Burkholderia glumae through a functional genomics approach. Front Cell Infect Microbiol. 2015 Mar 10;5:22. doi: 10.3389/fcimb.2015.00022. eCollection 2015. [PubMed:25806356 ]
Lee J, Park J, Kim S, Park I, Seo YS: Differential regulation of toxoflavin production and its role in the enhanced virulence of Burkholderia gladioli. Mol Plant Pathol. 2016 Jan;17(1):65-76. doi: 10.1111/mpp.12262. Epub 2015 May 7. [PubMed:25845410 ]

Showing NP-Card for Xanthothricin (NP0012535)

MOL for NP0012535 (Xanthothricin)

3D MOL for NP0012535 (Xanthothricin)

3D SDF for NP0012535 (Xanthothricin)

3D-SDF for NP0012535 (Xanthothricin)

PDB for NP0012535 (Xanthothricin)

3D PDB for NP0012535 (Xanthothricin)

SMILES for NP0012535 (Xanthothricin)

INCHI for NP0012535 (Xanthothricin)

Structure for NP0012535 (Xanthothricin)

3D Structure for NP0012535 (Xanthothricin)