NP-MRD: Showing NP-Card for Tropodithietic acid (NP0005236)

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Record Information

Version

2.0

Created at

2020-12-09 02:32:21 UTC

Updated at

2021-07-15 16:51:25 UTC

NP-MRD ID

NP0005236

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Tropodithietic acid

Provided By

NPAtlas

Description

Tropodithietic acid belongs to the class of organic compounds known as tropones. Tropones are compounds containing a tropone ring, which is a cycloheptatrienone ring bearing a ketone group. Tropodithietic acid 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. Tropodithietic acid is found in Phaeobacter inhibens and Roseobacter sp.. Tropodithietic acid was first documented in 2004 (PMID: 15066861). Based on a literature review a small amount of articles have been published on tropodithietic acid (PMID: 18062698) (PMID: 18192410) (PMID: 20601479) (PMID: 21263047).

Structure

MOL 3D MOL SDF 3D SDF PDB SMILES InChI


  Mrv1652306242118173D          

 17 18  0  0  0  0            999 V2000
    3.0314   -0.6997   -1.2048 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.3355   -0.5455   -0.1831 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9053   -0.6976    1.0612 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.9314   -0.2076   -0.2801 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0455   -1.2931   -0.3362 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6113   -2.4251   -0.4414 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3365   -1.3079   -0.2939 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1885   -0.3167    0.1737 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8745    1.0296    0.3766 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7207    1.6770   -0.0181 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3800    3.3449   -0.2940 S   0  0  0  0  0  0  0  0  0  0  0  0
    1.4165    2.5472   -0.7139 S   0  0  0  0  0  0  0  0  0  0  0  0
    0.5338    1.1204   -0.3113 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3436   -1.0183    1.8227 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8115   -2.1960   -0.6688 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2029   -0.5971    0.4110 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6396    1.5855    0.9002 H   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
  2  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  2  0  0  0  0
  5  7  1  0  0  0  0
  7  8  2  0  0  0  0
  8  9  1  0  0  0  0
  9 10  2  0  0  0  0
 10 11  1  0  0  0  0
 11 12  1  0  0  0  0
 12 13  1  0  0  0  0
 13  4  2  0  0  0  0
 13 10  1  0  0  0  0
  3 14  1  0  0  0  0
  7 15  1  0  0  0  0
  8 16  1  0  0  0  0
  9 17  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0005236

> <DATABASE_NAME>
NP-MRD

> <SMILES>
[H]OC(=O)C1=C2SSC2=C([H])C([H])=C([H])C1=O

> <INCHI_IDENTIFIER>
InChI=1S/C8H4O3S2/c9-4-2-1-3-5-7(13-12-5)6(4)8(10)11/h1-3H,(H,10,11)

> <INCHI_KEY>
BLFCMITWMARUSM-UHFFFAOYSA-N

> <FORMULA>
C8H4O3S2

> <MOLECULAR_WEIGHT>
212.24

> <EXACT_MASS>
211.960186337

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_ATOM_COUNT>
17

> <JCHEM_AVERAGE_POLARIZABILITY>
18.89248968325917

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
3-oxo-8,9-dithiabicyclo[5.2.0]nona-1,4,6-triene-2-carboxylic acid

> <ALOGPS_LOGP>
1.76

> <JCHEM_LOGP>
1.2954037106666667

> <ALOGPS_LOGS>
-2.02

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.880422117249022

> <JCHEM_PKA_STRONGEST_BASIC>
-5.094170393383815

> <JCHEM_POLAR_SURFACE_AREA>
54.37

> <JCHEM_REFRACTIVITY>
56.468300000000006

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
2.02e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
3-oxo-8,9-dithiabicyclo[5.2.0]nona-1,4,6-triene-2-carboxylic acid

> <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  O   UNK     0       3.031  -0.700  -1.205  0.00  0.00           O+0
HETATM    2  C   UNK     0       2.336  -0.546  -0.183  0.00  0.00           C+0
HETATM    3  O   UNK     0       2.905  -0.698   1.061  0.00  0.00           O+0
HETATM    4  C   UNK     0       0.931  -0.208  -0.280  0.00  0.00           C+0
HETATM    5  C   UNK     0       0.046  -1.293  -0.336  0.00  0.00           C+0
HETATM    6  O   UNK     0       0.611  -2.425  -0.441  0.00  0.00           O+0
HETATM    7  C   UNK     0      -1.337  -1.308  -0.294  0.00  0.00           C+0
HETATM    8  C   UNK     0      -2.188  -0.317   0.174  0.00  0.00           C+0
HETATM    9  C   UNK     0      -1.875   1.030   0.377  0.00  0.00           C+0
HETATM   10  C   UNK     0      -0.721   1.677  -0.018  0.00  0.00           C+0
HETATM   11  S   UNK     0      -0.380   3.345  -0.294  0.00  0.00           S+0
HETATM   12  S   UNK     0       1.417   2.547  -0.714  0.00  0.00           S+0
HETATM   13  C   UNK     0       0.534   1.120  -0.311  0.00  0.00           C+0
HETATM   14  H   UNK     0       2.344  -1.018   1.823  0.00  0.00           H+0
HETATM   15  H   UNK     0      -1.812  -2.196  -0.669  0.00  0.00           H+0
HETATM   16  H   UNK     0      -3.203  -0.597   0.411  0.00  0.00           H+0
HETATM   17  H   UNK     0      -2.640   1.585   0.900  0.00  0.00           H+0
CONECT    1    2                                                            
CONECT    2    1    3    4                                                  
CONECT    3    2   14                                                       
CONECT    4    2    5   13                                                  
CONECT    5    4    6    7                                                  
CONECT    6    5                                                            
CONECT    7    5    8   15                                                  
CONECT    8    7    9   16                                                  
CONECT    9    8   10   17                                                  
CONECT   10    9   11   13                                                  
CONECT   11   10   12                                                       
CONECT   12   11   13                                                       
CONECT   13   12    4   10                                                  
CONECT   14    3                                                            
CONECT   15    7                                                            
CONECT   16    8                                                            
CONECT   17    9                                                            
MASTER        0    0    0    0    0    0    0    0   17    0   36    0
END

View in JSmol View NMR Assignments

Synonyms

Value	Source
Tropodithietate	Generator

Chemical Formula

C₈H₄O₃S₂

Average Mass

212.2400 Da

Monoisotopic Mass

211.96019 Da

IUPAC Name

3-oxo-8,9-dithiabicyclo[5.2.0]nona-1,4,6-triene-2-carboxylic acid

Traditional Name

3-oxo-8,9-dithiabicyclo[5.2.0]nona-1,4,6-triene-2-carboxylic acid

CAS Registry Number

Not Available

SMILES

OC(=O)C1=C2SSC2=CC=CC1=O

InChI Identifier

InChI=1S/C8H4O3S2/c9-4-2-1-3-5-7(13-12-5)6(4)8(10)11/h1-3H,(H,10,11)

InChI Key

BLFCMITWMARUSM-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
Phaeobacter inhibens	LOTUS Database	35616633
Roseobacter sp.	NPAtlas	15066861

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as tropones. Tropones are compounds containing a tropone ring, which is a cycloheptatrienone ring bearing a ketone group.

Kingdom

Organic compounds

Super Class

Hydrocarbon derivatives

Class

Tropones

Sub Class

Not Available

Direct Parent

Tropones

Alternative Parents

Substituents

Tropone
Heteroaromatic compound
Cyclic ketone
Organoheterocyclic compound
Carboxylic acid
Carboxylic acid derivative
Organic oxygen compound
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	1.76	ALOGPS
logP	1.3	ChemAxon
logS	-2	ALOGPS
pKa (Strongest Acidic)	3.88	ChemAxon
pKa (Strongest Basic)	-5.1	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	3	ChemAxon
Hydrogen Donor Count	1	ChemAxon
Polar Surface Area	54.37 Å²	ChemAxon
Rotatable Bond Count	1	ChemAxon
Refractivity	56.47 m³·mol⁻¹	ChemAxon
Polarizability	18.89 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

NPA024788

HMDB ID

Not Available

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

Not Available

KNApSAcK ID

Not Available

Chemspider ID

27025853

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Tropodithietic acid

METLIN ID

Not Available

PubChem Compound

44632924

PDB ID

Not Available

ChEBI ID

156455

Good Scents ID

Not Available

References

General References

Brinkhoff T, Bach G, Heidorn T, Liang L, Schlingloff A, Simon M: Antibiotic production by a Roseobacter clade-affiliated species from the German Wadden Sea and its antagonistic effects on indigenous isolates. Appl Environ Microbiol. 2004 Apr;70(4):2560-5. doi: 10.1128/aem.70.4.2560-2565.2003. [PubMed:15066861 ]
Greer EM, Aebisher D, Greer A, Bentley R: Computational studies of the tropone natural products, thiotropocin, tropodithietic acid, and troposulfenin. Significance of thiocarbonyl-enol tautomerism. J Org Chem. 2008 Jan 4;73(1):280-3. doi: 10.1021/jo7018416. Epub 2007 Dec 7. [PubMed:18062698 ]
Geng H, Bruhn JB, Nielsen KF, Gram L, Belas R: Genetic dissection of tropodithietic acid biosynthesis by marine roseobacters. Appl Environ Microbiol. 2008 Mar;74(5):1535-45. doi: 10.1128/AEM.02339-07. Epub 2008 Jan 11. [PubMed:18192410 ]
Geng H, Belas R: Expression of tropodithietic acid biosynthesis is controlled by a novel autoinducer. J Bacteriol. 2010 Sep;192(17):4377-87. doi: 10.1128/JB.00410-10. Epub 2010 Jul 2. [PubMed:20601479 ]
Porsby CH, Webber MA, Nielsen KF, Piddock LJ, Gram L: Resistance and tolerance to tropodithietic acid, an antimicrobial in aquaculture, is hard to select. Antimicrob Agents Chemother. 2011 Apr;55(4):1332-7. doi: 10.1128/AAC.01222-10. Epub 2011 Jan 24. [PubMed:21263047 ]

Showing NP-Card for Tropodithietic acid (NP0005236)

MOL for NP0005236 (Tropodithietic acid)

3D MOL for NP0005236 (Tropodithietic acid)

3D SDF for NP0005236 (Tropodithietic acid)

3D-SDF for NP0005236 (Tropodithietic acid)

PDB for NP0005236 (Tropodithietic acid)

3D PDB for NP0005236 (Tropodithietic acid)

SMILES for NP0005236 (Tropodithietic acid)

INCHI for NP0005236 (Tropodithietic acid)

Structure for NP0005236 (Tropodithietic acid)

3D Structure for NP0005236 (Tropodithietic acid)