MiMeDB: Showing metabocard for Trichodermatide D (MMDBc0018220)

Record Information

Version

2.0

Status

Detected and Quantified

Creation Date

2021-05-15 08:27:21 UTC

Update Date

2025-10-07 16:06:48 UTC

Metabolite ID

MMDBc0018220

Metabolite Identification

Common Name

Trichodermatide D

Description

Trichodermatide D is a polyketide, a class of compounds characterized by their biosynthesis through the polyketide synthase pathway. This metabolite has been isolated from various species of the Trichoderma genus, particularly during interactions with bacteria, as evidenced by its exclusive detection in co-cultures with bacterial strains (PMID:38980562 ). The chemical structure of Trichodermatide D features a complex arrangement of carbon chains and functional groups typical of polyketides, contributing to its diverse biological activities. In addition to its isolation from Trichoderma species, Trichodermatide D has been identified alongside other compounds in extracts from fungi, indicating its potential role in the ecological interactions within its habitat (PMID:36250229 ). While the specific biological pathways involving Trichodermatide D are not detailed, polyketides are generally known for their involvement in various metabolic processes, including antifungal and antibacterial activities, which may play a role in the organism's survival and competitive advantage in its environment.

Structure

MOL SDF PDB SMILES InChI


  Mrv1652305152110272D          

 22 23  0  0  1  0            999 V2000
    4.2868    2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0013    2.8875    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 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.1447    2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.8592    2.8875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.7171    2.8875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.0026    2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.4315    4.9500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.0026    4.9500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.7171    5.3625    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   10.7171    3.7125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.5737    2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.4315    4.1250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.2881    2.8875    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   10.0026    4.1250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.7171    6.1875    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    8.5737    1.6500    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   12.1460    3.7125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    9.2881    3.7125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   10.0026    5.7750    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    9.2881    2.0625    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  0  0  0  0
  3  2  1  0  0  0  0
  4  3  1  0  0  0  0
  5  4  1  0  0  0  0
  6  5  1  0  0  0  0
  8  7  1  0  0  0  0
 11  9  1  0  0  0  0
 11 10  1  0  0  0  0
 12  7  1  0  0  0  0
 13  6  1  0  0  0  0
 14  9  1  0  0  0  0
 14 12  1  0  0  0  0
 15  8  1  0  0  0  0
 15 13  1  6  0  0  0
 16 10  1  0  0  0  0
 16 12  2  0  0  0  0
 11 17  1  1  0  0  0
 18 13  2  0  0  0  0
 19 14  2  0  0  0  0
 20 15  1  0  0  0  0
 20 16  1  0  0  0  0
 11 21  1  6  0  0  0
 15 22  1  1  0  0  0
M  END
> <DATABASE_ID>
MMDBc0018220

> <DATABASE_NAME>
MIME

> <SMILES>
[H][C@]1(O)CC(=O)C2=C(C1)O[C@]([H])(CC2)C(=O)CCCCCC

> <INCHI_IDENTIFIER>
InChI=1S/C16H24O4/c1-2-3-4-5-6-13(18)15-8-7-12-14(19)9-11(17)10-16(12)20-15/h11,15,17H,2-10H2,1H3/t11-,15+/m0/s1

> <INCHI_KEY>
KERJAKAVUGWYGC-XHDPSFHLSA-N

> <FORMULA>
C16H24O4

> <MOLECULAR_WEIGHT>
280.364

> <EXACT_MASS>
280.167459253

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_ATOM_COUNT>
44

> <JCHEM_AVERAGE_POLARIZABILITY>
31.82690653633901

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
(2R,7R)-2-heptanoyl-7-hydroxy-3,4,5,6,7,8-hexahydro-2H-1-benzopyran-5-one

> <ALOGPS_LOGP>
2.08

> <JCHEM_LOGP>
2.333447608666666

> <ALOGPS_LOGS>
-2.89

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
17.103101697381568

> <JCHEM_PKA_STRONGEST_ACIDIC>
14.897385933085019

> <JCHEM_PKA_STRONGEST_BASIC>
-2.830365320625135

> <JCHEM_POLAR_SURFACE_AREA>
63.599999999999994

> <JCHEM_REFRACTIVITY>
77.24849999999999

> <JCHEM_ROTATABLE_BOND_COUNT>
6

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
3.63e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(2R,7R)-2-heptanoyl-7-hydroxy-2,3,4,6,7,8-hexahydro-1-benzopyran-5-one

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 15-MAY-21   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   15-MAY-21         0                                  
HETATM    1  C   UNK     0       8.002   4.620   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       9.336   5.390   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      10.669   4.620   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      12.003   5.390   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      13.337   4.620   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      14.670   5.390   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      20.005   5.390   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      18.672   4.620   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      21.339   9.240   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      18.672   9.240   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      20.005  10.010   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      20.005   6.930   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      16.004   4.620   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      21.339   7.700   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0      17.338   5.390   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0      18.672   7.700   0.000  0.00  0.00           C+0
HETATM   17  O   UNK     0      20.005  11.550   0.000  0.00  0.00           O+0
HETATM   18  O   UNK     0      16.004   3.080   0.000  0.00  0.00           O+0
HETATM   19  O   UNK     0      22.673   6.930   0.000  0.00  0.00           O+0
HETATM   20  O   UNK     0      17.338   6.930   0.000  0.00  0.00           O+0
HETATM   21  H   UNK     0      18.672  10.780   0.000  0.00  0.00           H+0
HETATM   22  H   UNK     0      17.338   3.850   0.000  0.00  0.00           H+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4    6                                                       
CONECT    6    5   13                                                       
CONECT    7    8   12                                                       
CONECT    8    7   15                                                       
CONECT    9   11   14                                                       
CONECT   10   11   16                                                       
CONECT   11    9   10   17   21                                             
CONECT   12    7   14   16                                                  
CONECT   13    6   15   18                                                  
CONECT   14    9   12   19                                                  
CONECT   15    8   13   20   22                                             
CONECT   16   10   12   20                                                  
CONECT   17   11                                                            
CONECT   18   13                                                            
CONECT   19   14                                                            
CONECT   20   15   16                                                       
CONECT   21   11                                                            
CONECT   22   15                                                            
MASTER        0    0    0    0    0    0    0    0   22    0   46    0
END

Synonyms

Not Available

Molecular Formula

C₁₆H₂₄O₄

Average Mass

280.364

Monoisotopic Mass

280.167459253

IUPAC Name

(2R,7R)-2-heptanoyl-7-hydroxy-3,4,5,6,7,8-hexahydro-2H-1-benzopyran-5-one

Traditional Name

(2R,7R)-2-heptanoyl-7-hydroxy-2,3,4,6,7,8-hexahydro-1-benzopyran-5-one

CAS Registry Number

Not Available

SMILES

[H][C@]1(O)CC(=O)C2=C(C1)O[C@]([H])(CC2)C(=O)CCCCCC

InChI Identifier

InChI=1S/C16H24O4/c1-2-3-4-5-6-13(18)15-8-7-12-14(19)9-11(17)10-16(12)20-15/h11,15,17H,2-10H2,1H3/t11-,15+/m0/s1

InChI Key

KERJAKAVUGWYGC-XHDPSFHLSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as benzopyrans. These are organic compounds containing a benzene ring fused to a pyran ring. Pyran a six-membered heterocyclic, non-aromatic ring, made up of five carbon atoms and one oxygen atom and containing two double bonds.

Kingdom

Organic compounds

Super Class

Organoheterocyclic compounds

Class

Benzopyrans

Sub Class

Not Available

Direct Parent

Benzopyrans

Alternative Parents

Substituents

Benzopyran
Cyclohexenone
Monosaccharide
Vinylogous ester
Secondary alcohol
Ketone
Oxacycle
Organic oxygen compound
Organic oxide
Hydrocarbon derivative
Organooxygen compound
Carbonyl group
Aldehyde
Alcohol
Aliphatic heteropolycyclic compound

Molecular Framework

Aliphatic heteropolycyclic compounds

External Descriptors

Not Available

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
Water Solubility	0.36 g/L	ALOGPS
logP	2.08	ALOGPS
logP	2.33	ChemAxon
logS	-2.9	ALOGPS
pKa (Strongest Acidic)	14.9	ChemAxon
pKa (Strongest Basic)	-2.8	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	4	ChemAxon
Hydrogen Donor Count	1	ChemAxon
Polar Surface Area	63.6 Å²	ChemAxon
Rotatable Bond Count	6	ChemAxon
Refractivity	77.25 m³·mol⁻¹	ChemAxon
Polarizability	31.83 Å³	ChemAxon
Number of Rings	2	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

Spectra

Spectrum Type	Description	Splash Key	Deposition Date	View
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_1_1) - 70eV, Positive	Not Available	2022-08-08	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	Not Available	2022-08-10	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	Not Available	2022-08-10	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	Not Available	2022-08-10	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	Not Available	2022-08-10	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	Not Available	2022-08-10	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	Not Available	2022-08-10	View Spectrum
MS	Mass Spectrum (Electron Ionization)	Not Available	2022-08-06	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 100 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 200 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 300 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 400 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 500 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 600 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 700 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 800 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 900 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, H₂O, predicted)		2022-08-18	View Spectrum

Biological Properties

Cellular Locations

Not Available

Biospecimen Locations

Not Available

Tissue Locations

Not Available

Associated OMIM IDs

114500 (Colorectal cancer)
610247 (Eosinophilic esophagitis)

Human Proteins and Enzymes

Protein ID	Protein Name	Protein Type	Uniprot ID	Species

Human Pathways

Pathways

Name	SMPDB/PathBank

Microbial Pathways

Pathways

Not Available

Metabolic Reactions

Reactions

This table shows at most 20 reactions. For the full list of associated reactions:

See All Associated Reactions

Reaction ID	Precursor	Product	Enzyme	Reaction Type	Data Source	Reference

Health Effects and Bioactivity

Health Outcome/Bioactivity	Metabolite Response/Effect	Evidence Type	Host and Biospecimen	Data Source	Reference

Microbial Sources

Superkingdom/Kingdom	Phylum	Total species	Hosts and Body Sites	Microbial Links
Eukaryota/Fungi	Ascomycota	1	Human feces	Metabolic reconstruction

Exposure Sources

Other Exposures

Source Type	Data Source	Reference

Host Biospecimen and Location

Host and Biospecimen	Status	Mean	Std	Min	Max	Units	Age	Sex	Health Condition	Data Source	Reference

External Links

HMDB ID

Not Available

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

Not Available

KNApSAcK ID

C00048888

Chemspider ID

27023224

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

24777197

PDB ID

Not Available

ChEBI ID

Not Available

Food Biomarker Ontology

Not Available

CMMC Knowledgebase

Not Available

General References

van Santen JA, Poynton EF, Iskakova D, McMann E, Alsup TA, Clark TN, Fergusson CH, Fewer DP, Hughes AH, McCadden CA, Parra J, Soldatou S, Rudolf JD, Janssen EM, Duncan KR, Linington RG: The Natural Products Atlas 2.0: a database of microbially-derived natural products. Nucleic Acids Res. 2022 Jan 7;50(D1):D1317-D1323. doi: 10.1093/nar/gkab941. [PubMed:34718710 ]

Showing metabocard for Trichodermatide D (MMDBc0018220)

MOL for #<Metabolite:0x00007f8db6a77920>

3D MOL for #<Metabolite:0x00007f8db6a77920>

3D SDF for #<Metabolite:0x00007f8db6a77920>

3D-SDF for #<Metabolite:0x00007f8db6a77920>

PDB for #<Metabolite:0x00007f8db6a77920>

3D PDB for #<Metabolite:0x00007f8db6a77920>

SMILES for #<Metabolite:0x00007f8db6a77920>

INCHI for #<Metabolite:0x00007f8db6a77920>

Structure for #<Metabolite:0x00007f8db6a77920>

3D Structure for #<Metabolite:0x00007f8db6a77920>