ContaminantDB: Trabectedin

Identification Taxonomy Biological Properties Physical Properties Toxicity Profile Spectra Concentrations Links References XML

Record Information

Version

1.0

Creation Date

2016-05-22 06:01:39 UTC

Update Date

2016-11-09 01:15:58 UTC

Accession Number

CHEM019326

Identification

Common Name

Trabectedin

Class

Small Molecule

Description

Trabectedin, also referred as Trabectedin during its development, is a marine-derived antitumor agent discovered in the Carribean tunicate _Ecteinascidia turbinata_ and now produced synthetically. Trabectedin has a unique mechanism of action. It binds to the minor groove of DNA interfering with cell division and genetic transcription processes and DNA repair machinery. It is approved for use in Europe, Russia and South Korea for the treatment of advanced soft tissue sarcoma. It is currently under evaluation for the treatment of breast cancer, prostate cancer, in addition to pediatric sarcomas. Both the European Commission and the U.S. Food and Drug Administration (FDA) have approved trabectedin as an orphan drug in soft tissue sarcomas and ovarian cancer. On October 23, 2015, the FDA approved trabectedin, (as Yondelis), for the treatment of specific soft tissue sarcomas.

Contaminant Sources

HMDB Contaminants - Urine
STOFF IDENT Compounds
ToxCast & Tox21 Chemicals

Contaminant Type

Not Available

Chemical Structure

MOL SDF PDB SMILES InChI

Synonyms

Value	Source
Ect 743	ChEBI
Ecteinascidin	ChEBI
Ecteinascidin 743	ChEBI
ET-743	ChEBI
ET743	ChEBI
Yondelis	ChEBI
NSC 684766	HMDB

Chemical Formula

C₃₉H₄₃N₃O₁₁S

Average Molecular Mass

761.837 g/mol

Monoisotopic Mass

761.262 g/mol

CAS Registry Number

114899-77-3

IUPAC Name

(1R,2R,3R,11S,12S,14R,26R)-5,6',12-trihydroxy-6,7'-dimethoxy-7,21,30-trimethyl-27-oxo-3',4'-dihydro-2'H-17,19,28-trioxa-24-thia-13,30-diazaspiro[heptacyclo[12.9.6.1³,¹¹.0²,¹³.0⁴,⁹.0¹⁵,²³.0¹⁶,²⁰]triacontane-26,1'-isoquinoline]-4,6,8,15,20,22-hexaen-22-yl acetate

Traditional Name

yondelis

SMILES

[H][C@@]12[C@@H]3SC[C@]4(NCCC5=C4C=C(OC)C(O)=C5)C(=O)OC[C@H](N1[C@@H](O)[C@@H]1CC4=CC(C)=C(OC)C(O)=C4[C@H]2N1C)C1=C2OCOC2=C(C)C(OC(C)=O)=C31

InChI Identifier

InChI=1S/C39H43N3O11S/c1-16-9-20-10-22-37(46)42-23-13-50-38(47)39(21-12-25(48-5)24(44)11-19(21)7-8-40-39)14-54-36(30(42)29(41(22)4)26(20)31(45)32(16)49-6)28-27(23)35-34(51-15-52-35)17(2)33(28)53-18(3)43/h9,11-12,22-23,29-30,36-37,40,44-46H,7-8,10,13-15H2,1-6H3/t22-,23-,29+,30+,36+,37-,39+/m0/s1

InChI Key

PKVRCIRHQMSYJX-AIFWHQITSA-N

Chemical Taxonomy

Description

belongs to the class of organic compounds known as benzazocines. These are organic compounds containing the benzazocine ring system, which consists of a benzene ring bound to an azocine ring.

Kingdom

Organic compounds

Super Class

Benzenoids

Class

Benzene and substituted derivatives

Sub Class

Benzazocines

Direct Parent

Benzazocines

Alternative Parents

Substituents

Benzazocine
Tetrahydroisoquinoline
Alpha-amino acid or derivatives
Benzodioxole
Anisole
Alkyl aryl ether
N-methylpiperazine
N-alkylpiperazine
Aralkylamine
1-hydroxy-4-unsubstituted benzenoid
1-hydroxy-2-unsubstituted benzenoid
Dicarboxylic acid or derivatives
Piperazine
1,4-diazinane
Hemiaminal
Lactone
Tertiary aliphatic amine
Carboxylic acid ester
Tertiary amine
Amino acid or derivatives
Acetal
Alkanolamine
Carboxylic acid derivative
Oxacycle
Secondary aliphatic amine
Azacycle
Organoheterocyclic compound
Ether
Dialkylthioether
Thioether
Polyol
Secondary amine
Amine
Organopnictogen compound
Organic oxide
Hydrocarbon derivative
Carbonyl group
Organonitrogen compound
Organooxygen compound
Organic nitrogen compound
Organic oxygen compound
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic heteropolycyclic compounds

External Descriptors

tertiary amino compound (CHEBI:84050 )
acetate ester (CHEBI:84050 )
polyphenol (CHEBI:84050 )
organic sulfide (CHEBI:84050 )
bridged compound (CHEBI:84050 )
isoquinoline alkaloid (CHEBI:84050 )
hemiaminal (CHEBI:84050 )
lactone (CHEBI:84050 )
azaspiro compound (CHEBI:84050 )
organic heteropolycyclic compound (CHEBI:84050 )
oxaspiro compound (CHEBI:84050 )

Biological Properties

Status

Detected and Not Quantified

Origin

Not Available

Cellular Locations

Not Available

Biofluid Locations

Not Available

Tissue Locations

Not Available

Pathways

Not Available

Applications

Not Available

Biological Roles

Not Available

Chemical Roles

Not Available

Physical Properties

State

Not Available

Appearance

Not Available

Experimental Properties

Property	Value
Melting Point	Not Available
Boiling Point	Not Available
Solubility	Not Available

Predicted Properties

Property	Value	Source
Water Solubility	0.33 g/L	ALOGPS
logP	2.04	ALOGPS
logP	3.99	ChemAxon
logS	-3.4	ALOGPS
pKa (Strongest Acidic)	9.27	ChemAxon
pKa (Strongest Basic)	7.66	ChemAxon
Physiological Charge	1	ChemAxon
Hydrogen Acceptor Count	12	ChemAxon
Hydrogen Donor Count	4	ChemAxon
Polar Surface Area	168.72 Å²	ChemAxon
Rotatable Bond Count	4	ChemAxon
Refractivity	196.92 m³·mol⁻¹	ChemAxon
Polarizability	77.72 Å³	ChemAxon
Number of Rings	9	ChemAxon
Bioavailability	0	ChemAxon
Rule of Five	No	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

Spectra

Spectrum Type	Description	Splash Key	View
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	splash10-0zgr-0090000100-1fbe6c879e491f9c397c	Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_1_1) - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_1_2) - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_1_3) - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_1_4) - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TBDMS_1_1) - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TBDMS_1_2) - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TBDMS_1_3) - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TBDMS_1_4) - 70eV, Positive	Not Available	Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-03di-0000000900-e91cca9b4689a68d194c	Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-0udi-0300002900-083c4ab0de6a8cbf080d	Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-0udl-2130029700-488b00bc8602ecbb0612	Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-03di-0000000900-5dd80d9620ee90346daa	Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-11ou-1000001900-ea86efb65818a8f27be5	Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-0kac-6050009800-1902e4760cf83e432109	Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-03di-0000000900-cf19b0cf6f95b02564a0	Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-03di-0000000900-3e1fdba9b1bd766aa3dc	Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-00vl-0010008900-6487d80738403778f792	Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-03di-0000000900-2edcd395ca8015613eae	Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-03di-0000000900-2874db466c2b035d495b	Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-01tl-0200016900-85e72ee9c89dddad28e0	Spectrum