Hmdb loader
Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2012-09-06 15:16:49 UTC
Update Date2022-03-07 02:51:39 UTC
HMDB IDHMDB0014529
Secondary Accession Numbers
  • HMDB14529
Metabolite Identification
Common NameValrubicin
DescriptionValrubicin is only found in individuals that have used or taken this drug. It is a chemotherapy drug used to treat bladder cancer. Valrubicin is a semisynthetic analog of the anthracycline doxorubicin, and is administered by infusion directly into the bladder. [Wikipedia ]Valrubicin is an anthracycline that affects a variety of inter-related biological functions, most of which involve nucleic acid metabolism. It readily penetrates into cells, where after DNA intercalation, it inhibits the incorporation of nucleosides into nucleic acids, causes extensive chromosomal damage, and arrests cell cycle in G2. Although valrubicin does not bind strongly to DNA, a principal mechanism of its action, mediated by valrubicin metabolites, is interference with the normal DNA breaking-resealing action of DNA topoisomerase II.
Structure
Data?1582753189
Synonyms
ValueSource
ValstarKegg
Antibiotic ad 32HMDB
N-Trifluoroacetyladriamycin 14-valerateHMDB
AD-32HMDB
Paladin brand OF valrubicinHMDB
ValtaxinHMDB
AD 32HMDB
2,2,2-Trifluoro-N-(3-hydroxy-2-methyl-6-{[(1S,3S)-3,5,12-trihydroxy-10-methoxy-6,11-dioxo-3-[2-(pentanoyloxy)acetyl]-1,2,3,4,6,11-hexahydrotetracen-1-yl]oxy}oxan-4-yl)ethanimidateHMDB
Chemical FormulaC34H36F3NO13
Average Molecular Weight723.6437
Monoisotopic Molecular Weight723.213874858
IUPAC Name2-oxo-2-[(2S,4S)-2,5,12-trihydroxy-4-{[5-hydroxy-6-methyl-4-(trifluoroacetamido)oxan-2-yl]oxy}-7-methoxy-6,11-dioxo-1,2,3,4,6,11-hexahydrotetracen-2-yl]ethyl pentanoate
Traditional Namevalrubicin
CAS Registry Number56124-62-0
SMILES
CCCCC(=O)OCC(=O)[C@@]1(O)C[C@H](OC2CC(NC(=O)C(F)(F)F)C(O)C(C)O2)C2=C(C1)C(O)=C1C(=O)C3=C(C(=O)C1=C2O)C(OC)=CC=C3
InChI Identifier
InChI=1S/C34H36F3NO13/c1-4-5-9-21(40)49-13-20(39)33(47)11-16-24(19(12-33)51-22-10-17(27(41)14(2)50-22)38-32(46)34(35,36)37)31(45)26-25(29(16)43)28(42)15-7-6-8-18(48-3)23(15)30(26)44/h6-8,14,17,19,22,27,41,43,45,47H,4-5,9-13H2,1-3H3,(H,38,46)/t14?,17?,19-,22?,27?,33-/m0/s1
InChI KeyZOCKGBMQLCSHFP-ZQUOIQDWSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as anthracyclines. These are polyketides containing a tetracenequinone ring structure with a sugar attached by glycosidic linkage.
KingdomOrganic compounds
Super ClassPhenylpropanoids and polyketides
ClassAnthracyclines
Sub ClassNot Available
Direct ParentAnthracyclines
Alternative Parents
Substituents
  • Anthracycline
  • Anthracyclinone-skeleton
  • Tetracenequinone
  • 9,10-anthraquinone
  • 1,4-anthraquinone
  • Anthracene
  • Glycosyl compound
  • O-glycosyl compound
  • Tetralin
  • Aryl ketone
  • Anisole
  • Alpha-acyloxy ketone
  • Fatty acid ester
  • Alkyl aryl ether
  • Benzenoid
  • Fatty acyl
  • Monosaccharide
  • Oxane
  • Vinylogous acid
  • Tertiary alcohol
  • Alpha-hydroxy ketone
  • Carboxamide group
  • Carboxylic acid ester
  • Secondary alcohol
  • Secondary carboxylic acid amide
  • Ketone
  • Oxacycle
  • Organoheterocyclic compound
  • Polyol
  • Carboxylic acid derivative
  • Ether
  • Acetal
  • Monocarboxylic acid or derivatives
  • Carbonyl group
  • Hydrocarbon derivative
  • Organic oxide
  • Organopnictogen compound
  • Organic oxygen compound
  • Organic nitrogen compound
  • Organofluoride
  • Alkyl fluoride
  • Organohalogen compound
  • Alkyl halide
  • Alcohol
  • Organooxygen compound
  • Organonitrogen compound
  • Aromatic heteropolycyclic compound
Molecular FrameworkAromatic heteropolycyclic compounds
External DescriptorsNot Available
Ontology
Physiological effectNot Available
Disposition
ProcessNot Available
RoleNot Available
Physical Properties
StateSolid
Experimental Molecular Properties
PropertyValueReference
Melting Point116 - 117 °CNot Available
Boiling PointNot AvailableNot Available
Water Solubility0.032 g/LNot Available
LogP2.2Not Available
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
PropertyValueSource
Water Solubility0.032 g/LALOGPS
logP2.67ALOGPS
logP4.49ChemAxon
logS-4.4ALOGPS
pKa (Strongest Acidic)5.39ChemAxon
pKa (Strongest Basic)-3.4ChemAxon
Physiological Charge-1ChemAxon
Hydrogen Acceptor Count12ChemAxon
Hydrogen Donor Count5ChemAxon
Polar Surface Area215.22 ŲChemAxon
Rotatable Bond Count12ChemAxon
Refractivity168.03 m³·mol⁻¹ChemAxon
Polarizability68.86 ųChemAxon
Number of Rings5ChemAxon
BioavailabilityNoChemAxon
Rule of FiveNoChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleYesChemAxon
Predicted Chromatographic Properties

Predicted Collision Cross Sections

PredictorAdduct TypeCCS Value (Å2)Reference
DeepCCS[M+H]+247.75930932474
DeepCCS[M-H]-245.67330932474
DeepCCS[M-2H]-279.65330932474
DeepCCS[M+Na]+253.9630932474
AllCCS[M+H]+248.232859911
AllCCS[M+H-H2O]+247.732859911
AllCCS[M+NH4]+248.632859911
AllCCS[M+Na]+248.732859911
AllCCS[M-H]-247.532859911
AllCCS[M+Na-2H]-251.032859911
AllCCS[M+HCOO]-255.032859911

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
ValrubicinCCCCC(=O)OCC(=O)[C@@]1(O)C[C@H](OC2CC(NC(=O)C(F)(F)F)C(O)C(C)O2)C2=C(C1)C(O)=C1C(=O)C3=C(C(=O)C1=C2O)C(OC)=CC=C35364.0Standard polar33892256
ValrubicinCCCCC(=O)OCC(=O)[C@@]1(O)C[C@H](OC2CC(NC(=O)C(F)(F)F)C(O)C(C)O2)C2=C(C1)C(O)=C1C(=O)C3=C(C(=O)C1=C2O)C(OC)=CC=C33909.3Standard non polar33892256
ValrubicinCCCCC(=O)OCC(=O)[C@@]1(O)C[C@H](OC2CC(NC(=O)C(F)(F)F)C(O)C(C)O2)C2=C(C1)C(O)=C1C(=O)C3=C(C(=O)C1=C2O)C(OC)=CC=C34796.1Semi standard non polar33892256
Spectra

GC-MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted GC-MSPredicted GC-MS Spectrum - Valrubicin GC-MS (Non-derivatized) - 70eV, Positivesplash10-052r-9721263000-df206296c65be0a6cbb12017-11-06Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Valrubicin GC-MS (TMS_1_1) - 70eV, PositiveNot Available2021-10-18Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Valrubicin GC-MS (TMS_1_2) - 70eV, PositiveNot Available2021-10-18Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Valrubicin GC-MS (TMS_1_3) - 70eV, PositiveNot Available2021-10-18Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Valrubicin GC-MS (TMS_1_4) - 70eV, PositiveNot Available2021-10-18Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Valrubicin GC-MS (TMS_1_5) - 70eV, PositiveNot Available2021-10-18Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Valrubicin GC-MS (TMS_1_6) - 70eV, PositiveNot Available2021-10-18Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Valrubicin GC-MS (TMS_2_1) - 70eV, PositiveNot Available2021-10-18Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Valrubicin GC-MS (TMS_2_2) - 70eV, PositiveNot Available2021-10-18Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Valrubicin GC-MS (TMS_2_3) - 70eV, PositiveNot Available2021-10-18Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Valrubicin GC-MS (TMS_2_4) - 70eV, PositiveNot Available2021-10-18Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Valrubicin GC-MS (TMS_2_5) - 70eV, PositiveNot Available2021-10-18Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Valrubicin GC-MS (TMS_2_6) - 70eV, PositiveNot Available2021-10-18Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Valrubicin GC-MS (TMS_2_7) - 70eV, PositiveNot Available2021-10-18Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Valrubicin GC-MS (TMS_2_8) - 70eV, PositiveNot Available2021-10-18Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Valrubicin GC-MS (TMS_2_9) - 70eV, PositiveNot Available2021-10-18Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Valrubicin GC-MS (TMS_2_10) - 70eV, PositiveNot Available2021-10-18Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Valrubicin GC-MS (TMS_2_11) - 70eV, PositiveNot Available2021-10-18Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Valrubicin GC-MS (TMS_2_12) - 70eV, PositiveNot Available2021-10-18Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Valrubicin GC-MS (TMS_2_13) - 70eV, PositiveNot Available2021-10-18Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Valrubicin GC-MS (TMS_2_14) - 70eV, PositiveNot Available2021-10-18Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Valrubicin GC-MS (TMS_2_15) - 70eV, PositiveNot Available2021-10-18Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Valrubicin GC-MS (TBDMS_1_1) - 70eV, PositiveNot Available2021-10-18Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Valrubicin GC-MS (TBDMS_1_2) - 70eV, PositiveNot Available2021-10-18Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Valrubicin GC-MS (TBDMS_1_3) - 70eV, PositiveNot Available2021-10-18Wishart LabView Spectrum

MS/MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Valrubicin 10V, Positive-QTOFsplash10-006t-9002402500-9e90dc5748fa5422239d2017-09-01Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Valrubicin 20V, Positive-QTOFsplash10-000b-8227901100-a76d64d39b73899671a72017-09-01Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Valrubicin 40V, Positive-QTOFsplash10-0002-9001100000-d7784aa32a024191964b2017-09-01Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Valrubicin 10V, Negative-QTOFsplash10-0ul0-8900213600-4a94b36c9ac08d2235e22017-09-01Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Valrubicin 20V, Negative-QTOFsplash10-0udi-6913111100-ab3c6472a1ac3db4d29d2017-09-01Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Valrubicin 40V, Negative-QTOFsplash10-0udi-5900300000-86e9d02455d0203aaac32017-09-01Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Valrubicin 10V, Positive-QTOFsplash10-0059-0075902300-624df39e91c9d410f3402021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Valrubicin 20V, Positive-QTOFsplash10-004i-2193204100-ba55844b0b476519af812021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Valrubicin 40V, Positive-QTOFsplash10-01r2-1930000000-d31c90e59f9f10e6040c2021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Valrubicin 10V, Negative-QTOFsplash10-00dj-8200701900-4541a3e4bf0ecf30a9d72021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Valrubicin 20V, Negative-QTOFsplash10-0204-4405902500-50fd3b26dea6e4d410dc2021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Valrubicin 40V, Negative-QTOFsplash10-066r-9000000000-65d1acb50c8427e363af2021-09-22Wishart LabView Spectrum
Biological Properties
Cellular Locations
  • Cytoplasm
Biospecimen Locations
  • Blood
  • Urine
Tissue LocationsNot Available
Pathways
Normal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
BloodExpected but not QuantifiedNot QuantifiedNot AvailableNot AvailableTaking drug identified by DrugBank entry DB00385 details
UrineExpected but not QuantifiedNot QuantifiedNot AvailableNot AvailableTaking drug identified by DrugBank entry DB00385 details
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDNot Available
KNApSAcK IDNot Available
Chemspider ID38088
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkValrubicin
METLIN IDNot Available
PubChem Compound41744
PDB IDNot Available
ChEBI ID125161
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDNot Available
Good Scents IDNot Available
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Not Available
General ReferencesNot Available

Enzymes

General function:
Involved in sequence-specific DNA binding transcription factor activity
Specific function:
Control of topological states of DNA by transient breakage and subsequent rejoining of DNA strands. Topoisomerase II makes double-strand breaks
Gene Name:
TOP2A
Uniprot ID:
P11388
Molecular weight:
174383.9
References
  1. Chen X, Ji ZL, Chen YZ: TTD: Therapeutic Target Database. Nucleic Acids Res. 2002 Jan 1;30(1):412-5. [PubMed:11752352 ]
  2. Perabo FG, Muller SC: New agents in intravesical chemotherapy of superficial bladder cancer. Scand J Urol Nephrol. 2005;39(2):108-16. [PubMed:16019763 ]