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Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2012-09-06 15:16:49 UTC
Update Date2022-03-07 02:51:38 UTC
HMDB IDHMDB0014505
Secondary Accession Numbers
  • HMDB14505
Metabolite Identification
Common NameVinorelbine
DescriptionVinorelbine is only found in individuals that have used or taken this drug. It is an anti-mitotic chemotherapy drug that is given as a treatment for some types of cancer, including breast cancer and non-small cell lung cancer. [Wikipedia ]The antitumor activity of vinorelbine is thought to be due primarily to inhibition of mitosis at metaphase through its interaction with tubulin. Vinorelbine binds to the microtubular proteins of the mitotic spindle, leading to crystallization of the microtubule and mitotic arrest or cell death. Like other vinca alkaloids, vinorelbine may also interfere with: 1) amino acid, cyclic AMP, and glutathione metabolism, 2) calmodulin-dependent Ca2+-transport ATPase activity, 3) cellular respiration, and 4) nucleic acid and lipid biosynthesis.
Structure
Data?1582753187
Synonyms
ValueSource
VinorelbinHMDB
Vinorelbine bitartrateHMDB
Vinorelbine ditartarateHMDB
Vinorelbine ditartrateHMDB
Vinorelbine tartrateHMDB
5'-Nor-anhydrovinblastineHMDB
NavelbineHMDB
5' Nor anhydrovinblastineHMDB
Chemical FormulaC45H54N4O8
Average Molecular Weight778.9323
Monoisotopic Molecular Weight778.394164724
IUPAC Namemethyl (1R,9R,10R,11R,12R,19R)-11-(acetyloxy)-12-ethyl-4-[(12S,14R)-16-ethyl-12-(methoxycarbonyl)-1,10-diazatetracyclo[12.3.1.0³,¹¹.0⁴,⁹]octadeca-3(11),4,6,8,15-pentaen-12-yl]-10-hydroxy-5-methoxy-8-methyl-8,16-diazapentacyclo[10.6.1.0¹,⁹.0²,⁷.0¹⁶,¹⁹]nonadeca-2,4,6,13-tetraene-10-carboxylate
Traditional Namenor-5'-anhydrovinblastine
CAS Registry Number71486-22-1
SMILES
[H][C@@]12N(C)C3=CC(OC)=C(C=C3[C@@]11CCN3CC=C[C@@](CC)([C@@H](OC(C)=O)[C@@]2(O)C(=O)OC)[C@@]13[H])[C@]1(C[C@@]2([H])CN(CC(CC)=C2)CC2=C1NC1=CC=CC=C21)C(=O)OC
InChI Identifier
InChI=1S/C45H54N4O8/c1-8-27-19-28-22-44(40(51)55-6,36-30(25-48(23-27)24-28)29-13-10-11-14-33(29)46-36)32-20-31-34(21-35(32)54-5)47(4)38-43(31)16-18-49-17-12-15-42(9-2,37(43)49)39(57-26(3)50)45(38,53)41(52)56-7/h10-15,19-21,28,37-39,46,53H,8-9,16-18,22-25H2,1-7H3/t28-,37-,38+,39+,42+,43+,44-,45+/m0/s1
InChI KeyGBABOYUKABKIAF-GHYRFKGUSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as vinca alkaloids. These are alkaloids with a dimeric chemical structure composed of an indole nucleus (catharanthine), and a dihydroindole nucleus (vindoline), joined together.
KingdomOrganic compounds
Super ClassAlkaloids and derivatives
ClassVinca alkaloids
Sub ClassNot Available
Direct ParentVinca alkaloids
Alternative Parents
Substituents
  • Vinca alkaloid skeleton
  • Catharanthine skeleton
  • Carbazole
  • 3-alkylindole
  • Indole
  • Indole or derivatives
  • Tricarboxylic acid or derivatives
  • Anisole
  • Tertiary aliphatic/aromatic amine
  • Dialkylarylamine
  • Alkyl aryl ether
  • Aralkylamine
  • Benzenoid
  • N-alkylpyrrolidine
  • Cyclic alcohol
  • Heteroaromatic compound
  • Pyrrole
  • Pyrrolidine
  • Tertiary alcohol
  • Methyl ester
  • Amino acid or derivatives
  • Tertiary aliphatic amine
  • Tertiary amine
  • Carboxylic acid ester
  • Organoheterocyclic compound
  • Azacycle
  • Carboxylic acid derivative
  • Ether
  • Alcohol
  • Organonitrogen compound
  • Amine
  • Carbonyl group
  • Organopnictogen compound
  • Organic oxygen compound
  • Organooxygen compound
  • Organic oxide
  • Hydrocarbon derivative
  • Organic nitrogen compound
  • Aromatic heteropolycyclic compound
Molecular FrameworkAromatic heteropolycyclic compounds
External DescriptorsNot Available
Ontology
Physiological effectNot Available
Disposition
Process
RoleNot Available
Physical Properties
StateSolid
Experimental Molecular Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water Solubility0.012 g/LNot Available
LogP4Not Available
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
PropertyValueSource
Water Solubility0.012 g/LALOGPS
logP4.39ALOGPS
logP4.65ChemAxon
logS-4.8ALOGPS
pKa (Strongest Acidic)10.87ChemAxon
pKa (Strongest Basic)8.72ChemAxon
Physiological Charge2ChemAxon
Hydrogen Acceptor Count8ChemAxon
Hydrogen Donor Count2ChemAxon
Polar Surface Area133.87 ŲChemAxon
Rotatable Bond Count10ChemAxon
Refractivity216.99 m³·mol⁻¹ChemAxon
Polarizability84.7 ųChemAxon
Number of Rings9ChemAxon
BioavailabilityYesChemAxon
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-2H]-304.95430932474
DeepCCS[M+Na]+278.42330932474
AllCCS[M+H]+269.632859911
AllCCS[M+H-H2O]+268.932859911
AllCCS[M+NH4]+270.132859911
AllCCS[M+Na]+270.332859911
AllCCS[M-H]-252.232859911
AllCCS[M+Na-2H]-257.032859911
AllCCS[M+HCOO]-262.332859911

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
Vinorelbine[H][C@@]12N(C)C3=CC(OC)=C(C=C3[C@@]11CCN3CC=C[C@@](CC)([C@@H](OC(C)=O)[C@@]2(O)C(=O)OC)[C@@]13[H])[C@]1(C[C@@]2([H])CN(CC(CC)=C2)CC2=C1NC1=CC=CC=C21)C(=O)OC5476.5Standard polar33892256
Vinorelbine[H][C@@]12N(C)C3=CC(OC)=C(C=C3[C@@]11CCN3CC=C[C@@](CC)([C@@H](OC(C)=O)[C@@]2(O)C(=O)OC)[C@@]13[H])[C@]1(C[C@@]2([H])CN(CC(CC)=C2)CC2=C1NC1=CC=CC=C21)C(=O)OC4714.5Standard non polar33892256
Vinorelbine[H][C@@]12N(C)C3=CC(OC)=C(C=C3[C@@]11CCN3CC=C[C@@](CC)([C@@H](OC(C)=O)[C@@]2(O)C(=O)OC)[C@@]13[H])[C@]1(C[C@@]2([H])CN(CC(CC)=C2)CC2=C1NC1=CC=CC=C21)C(=O)OC5228.8Semi standard non polar33892256
Spectra

GC-MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted GC-MSPredicted GC-MS Spectrum - Vinorelbine GC-MS (TMS_1_1) - 70eV, PositiveNot Available2021-10-18Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Vinorelbine GC-MS (TMS_1_2) - 70eV, PositiveNot Available2021-10-18Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Vinorelbine GC-MS (TBDMS_1_1) - 70eV, PositiveNot Available2021-10-18Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Vinorelbine GC-MS (TBDMS_1_2) - 70eV, PositiveNot Available2021-10-18Wishart LabView Spectrum

MS/MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Vinorelbine 10V, Positive-QTOFsplash10-00p0-0000001900-dbd6ff15d62211800a682016-08-01Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Vinorelbine 20V, Positive-QTOFsplash10-02t9-0121002900-3866c7af52c9c4f9a5cb2016-08-01Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Vinorelbine 40V, Positive-QTOFsplash10-0adu-2211009200-713a97aafaac3eca57c52016-08-01Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Vinorelbine 10V, Negative-QTOFsplash10-00vi-1003001900-588c32e4825e044c3d652016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Vinorelbine 20V, Negative-QTOFsplash10-00dl-1059000300-a6cf8884b788e19e37352016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Vinorelbine 40V, Negative-QTOFsplash10-0a6r-9015107200-d6f834659529a27173562016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Vinorelbine 10V, Negative-QTOFsplash10-056r-1000001900-e530ac740e5ea2e887e92021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Vinorelbine 20V, Negative-QTOFsplash10-0a4i-2000009000-3710c717c2a01768e2b72021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Vinorelbine 40V, Negative-QTOFsplash10-0a4i-6070009400-2dd2c86c6ea7cafd5fd62021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Vinorelbine 10V, Positive-QTOFsplash10-004i-0000000900-9149460c568e3b97e0f82021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Vinorelbine 20V, Positive-QTOFsplash10-004i-0000000900-a4f4254d6b25530d6f882021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Vinorelbine 40V, Positive-QTOFsplash10-0040-0940311700-ca3bd0e6004f26e658e22021-09-22Wishart LabView Spectrum
Biological Properties
Cellular Locations
  • Cytoplasm
  • Membrane
Biospecimen Locations
  • Blood
  • Urine
Tissue LocationsNot Available
Pathways
Normal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
BloodExpected but not QuantifiedNot QuantifiedNot AvailableNot AvailableTaking drug identified by DrugBank entry DB00361 details
UrineExpected but not QuantifiedNot QuantifiedNot AvailableNot AvailableTaking drug identified by DrugBank entry DB00361 details
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDDB00361
Phenol Explorer Compound IDNot Available
FooDB IDNot Available
KNApSAcK IDNot Available
Chemspider ID23284827
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkVinorelbine
METLIN IDNot Available
PubChem Compound44424639
PDB IDNot Available
ChEBI ID480999
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 References
  1. Marty M, Fumoleau P, Adenis A, Rousseau Y, Merrouche Y, Robinet G, Senac I, Puozzo C: Oral vinorelbine pharmacokinetics and absolute bioavailability study in patients with solid tumors. Ann Oncol. 2001 Nov;12(11):1643-9. [PubMed:11822766 ]

Enzymes

General function:
Involved in monooxygenase activity
Specific function:
Cytochromes P450 are a group of heme-thiolate monooxygenases. In liver microsomes, this enzyme is involved in an NADPH-dependent electron transport pathway. It performs a variety of oxidation reactions (e.g. caffeine 8-oxidation, omeprazole sulphoxidation, midazolam 1'-hydroxylation and midazolam 4-hydroxylation) of structurally unrelated compounds, including steroids, fatty acids, and xenobiotics. Acts as a 1,8-cineole 2-exo-monooxygenase. The enzyme also hydroxylates etoposide.
Gene Name:
CYP3A4
Uniprot ID:
P08684
Molecular weight:
57255.585
References
  1. Preissner S, Kroll K, Dunkel M, Senger C, Goldsobel G, Kuzman D, Guenther S, Winnenburg R, Schroeder M, Preissner R: SuperCYP: a comprehensive database on Cytochrome P450 enzymes including a tool for analysis of CYP-drug interactions. Nucleic Acids Res. 2010 Jan;38(Database issue):D237-43. doi: 10.1093/nar/gkp970. Epub 2009 Nov 24. [PubMed:19934256 ]
General function:
Involved in monooxygenase activity
Specific function:
Responsible for the metabolism of many drugs and environmental chemicals that it oxidizes. It is involved in the metabolism of drugs such as antiarrhythmics, adrenoceptor antagonists, and tricyclic antidepressants.
Gene Name:
CYP2D6
Uniprot ID:
P10635
Molecular weight:
55768.94
References
  1. Preissner S, Kroll K, Dunkel M, Senger C, Goldsobel G, Kuzman D, Guenther S, Winnenburg R, Schroeder M, Preissner R: SuperCYP: a comprehensive database on Cytochrome P450 enzymes including a tool for analysis of CYP-drug interactions. Nucleic Acids Res. 2010 Jan;38(Database issue):D237-43. doi: 10.1093/nar/gkp970. Epub 2009 Nov 24. [PubMed:19934256 ]
General function:
Involved in structural molecule activity
Specific function:
Tubulin is the major constituent of microtubules. It binds two moles of GTP, one at an exchangeable site on the beta chain and one at a non-exchangeable site on the alpha-chain
Gene Name:
TUBB
Uniprot ID:
P07437
Molecular weight:
49670.5
References
  1. Overington JP, Al-Lazikani B, Hopkins AL: How many drug targets are there? Nat Rev Drug Discov. 2006 Dec;5(12):993-6. [PubMed:17139284 ]
  2. Imming P, Sinning C, Meyer A: Drugs, their targets and the nature and number of drug targets. Nat Rev Drug Discov. 2006 Oct;5(10):821-34. [PubMed:17016423 ]
  3. Kruczynski A, Barret JM, Etievant C, Colpaert F, Fahy J, Hill BT: Antimitotic and tubulin-interacting properties of vinflunine, a novel fluorinated Vinca alkaloid. Biochem Pharmacol. 1998 Mar 1;55(5):635-48. [PubMed:9515574 ]
  4. Chang AY, Garrow GC: Pilot study of vinorelbine (Navelbine) and paclitaxel (Taxol) in patients with refractory breast cancer and lung cancer. Semin Oncol. 1995 Apr;22(2 Suppl 5):66-70; discussion 70-1. [PubMed:7740336 ]
  5. Seve P, Dumontet C: [Class III beta tubulin expression in nonsmall cell lung cancer]. Rev Mal Respir. 2010 Apr;27(4):383-6. doi: 10.1016/j.rmr.2010.03.006. Epub 2010 Mar 25. [PubMed:20403547 ]

Transporters

General function:
Involved in ATP binding
Specific function:
Energy-dependent efflux pump responsible for decreased drug accumulation in multidrug-resistant cells
Gene Name:
ABCB1
Uniprot ID:
P08183
Molecular weight:
141477.3
References
  1. Polli JW, Wring SA, Humphreys JE, Huang L, Morgan JB, Webster LO, Serabjit-Singh CS: Rational use of in vitro P-glycoprotein assays in drug discovery. J Pharmacol Exp Ther. 2001 Nov;299(2):620-8. [PubMed:11602674 ]