You are using an unsupported browser. Please upgrade your browser to a newer version to get the best experience on Human Metabolome Database.

Showing metabocard for Lenalidomide (HMDB0014623)

Jump To Section:
IdentificationTaxonomyOntologyPhysical propertiesSpectraBiological propertiesConcentrationsLinksReferencesenzymes (3) Show 3 proteinsXML
enzymes (3) Show 3 proteins
Record Information
Version4.0
StatusExpected but not Quantified
Creation Date2012-09-06 15:16:49 UTC
Update Date2020-02-26 21:40:00 UTC
HMDB IDHMDB0014623
Secondary Accession Numbers
  • HMDB14623
Metabolite Identification
Common NameLenalidomide
DescriptionLenalidomide, also known as revlimid or IMID3, belongs to the class of organic compounds known as isoindolones. These are aromatic polycyclic compounds that an isoindole bearing a ketone. Lenalidomide is a drug. Lenalidomide is a moderately basic compound (based on its pKa). A dicarboximide that consists of 1-oxoisoindoline bearing an amino substituent at position 4 and a 2,6-dioxopiperidin-3-yl group at position 2.
Structure
Data?1582753200
MOLSDF3D-SDFPDBSMILESInChI View 3D Structure
Synonyms
ValueSource
1-oxo-2-(2,6-Dioxopiperidin-3-yl)-4-aminoisoindolineChEBI
3-(4-Amino-1-oxoisoindolin-2-yl)piperidine-2,6-dioneChEBI
RevlimidChEBI
CC-5013HMDB
CDC 501HMDB
IMiD3HMDB
RevimidHMDB
Celgene brand OF lenalidomideHMDB
IMiD3 CPDHMDB
Chemical FormulaC13H13N3O3
Average Molecular Weight259.2606
Monoisotopic Molecular Weight259.095691297
IUPAC Name3-(4-amino-1-oxo-2,3-dihydro-1H-isoindol-2-yl)piperidine-2,6-dione
Traditional Namelenalidomide
CAS Registry Number191732-72-6
SMILES
NC1=CC=CC2=C1CN(C1CCC(=O)NC1=O)C2=O
InChI Identifier
InChI=1S/C13H13N3O3/c14-9-3-1-2-7-8(9)6-16(13(7)19)10-4-5-11(17)15-12(10)18/h1-3,10H,4-6,14H2,(H,15,17,18)
InChI KeyGOTYRUGSSMKFNF-UHFFFAOYSA-N
Chemical Taxonomy
Description belongs to the class of organic compounds known as isoindolones. These are aromatic polycyclic compounds that an isoindole bearing a ketone.
KingdomOrganic compounds
Super ClassOrganoheterocyclic compounds
ClassIsoindoles and derivatives
Sub ClassIsoindolines
Direct ParentIsoindolones
Alternative Parents
Substituents
  • Alpha-amino acid or derivatives
  • Isoindolone
  • Isoindole
  • Piperidinedione
  • Delta-lactam
  • Piperidinone
  • Piperidine
  • Benzenoid
  • Carboxylic acid imide
  • Dicarboximide
  • Carboxylic acid imide, n-unsubstituted
  • Tertiary carboxylic acid amide
  • Amino acid or derivatives
  • Lactam
  • Carboxamide group
  • Carboxylic acid derivative
  • Azacycle
  • Organooxygen compound
  • Organonitrogen compound
  • Organic oxide
  • Organopnictogen compound
  • Amine
  • Organic oxygen compound
  • Organic nitrogen compound
  • Carbonyl group
  • Hydrocarbon derivative
  • Primary amine
  • Aromatic heteropolycyclic compound
Molecular FrameworkAromatic heteropolycyclic compounds
External Descriptors
Ontology
Disposition

Biological location:

Role

Industrial application:

Physical Properties
StateSolid
Experimental Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water Solubility2.33 g/LNot Available
LogP-0.4Not Available
Predicted Properties
PropertyValueSource
Water Solubility2.33 g/LALOGPS
logP-0.43ALOGPS
logP-0.71ChemAxon
logS-2ALOGPS
pKa (Strongest Acidic)11.61ChemAxon
pKa (Strongest Basic)2.31ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count4ChemAxon
Hydrogen Donor Count2ChemAxon
Polar Surface Area92.5 ŲChemAxon
Rotatable Bond Count1ChemAxon
Refractivity68.3 m³·mol⁻¹ChemAxon
Polarizability25.55 ųChemAxon
Number of Rings3ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
Spectra
Spectrum TypeDescriptionSplash KeyView
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positivesplash10-01si-4950000000-d56c036a1d29e5a9442fSpectrum
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-qTof , Positivesplash10-0002-1920000000-c10c48acd9b8123e3505Spectrum
LC-MS/MSLC-MS/MS Spectrum - , positivesplash10-0002-1920000000-c10c48acd9b8123e3505Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-03dl-0090000000-2431a4e4063fb866e502Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-03dl-0590000000-3bd8341d78d9f0bb2185Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-0006-5900000000-ede52ce7143fcbe39e3cSpectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-0a4i-0190000000-a51e8a05d578a97d3916Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-0btc-2980000000-9fa6887f8d1dd5044b78Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-000f-9500000000-60ff64f6a1048a417538Spectrum
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 DB00480 details
UrineExpected but not QuantifiedNot QuantifiedNot AvailableNot AvailableTaking drug identified by DrugBank entry DB00480 details
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDDB00480
Phenol Explorer Compound IDNot Available
FooDB IDNot Available
KNApSAcK IDNot Available
Chemspider ID187515
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkLenalidomide
METLIN IDNot Available
PubChem Compound216326
PDB IDNot Available
ChEBI ID63791
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB ID
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Not Available
General References
  1. List A, Kurtin S, Roe DJ, Buresh A, Mahadevan D, Fuchs D, Rimsza L, Heaton R, Knight R, Zeldis JB: Efficacy of lenalidomide in myelodysplastic syndromes. N Engl J Med. 2005 Feb 10;352(6):549-57. [PubMed:15703420 ]
  2. Anderson KC: Lenalidomide and thalidomide: mechanisms of action--similarities and differences. Semin Hematol. 2005 Oct;42(4 Suppl 4):S3-8. [PubMed:16344099 ]
  3. Chang DH, Liu N, Klimek V, Hassoun H, Mazumder A, Nimer SD, Jagannath S, Dhodapkar MV: Enhancement of ligand-dependent activation of human natural killer T cells by lenalidomide: therapeutic implications. Blood. 2006 Jul 15;108(2):618-21. Epub 2006 Mar 28. [PubMed:16569772 ]

Enzymes

Enzyme Details
1. Prostaglandin G/H synthase 2
General function:
Involved in peroxidase activity
Specific function:
Mediates the formation of prostaglandins from arachidonate. May have a role as a major mediator of inflammation and/or a role for prostanoid signaling in activity-dependent plasticity.
Gene Name:
PTGS2
Uniprot ID:
P35354
Molecular weight:
68995.625
References
  1. Payvandi F, Wu L, Haley M, Schafer PH, Zhang LH, Chen RS, Muller GW, Stirling DI: Immunomodulatory drugs inhibit expression of cyclooxygenase-2 from TNF-alpha, IL-1beta, and LPS-stimulated human PBMC in a partially IL-10-dependent manner. Cell Immunol. 2004 Aug;230(2):81-8. [PubMed:15598423 ]
  2. Zeldis JB, Schafer PH, Bennett BL, Mercurio F, Stirling DI: Potential new therapeutics for Waldenstrom's macroglobulinemia. Semin Oncol. 2003 Apr;30(2):275-81. [PubMed:12720152 ]
Enzyme Details
2. Tumor necrosis factor ligand superfamily member 11
General function:
Involved in tumor necrosis factor receptor binding
Specific function:
Cytokine that binds to TNFRSF11B/OPG and to TNFRSF11A/RANK. Osteoclast differentiation and activation factor. Augments the ability of dendritic cells to stimulate naive T-cell proliferation. May be an important regulator of interactions between T-cells and dendritic cells and may play a role in the regulation of the T-cell-dependent immune response. May also play an important role in enhanced bone-resorption in humoral hypercalcemia of malignancy
Gene Name:
TNFSF11
Uniprot ID:
O14788
Molecular weight:
35477.8
References
  1. Akobeng AK, Stokkers PC: Thalidomide and thalidomide analogues for maintenance of remission in Crohn's disease. Cochrane Database Syst Rev. 2009 Apr 15;(2):CD007351. doi: 10.1002/14651858.CD007351.pub2. [PubMed:19370685 ]
  2. Melchert M, List A: The thalidomide saga. Int J Biochem Cell Biol. 2007;39(7-8):1489-99. Epub 2007 Jan 30. [PubMed:17369076 ]
Enzyme Details
3. Cadherin-5
General function:
Involved in calcium ion binding
Specific function:
Cadherins are calcium dependent cell adhesion proteins. They preferentially interact with themselves in a homophilic manner in connecting cells; cadherins may thus contribute to the sorting of heterogeneous cell types. This cadherin may play a important role in endothelial cell biology through control of the cohesion and organization of the intercellular junctions. It associates with alpha-catenin forming a link to the cytoskeleton
Gene Name:
CDH5
Uniprot ID:
P33151
Molecular weight:
87515.7
References
  1. Lu L, Payvandi F, Wu L, Zhang LH, Hariri RJ, Man HW, Chen RS, Muller GW, Hughes CC, Stirling DI, Schafer PH, Bartlett JB: The anti-cancer drug lenalidomide inhibits angiogenesis and metastasis via multiple inhibitory effects on endothelial cell function in normoxic and hypoxic conditions. Microvasc Res. 2009 Mar;77(2):78-86. doi: 10.1016/j.mvr.2008.08.003. Epub 2008 Sep 4. [PubMed:18805433 ]