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Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2012-09-06 15:16:49 UTC
Update Date2022-03-07 02:51:41 UTC
HMDB IDHMDB0014623
Secondary Accession Numbers
  • HMDB14623
Metabolite Identification
Common NameLenalidomide
DescriptionLenalidomide (initially known as CC-5013 and marketed as Revlimid by Celgene) is a derivative of thalidomide introduced in 2004. It was initially intended as a treatment for multiple myeloma, for which thalidomide is an accepted therapeutic modality, but has also shown efficacy in the hematological disorders known as the myelodysplastic syndromes. [Wikipedia ]
Structure
Data?1582753200
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
RevimidMeSH, HMDB
Celgene brand OF lenalidomideMeSH, HMDB
IMiD3 CPDMeSH, HMDB
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
  • Isoindolone
  • Alpha-amino acid or derivatives
  • Isoindole
  • Piperidinedione
  • Piperidinone
  • Delta-lactam
  • Benzenoid
  • Piperidine
  • Tertiary carboxylic acid amide
  • Carboxylic acid imide, n-unsubstituted
  • Dicarboximide
  • Carboxylic acid imide
  • Lactam
  • Carboxamide group
  • Amino acid or derivatives
  • Azacycle
  • Carboxylic acid derivative
  • Organic nitrogen compound
  • Organic oxygen compound
  • Organopnictogen compound
  • Organic oxide
  • Hydrocarbon derivative
  • Primary amine
  • Organooxygen compound
  • Organonitrogen compound
  • Carbonyl group
  • Amine
  • Aromatic heteropolycyclic compound
Molecular FrameworkAromatic heteropolycyclic compounds
External Descriptors
Ontology
Physiological effectNot Available
Disposition
ProcessNot Available
RoleNot Available
Physical Properties
StateSolid
Experimental Molecular Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water Solubility2.33 g/LNot Available
LogP-0.4Not Available
Experimental Chromatographic PropertiesNot Available
Predicted Molecular 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
Predicted Chromatographic Properties

Predicted Collision Cross Sections

PredictorAdduct TypeCCS Value (Å2)Reference
DarkChem[M+H]+160.34731661259
DarkChem[M-H]-157.53731661259
DeepCCS[M+H]+161.0930932474
DeepCCS[M-H]-158.73230932474
DeepCCS[M-2H]-191.65930932474
DeepCCS[M+Na]+167.18430932474
AllCCS[M+H]+159.032859911
AllCCS[M+H-H2O]+155.432859911
AllCCS[M+NH4]+162.332859911
AllCCS[M+Na]+163.332859911
AllCCS[M-H]-160.332859911
AllCCS[M+Na-2H]-159.932859911
AllCCS[M+HCOO]-159.532859911

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
LenalidomideNC1=CC=CC2=C1CN(C1CCC(=O)NC1=O)C2=O4149.2Standard polar33892256
LenalidomideNC1=CC=CC2=C1CN(C1CCC(=O)NC1=O)C2=O2572.0Standard non polar33892256
LenalidomideNC1=CC=CC2=C1CN(C1CCC(=O)NC1=O)C2=O2817.3Semi standard non polar33892256

Derivatized

Derivative Name / StructureSMILESKovats RI ValueColumn TypeReference
Lenalidomide,1TMS,isomer #1C[Si](C)(C)NC1=CC=CC2=C1CN(C1CCC(=O)NC1=O)C2=O2796.3Semi standard non polar33892256
Lenalidomide,1TMS,isomer #1C[Si](C)(C)NC1=CC=CC2=C1CN(C1CCC(=O)NC1=O)C2=O2726.2Standard non polar33892256
Lenalidomide,1TMS,isomer #1C[Si](C)(C)NC1=CC=CC2=C1CN(C1CCC(=O)NC1=O)C2=O4146.3Standard polar33892256
Lenalidomide,1TMS,isomer #2C[Si](C)(C)N1C(=O)CCC(N2CC3=C(N)C=CC=C3C2=O)C1=O2618.4Semi standard non polar33892256
Lenalidomide,1TMS,isomer #2C[Si](C)(C)N1C(=O)CCC(N2CC3=C(N)C=CC=C3C2=O)C1=O2639.2Standard non polar33892256
Lenalidomide,1TMS,isomer #2C[Si](C)(C)N1C(=O)CCC(N2CC3=C(N)C=CC=C3C2=O)C1=O4008.2Standard polar33892256
Lenalidomide,2TMS,isomer #1C[Si](C)(C)N(C1=CC=CC2=C1CN(C1CCC(=O)NC1=O)C2=O)[Si](C)(C)C2721.8Semi standard non polar33892256
Lenalidomide,2TMS,isomer #1C[Si](C)(C)N(C1=CC=CC2=C1CN(C1CCC(=O)NC1=O)C2=O)[Si](C)(C)C2793.7Standard non polar33892256
Lenalidomide,2TMS,isomer #1C[Si](C)(C)N(C1=CC=CC2=C1CN(C1CCC(=O)NC1=O)C2=O)[Si](C)(C)C3902.1Standard polar33892256
Lenalidomide,2TMS,isomer #2C[Si](C)(C)NC1=CC=CC2=C1CN(C1CCC(=O)N([Si](C)(C)C)C1=O)C2=O2686.8Semi standard non polar33892256
Lenalidomide,2TMS,isomer #2C[Si](C)(C)NC1=CC=CC2=C1CN(C1CCC(=O)N([Si](C)(C)C)C1=O)C2=O2741.1Standard non polar33892256
Lenalidomide,2TMS,isomer #2C[Si](C)(C)NC1=CC=CC2=C1CN(C1CCC(=O)N([Si](C)(C)C)C1=O)C2=O3583.7Standard polar33892256
Lenalidomide,3TMS,isomer #1C[Si](C)(C)N1C(=O)CCC(N2CC3=C(C=CC=C3N([Si](C)(C)C)[Si](C)(C)C)C2=O)C1=O2571.5Semi standard non polar33892256
Lenalidomide,3TMS,isomer #1C[Si](C)(C)N1C(=O)CCC(N2CC3=C(C=CC=C3N([Si](C)(C)C)[Si](C)(C)C)C2=O)C1=O2837.6Standard non polar33892256
Lenalidomide,3TMS,isomer #1C[Si](C)(C)N1C(=O)CCC(N2CC3=C(C=CC=C3N([Si](C)(C)C)[Si](C)(C)C)C2=O)C1=O3315.5Standard polar33892256
Lenalidomide,1TBDMS,isomer #1CC(C)(C)[Si](C)(C)NC1=CC=CC2=C1CN(C1CCC(=O)NC1=O)C2=O3050.7Semi standard non polar33892256
Lenalidomide,1TBDMS,isomer #1CC(C)(C)[Si](C)(C)NC1=CC=CC2=C1CN(C1CCC(=O)NC1=O)C2=O2961.8Standard non polar33892256
Lenalidomide,1TBDMS,isomer #1CC(C)(C)[Si](C)(C)NC1=CC=CC2=C1CN(C1CCC(=O)NC1=O)C2=O4137.0Standard polar33892256
Lenalidomide,1TBDMS,isomer #2CC(C)(C)[Si](C)(C)N1C(=O)CCC(N2CC3=C(N)C=CC=C3C2=O)C1=O2869.2Semi standard non polar33892256
Lenalidomide,1TBDMS,isomer #2CC(C)(C)[Si](C)(C)N1C(=O)CCC(N2CC3=C(N)C=CC=C3C2=O)C1=O2871.9Standard non polar33892256
Lenalidomide,1TBDMS,isomer #2CC(C)(C)[Si](C)(C)N1C(=O)CCC(N2CC3=C(N)C=CC=C3C2=O)C1=O4002.8Standard polar33892256
Lenalidomide,2TBDMS,isomer #1CC(C)(C)[Si](C)(C)N(C1=CC=CC2=C1CN(C1CCC(=O)NC1=O)C2=O)[Si](C)(C)C(C)(C)C3181.7Semi standard non polar33892256
Lenalidomide,2TBDMS,isomer #1CC(C)(C)[Si](C)(C)N(C1=CC=CC2=C1CN(C1CCC(=O)NC1=O)C2=O)[Si](C)(C)C(C)(C)C3247.6Standard non polar33892256
Lenalidomide,2TBDMS,isomer #1CC(C)(C)[Si](C)(C)N(C1=CC=CC2=C1CN(C1CCC(=O)NC1=O)C2=O)[Si](C)(C)C(C)(C)C3874.6Standard polar33892256
Lenalidomide,2TBDMS,isomer #2CC(C)(C)[Si](C)(C)NC1=CC=CC2=C1CN(C1CCC(=O)N([Si](C)(C)C(C)(C)C)C1=O)C2=O3131.6Semi standard non polar33892256
Lenalidomide,2TBDMS,isomer #2CC(C)(C)[Si](C)(C)NC1=CC=CC2=C1CN(C1CCC(=O)N([Si](C)(C)C(C)(C)C)C1=O)C2=O3194.0Standard non polar33892256
Lenalidomide,2TBDMS,isomer #2CC(C)(C)[Si](C)(C)NC1=CC=CC2=C1CN(C1CCC(=O)N([Si](C)(C)C(C)(C)C)C1=O)C2=O3589.3Standard polar33892256
Lenalidomide,3TBDMS,isomer #1CC(C)(C)[Si](C)(C)N1C(=O)CCC(N2CC3=C(C=CC=C3N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C)C2=O)C1=O3262.2Semi standard non polar33892256
Lenalidomide,3TBDMS,isomer #1CC(C)(C)[Si](C)(C)N1C(=O)CCC(N2CC3=C(C=CC=C3N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C)C2=O)C1=O3481.9Standard non polar33892256
Lenalidomide,3TBDMS,isomer #1CC(C)(C)[Si](C)(C)N1C(=O)CCC(N2CC3=C(C=CC=C3N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C)C2=O)C1=O3449.2Standard polar33892256
Spectra

GC-MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted GC-MSPredicted GC-MS Spectrum - Lenalidomide GC-MS (Non-derivatized) - 70eV, Positivesplash10-01si-4950000000-d56c036a1d29e5a9442f2017-09-01Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Lenalidomide GC-MS (Non-derivatized) - 70eV, PositiveNot Available2021-10-12Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Lenalidomide GC-MS (Non-derivatized) - 70eV, PositiveNot Available2021-10-12Wishart LabView Spectrum

MS/MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Experimental LC-MS/MSLC-MS/MS Spectrum - Lenalidomide LC-ESI-qTof , Positive-QTOFsplash10-0002-1920000000-c10c48acd9b8123e35052017-09-14HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Lenalidomide , positive-QTOFsplash10-0002-1920000000-c10c48acd9b8123e35052017-09-14HMDB team, MONAView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Lenalidomide 10V, Positive-QTOFsplash10-03dl-0090000000-2431a4e4063fb866e5022016-08-01Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Lenalidomide 20V, Positive-QTOFsplash10-03dl-0590000000-3bd8341d78d9f0bb21852016-08-01Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Lenalidomide 40V, Positive-QTOFsplash10-0006-5900000000-ede52ce7143fcbe39e3c2016-08-01Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Lenalidomide 10V, Negative-QTOFsplash10-0a4i-0190000000-a51e8a05d578a97d39162016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Lenalidomide 20V, Negative-QTOFsplash10-0btc-2980000000-9fa6887f8d1dd5044b782016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Lenalidomide 40V, Negative-QTOFsplash10-000f-9500000000-60ff64f6a1048a4175382016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Lenalidomide 10V, Positive-QTOFsplash10-03dj-0590000000-f93c028e30eeeb33fb072021-09-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Lenalidomide 20V, Positive-QTOFsplash10-01pk-0970000000-62ad8f815b005ef334f62021-09-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Lenalidomide 40V, Positive-QTOFsplash10-001j-2900000000-882d6b2043b051c57a332021-09-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Lenalidomide 10V, Negative-QTOFsplash10-0a4i-0090000000-7a47503a13a4776dc84e2021-09-25Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Lenalidomide 20V, Negative-QTOFsplash10-0a4u-1690000000-9c997f4a738ff527b14a2021-09-25Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Lenalidomide 40V, Negative-QTOFsplash10-0006-6910000000-618785cddde3e646877b2021-09-25Wishart LabView Spectrum

NMR Spectra

Spectrum TypeDescriptionDeposition DateSourceView
Predicted 1D NMR13C NMR Spectrum (1D, 100 MHz, D2O, predicted)2021-09-16Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 100 MHz, D2O, predicted)2021-09-16Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 200 MHz, D2O, predicted)2021-09-16Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 200 MHz, D2O, predicted)2021-09-16Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 300 MHz, D2O, predicted)2021-09-16Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 300 MHz, D2O, predicted)2021-09-16Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 400 MHz, D2O, predicted)2021-09-16Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 400 MHz, D2O, predicted)2021-09-16Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 500 MHz, D2O, predicted)2021-09-16Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 500 MHz, D2O, predicted)2021-09-16Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 600 MHz, D2O, predicted)2021-09-16Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 600 MHz, D2O, predicted)2021-09-16Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 700 MHz, D2O, predicted)2021-09-16Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 700 MHz, D2O, predicted)2021-09-16Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 800 MHz, D2O, predicted)2021-09-16Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 800 MHz, D2O, predicted)2021-09-16Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 900 MHz, D2O, predicted)2021-09-16Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 900 MHz, D2O, predicted)2021-09-16Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 1000 MHz, D2O, predicted)2021-09-16Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 1000 MHz, D2O, predicted)2021-09-16Wishart 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 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 CompoundNot Available
PDB IDNot Available
ChEBI ID63791
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. 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

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 ]
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 ]
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 ]