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Record Information
Version5.0
StatusDetected but not Quantified
Creation Date2021-09-11 17:58:40 UTC
Update Date2021-09-26 23:13:26 UTC
HMDB IDHMDB0257211
Secondary Accession NumbersNone
Metabolite Identification
Common NameRibociclib
DescriptionRibociclib belongs to the class of organic compounds known as pyridinylpiperazines. Pyridinylpiperazines are compounds containing a pyridinylpiperazine skeleton, which consists of a pyridine linked (not fused) to a piperazine by a bond by a single bond that is not part of a ring. Based on a literature review a significant number of articles have been published on Ribociclib. This compound has been identified in human blood as reported by (PMID: 31557052 ). Ribociclib is not a naturally occurring metabolite and is only found in those individuals exposed to this compound or its derivatives. Technically Ribociclib is part of the human exposome. The exposome can be defined as the collection of all the exposures of an individual in a lifetime and how those exposures relate to health. An individual's exposure begins before birth and includes insults from environmental and occupational sources.
Structure
Thumb
Synonyms
ValueSource
LEE-011NVP-lee011ChEMBL
Chemical FormulaC23H30N8O
Average Molecular Weight434.548
Monoisotopic Molecular Weight434.254257618
IUPAC Name7-cyclopentyl-N,N-dimethyl-2-{[5-(piperazin-1-yl)pyridin-2-yl]amino}-7H-pyrrolo[2,3-d]pyrimidine-6-carboxamide
Traditional Name7-cyclopentyl-N,N-dimethyl-2-{[5-(piperazin-1-yl)pyridin-2-yl]amino}pyrrolo[2,3-d]pyrimidine-6-carboxamide
CAS Registry NumberNot Available
SMILES
CN(C)C(=O)C1=CC2=CN=C(NC3=CC=C(C=N3)N3CCNCC3)N=C2N1C1CCCC1
InChI Identifier
InChI=1S/C23H30N8O/c1-29(2)22(32)19-13-16-14-26-23(28-21(16)31(19)17-5-3-4-6-17)27-20-8-7-18(15-25-20)30-11-9-24-10-12-30/h7-8,13-15,17,24H,3-6,9-12H2,1-2H3,(H,25,26,27,28)
InChI KeyRHXHGRAEPCAFML-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as pyridinylpiperazines. Pyridinylpiperazines are compounds containing a pyridinylpiperazine skeleton, which consists of a pyridine linked (not fused) to a piperazine by a bond by a single bond that is not part of a ring.
KingdomOrganic compounds
Super ClassOrganoheterocyclic compounds
ClassDiazinanes
Sub ClassPiperazines
Direct ParentPyridinylpiperazines
Alternative Parents
Substituents
  • Pyridinylpiperazine
  • N-arylpiperazine
  • Pyrimidinecarboxamide
  • Pyrrolopyrimidine
  • Pyrrolo[2,3-d]pyrimidine
  • 2-heteroaryl carboxamide
  • Pyrrole-2-carboxamide
  • Pyrrole-2-carboxylic acid or derivatives
  • Tertiary aliphatic/aromatic amine
  • Dialkylarylamine
  • Aminopyrimidine
  • Aminopyridine
  • Substituted pyrrole
  • Imidolactam
  • Pyrimidine
  • Pyridine
  • Heteroaromatic compound
  • Tertiary carboxylic acid amide
  • Pyrrole
  • Tertiary amine
  • Carboxamide group
  • Amino acid or derivatives
  • Azacycle
  • Secondary amine
  • Carboxylic acid derivative
  • Secondary aliphatic amine
  • Hydrocarbon derivative
  • Organic oxygen compound
  • Organic oxide
  • Organonitrogen compound
  • Organooxygen compound
  • Organic nitrogen compound
  • Amine
  • Aromatic heteropolycyclic compound
Molecular FrameworkAromatic heteropolycyclic compounds
External DescriptorsNot Available
Ontology
Physiological effectNot Available
Disposition
ProcessNot Available
RoleNot Available
Physical Properties
StateNot Available
Experimental Molecular Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
PropertyValueSource
logP2.5ALOGPS
logP2.38ChemAxon
logS-3.3ALOGPS
pKa (Strongest Acidic)11.59ChemAxon
pKa (Strongest Basic)8.87ChemAxon
Physiological Charge1ChemAxon
Hydrogen Acceptor Count7ChemAxon
Hydrogen Donor Count2ChemAxon
Polar Surface Area91.21 ŲChemAxon
Rotatable Bond Count5ChemAxon
Refractivity125.59 m³·mol⁻¹ChemAxon
Polarizability49.13 ųChemAxon
Number of Rings5ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
Predicted Chromatographic Properties

Predicted Collision Cross Sections

PredictorAdduct TypeCCS Value (Å2)Reference
DeepCCS[M+H]+205.14230932474
DeepCCS[M-H]-202.78430932474
DeepCCS[M-2H]-236.64830932474
DeepCCS[M+Na]+211.6830932474
AllCCS[M+H]+205.332859911
AllCCS[M+H-H2O]+203.232859911
AllCCS[M+NH4]+207.232859911
AllCCS[M+Na]+207.732859911
AllCCS[M-H]-196.832859911
AllCCS[M+Na-2H]-197.532859911
AllCCS[M+HCOO]-198.332859911

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
RibociclibCN(C)C(=O)C1=CC2=CN=C(NC3=CC=C(C=N3)N3CCNCC3)N=C2N1C1CCCC14205.3Standard polar33892256
RibociclibCN(C)C(=O)C1=CC2=CN=C(NC3=CC=C(C=N3)N3CCNCC3)N=C2N1C1CCCC13757.9Standard non polar33892256
RibociclibCN(C)C(=O)C1=CC2=CN=C(NC3=CC=C(C=N3)N3CCNCC3)N=C2N1C1CCCC14336.2Semi standard non polar33892256

Derivatized

Derivative Name / StructureSMILESKovats RI ValueColumn TypeReference
Ribociclib,1TMS,isomer #1CN(C)C(=O)C1=CC2=CN=C(N(C3=CC=C(N4CCNCC4)C=N3)[Si](C)(C)C)N=C2N1C1CCCC13988.1Semi standard non polar33892256
Ribociclib,1TMS,isomer #1CN(C)C(=O)C1=CC2=CN=C(N(C3=CC=C(N4CCNCC4)C=N3)[Si](C)(C)C)N=C2N1C1CCCC13819.8Standard non polar33892256
Ribociclib,1TMS,isomer #1CN(C)C(=O)C1=CC2=CN=C(N(C3=CC=C(N4CCNCC4)C=N3)[Si](C)(C)C)N=C2N1C1CCCC15219.3Standard polar33892256
Ribociclib,1TMS,isomer #2CN(C)C(=O)C1=CC2=CN=C(NC3=CC=C(N4CCN([Si](C)(C)C)CC4)C=N3)N=C2N1C1CCCC14292.3Semi standard non polar33892256
Ribociclib,1TMS,isomer #2CN(C)C(=O)C1=CC2=CN=C(NC3=CC=C(N4CCN([Si](C)(C)C)CC4)C=N3)N=C2N1C1CCCC14060.3Standard non polar33892256
Ribociclib,1TMS,isomer #2CN(C)C(=O)C1=CC2=CN=C(NC3=CC=C(N4CCN([Si](C)(C)C)CC4)C=N3)N=C2N1C1CCCC15583.6Standard polar33892256
Ribociclib,2TMS,isomer #1CN(C)C(=O)C1=CC2=CN=C(N(C3=CC=C(N4CCN([Si](C)(C)C)CC4)C=N3)[Si](C)(C)C)N=C2N1C1CCCC14054.5Semi standard non polar33892256
Ribociclib,2TMS,isomer #1CN(C)C(=O)C1=CC2=CN=C(N(C3=CC=C(N4CCN([Si](C)(C)C)CC4)C=N3)[Si](C)(C)C)N=C2N1C1CCCC13991.3Standard non polar33892256
Ribociclib,2TMS,isomer #1CN(C)C(=O)C1=CC2=CN=C(N(C3=CC=C(N4CCN([Si](C)(C)C)CC4)C=N3)[Si](C)(C)C)N=C2N1C1CCCC15086.0Standard polar33892256
Ribociclib,1TBDMS,isomer #1CN(C)C(=O)C1=CC2=CN=C(N(C3=CC=C(N4CCNCC4)C=N3)[Si](C)(C)C(C)(C)C)N=C2N1C1CCCC14173.8Semi standard non polar33892256
Ribociclib,1TBDMS,isomer #1CN(C)C(=O)C1=CC2=CN=C(N(C3=CC=C(N4CCNCC4)C=N3)[Si](C)(C)C(C)(C)C)N=C2N1C1CCCC14011.7Standard non polar33892256
Ribociclib,1TBDMS,isomer #1CN(C)C(=O)C1=CC2=CN=C(N(C3=CC=C(N4CCNCC4)C=N3)[Si](C)(C)C(C)(C)C)N=C2N1C1CCCC15242.6Standard polar33892256
Ribociclib,1TBDMS,isomer #2CN(C)C(=O)C1=CC2=CN=C(NC3=CC=C(N4CCN([Si](C)(C)C(C)(C)C)CC4)C=N3)N=C2N1C1CCCC14490.2Semi standard non polar33892256
Ribociclib,1TBDMS,isomer #2CN(C)C(=O)C1=CC2=CN=C(NC3=CC=C(N4CCN([Si](C)(C)C(C)(C)C)CC4)C=N3)N=C2N1C1CCCC14255.7Standard non polar33892256
Ribociclib,1TBDMS,isomer #2CN(C)C(=O)C1=CC2=CN=C(NC3=CC=C(N4CCN([Si](C)(C)C(C)(C)C)CC4)C=N3)N=C2N1C1CCCC15710.5Standard polar33892256
Ribociclib,2TBDMS,isomer #1CN(C)C(=O)C1=CC2=CN=C(N(C3=CC=C(N4CCN([Si](C)(C)C(C)(C)C)CC4)C=N3)[Si](C)(C)C(C)(C)C)N=C2N1C1CCCC14445.5Semi standard non polar33892256
Ribociclib,2TBDMS,isomer #1CN(C)C(=O)C1=CC2=CN=C(N(C3=CC=C(N4CCN([Si](C)(C)C(C)(C)C)CC4)C=N3)[Si](C)(C)C(C)(C)C)N=C2N1C1CCCC14366.4Standard non polar33892256
Ribociclib,2TBDMS,isomer #1CN(C)C(=O)C1=CC2=CN=C(N(C3=CC=C(N4CCN([Si](C)(C)C(C)(C)C)CC4)C=N3)[Si](C)(C)C(C)(C)C)N=C2N1C1CCCC15159.3Standard polar33892256
Spectra

GC-MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted GC-MSPredicted GC-MS Spectrum - Ribociclib GC-MS (Non-derivatized) - 70eV, Positivesplash10-014l-5198400000-05147fd0421bf0ce99e12021-09-24Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Ribociclib GC-MS (Non-derivatized) - 70eV, PositiveNot Available2021-10-12Wishart LabView Spectrum

MS/MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Ribociclib 10V, Positive-QTOFsplash10-000i-0134900000-19b75d4d2f13025353622017-07-25Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Ribociclib 20V, Positive-QTOFsplash10-03ka-2396000000-20a47b700b3c925447382017-07-25Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Ribociclib 40V, Positive-QTOFsplash10-0a6s-4960000000-aded5512d57e7004e3722017-07-25Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Ribociclib 10V, Negative-QTOFsplash10-001i-0111900000-1af9a7b18e2253421e442017-07-26Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Ribociclib 20V, Negative-QTOFsplash10-00gr-1289400000-77f6701252b94d31984a2017-07-26Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Ribociclib 40V, Negative-QTOFsplash10-0f6x-9475100000-becc0f6259eb8aaffc1c2017-07-26Wishart LabView Spectrum
Biological Properties
Cellular LocationsNot Available
Biospecimen Locations
  • Blood
Tissue LocationsNot Available
Pathways
Normal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
BloodDetected but not QuantifiedNot QuantifiedNot SpecifiedNot SpecifiedNormal details
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDDB11730
Phenol Explorer Compound IDNot Available
FooDB IDNot Available
KNApSAcK IDNot Available
Chemspider ID30798107
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkRibociclib
METLIN IDNot Available
PubChem CompoundNot Available
PDB IDNot Available
ChEBI IDNot Available
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. Barupal DK, Fiehn O: Generating the Blood Exposome Database Using a Comprehensive Text Mining and Database Fusion Approach. Environ Health Perspect. 2019 Sep;127(9):97008. doi: 10.1289/EHP4713. Epub 2019 Sep 26. [PubMed:31557052 ]