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Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2012-09-06 15:16:50 UTC
Update Date2022-03-07 02:51:44 UTC
HMDB IDHMDB0014787
Secondary Accession Numbers
  • HMDB14787
Metabolite Identification
Common NameStavudine
DescriptionStavudine, also known as D4T or sanilvudine, belongs to the class of organic compounds known as nucleoside and nucleotide analogues. These are analogues of nucleosides and nucleotides. These include phosphonated nucleosides, C-glycosylated nucleoside bases, analogues where the sugar unit is a pyranose, and carbocyclic nucleosides, among others. Stavudine is a drug which is used for the treatment of human immunovirus (hiv) infections. In humans, stavudine is involved in the stavudine action pathway. Stavudine is a primary metabolite. Primary metabolites are metabolically or physiologically essential metabolites. They are directly involved in an organism’s growth, development or reproduction. Based on a literature review very few articles have been published on Stavudine.
Structure
Data?1582753221
Synonyms
ValueSource
1-(2,3-Dideoxy-beta-D-glycero-pent-2-enofuranosyl)thymineChEBI
2',3'-Didehydro-3'-deoxythimidineChEBI
3'-Deoxy-2'-thymidineneChEBI
d4TChEBI
EstavudinaChEBI
SanilvudineChEBI
StavudinumChEBI
STVChEBI
ZeritKegg
ABBR D4TKegg
1-(2,3-Dideoxy-b-D-glycero-pent-2-enofuranosyl)thymineGenerator
1-(2,3-Dideoxy-β-D-glycero-pent-2-enofuranosyl)thymineGenerator
2',3'-Didehydro-2',3'-dideoxythmidineHMDB
2',3' Didehydro 3' deoxythymidineHMDB
2',3'-Didehydro-3'-deoxythymidineHMDB
Bristol-myers squibb brand OF stavudineHMDB
Bristol-myers brand OF stavudineHMDB
Stavudine, monosodium saltHMDB
Chemical FormulaC10H12N2O4
Average Molecular Weight224.2133
Monoisotopic Molecular Weight224.079706882
IUPAC Name1-[(2R,5S)-5-(hydroxymethyl)-2,5-dihydrofuran-2-yl]-5-methyl-1,2,3,4-tetrahydropyrimidine-2,4-dione
Traditional Namestavudine
CAS Registry Number3056-17-5
SMILES
CC1=CN([C@@H]2O[C@H](CO)C=C2)C(=O)NC1=O
InChI Identifier
InChI=1S/C10H12N2O4/c1-6-4-12(10(15)11-9(6)14)8-3-2-7(5-13)16-8/h2-4,7-8,13H,5H2,1H3,(H,11,14,15)/t7-,8+/m0/s1
InChI KeyXNKLLVCARDGLGL-JGVFFNPUSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as nucleoside and nucleotide analogues. These are analogues of nucleosides and nucleotides. These include phosphonated nucleosides, C-glycosylated nucleoside bases, analogues where the sugar unit is a pyranose, and carbocyclic nucleosides, among others.
KingdomOrganic compounds
Super ClassNucleosides, nucleotides, and analogues
ClassNucleoside and nucleotide analogues
Sub ClassNot Available
Direct ParentNucleoside and nucleotide analogues
Alternative Parents
Substituents
  • Pyrimidone
  • Hydropyrimidine
  • Pyrimidine
  • Dihydrofuran
  • Vinylogous amide
  • Heteroaromatic compound
  • Lactam
  • Urea
  • Organoheterocyclic compound
  • Azacycle
  • Oxacycle
  • Hydrocarbon derivative
  • Organic oxide
  • Organopnictogen compound
  • Primary alcohol
  • Organooxygen compound
  • Organonitrogen compound
  • Alcohol
  • Organic oxygen compound
  • Organic nitrogen compound
  • Aromatic heteromonocyclic compound
Molecular FrameworkAromatic heteromonocyclic compounds
External Descriptors
Ontology
Physiological effectNot Available
Disposition
Process
RoleNot Available
Physical Properties
StateSolid
Experimental Molecular Properties
PropertyValueReference
Melting Point159 - 160 °CNot Available
Boiling PointNot AvailableNot Available
Water Solubility40.5 g/LNot Available
LogP-0.8Not Available
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
PropertyValueSource
Water Solubility40.5 g/LALOGPS
logP-0.73ALOGPS
logP-0.23ChemAxon
logS-0.74ALOGPS
pKa (Strongest Acidic)9.95ChemAxon
pKa (Strongest Basic)-3ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count4ChemAxon
Hydrogen Donor Count2ChemAxon
Polar Surface Area78.87 ŲChemAxon
Rotatable Bond Count2ChemAxon
Refractivity55.32 m³·mol⁻¹ChemAxon
Polarizability21.33 ųChemAxon
Number of Rings2ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
Predicted Chromatographic Properties

Predicted Collision Cross Sections

PredictorAdduct TypeCCS Value (Å2)Reference
DarkChem[M+H]+151.87531661259
DarkChem[M-H]-151.33831661259
DeepCCS[M+H]+153.22630932474
DeepCCS[M-H]-150.83130932474
DeepCCS[M-2H]-183.87330932474
DeepCCS[M+Na]+159.13930932474
AllCCS[M+H]+149.732859911
AllCCS[M+H-H2O]+145.732859911
AllCCS[M+NH4]+153.432859911
AllCCS[M+Na]+154.532859911
AllCCS[M-H]-150.532859911
AllCCS[M+Na-2H]-150.632859911
AllCCS[M+HCOO]-150.832859911

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
StavudineCC1=CN([C@@H]2O[C@H](CO)C=C2)C(=O)NC1=O3022.5Standard polar33892256
StavudineCC1=CN([C@@H]2O[C@H](CO)C=C2)C(=O)NC1=O2129.1Standard non polar33892256
StavudineCC1=CN([C@@H]2O[C@H](CO)C=C2)C(=O)NC1=O2159.1Semi standard non polar33892256

Derivatized

Derivative Name / StructureSMILESKovats RI ValueColumn TypeReference
Stavudine,1TMS,isomer #1CC1=CN([C@H]2C=C[C@@H](CO[Si](C)(C)C)O2)C(=O)[NH]C1=O2127.5Semi standard non polar33892256
Stavudine,1TMS,isomer #2CC1=CN([C@H]2C=C[C@@H](CO)O2)C(=O)N([Si](C)(C)C)C1=O2166.9Semi standard non polar33892256
Stavudine,2TMS,isomer #1CC1=CN([C@H]2C=C[C@@H](CO[Si](C)(C)C)O2)C(=O)N([Si](C)(C)C)C1=O2237.6Semi standard non polar33892256
Stavudine,2TMS,isomer #1CC1=CN([C@H]2C=C[C@@H](CO[Si](C)(C)C)O2)C(=O)N([Si](C)(C)C)C1=O2266.9Standard non polar33892256
Stavudine,2TMS,isomer #1CC1=CN([C@H]2C=C[C@@H](CO[Si](C)(C)C)O2)C(=O)N([Si](C)(C)C)C1=O2764.3Standard polar33892256
Stavudine,1TBDMS,isomer #1CC1=CN([C@H]2C=C[C@@H](CO[Si](C)(C)C(C)(C)C)O2)C(=O)[NH]C1=O2387.1Semi standard non polar33892256
Stavudine,1TBDMS,isomer #2CC1=CN([C@H]2C=C[C@@H](CO)O2)C(=O)N([Si](C)(C)C(C)(C)C)C1=O2392.6Semi standard non polar33892256
Stavudine,2TBDMS,isomer #1CC1=CN([C@H]2C=C[C@@H](CO[Si](C)(C)C(C)(C)C)O2)C(=O)N([Si](C)(C)C(C)(C)C)C1=O2666.0Semi standard non polar33892256
Stavudine,2TBDMS,isomer #1CC1=CN([C@H]2C=C[C@@H](CO[Si](C)(C)C(C)(C)C)O2)C(=O)N([Si](C)(C)C(C)(C)C)C1=O2680.0Standard non polar33892256
Stavudine,2TBDMS,isomer #1CC1=CN([C@H]2C=C[C@@H](CO[Si](C)(C)C(C)(C)C)O2)C(=O)N([Si](C)(C)C(C)(C)C)C1=O2889.8Standard polar33892256
Spectra

GC-MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted GC-MSPredicted GC-MS Spectrum - Stavudine GC-MS (Non-derivatized) - 70eV, Positivesplash10-004i-9710000000-ec1b8accee7609d895af2017-09-01Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Stavudine GC-MS (1 TMS) - 70eV, Positivesplash10-0fi9-9710000000-a08eaef1e27e4362b56e2017-10-06Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Stavudine 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 - Stavudine 15V, Negative-QTOFsplash10-00di-0970000000-1b5ba27caa3ca46a5b792021-09-20HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Stavudine 30V, Negative-QTOFsplash10-0fk9-0910000000-0c32425ddc6552e762c72021-09-20HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Stavudine 90V, Positive-QTOFsplash10-053i-1900000000-8995ae3343a9f5bbbd7e2021-09-20HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Stavudine 75V, Positive-QTOFsplash10-052r-1900000000-b232bf6bd07c731257762021-09-20HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Stavudine 35V, Negative-QTOFsplash10-0006-9000000000-b6b8d8a7acd0cee4a6be2021-09-20HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Stavudine 35V, Positive-QTOFsplash10-004i-0900000000-bfecc35d096bfac410702021-09-20HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Stavudine 45V, Positive-QTOFsplash10-014r-0900000000-7eaff645bdf6c4509baf2021-09-20HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Stavudine 30V, Positive-QTOFsplash10-014i-0910000000-14958ea9ed30262a43132021-09-20HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Stavudine 75V, Negative-QTOFsplash10-0a4i-0900000000-f6122db2223358609e312021-09-20HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Stavudine 90V, Negative-QTOFsplash10-0a4i-0900000000-c3ebc31e7ad70d77da442021-09-20HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Stavudine 60V, Negative-QTOFsplash10-0a4i-0900000000-d5d5a96f8199343194ce2021-09-20HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Stavudine 45V, Negative-QTOFsplash10-0a4i-0900000000-2e40076ad350727ab3ef2021-09-20HMDB team, MONAView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Stavudine 10V, Positive-QTOFsplash10-004i-0900000000-a15778802feedb7e87022016-08-01Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Stavudine 20V, Positive-QTOFsplash10-004i-5900000000-1e77dd699ba1244d96dd2016-08-01Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Stavudine 40V, Positive-QTOFsplash10-0a7j-9600000000-42ce2a756eceb750ac462016-08-01Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Stavudine 10V, Negative-QTOFsplash10-00c0-2940000000-3e2b43ac1b4b3b11d5402016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Stavudine 20V, Negative-QTOFsplash10-01di-3920000000-0a634444532bc0df95492016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Stavudine 40V, Negative-QTOFsplash10-0006-9200000000-5a3e9da67f3d054c39c82016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Stavudine 10V, Positive-QTOFsplash10-004i-0910000000-3590697dc556ba789bc32021-10-11Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Stavudine 20V, Positive-QTOFsplash10-004i-4930000000-0d37f8daf0a0e84719bf2021-10-11Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Stavudine 40V, Positive-QTOFsplash10-0a59-9400000000-0f2472d56e156d73d0de2021-10-11Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Stavudine 10V, Negative-QTOFsplash10-00di-0090000000-2b6aa9078cee3df72a6f2021-10-11Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Stavudine 20V, Negative-QTOFsplash10-00bc-7960000000-a5ae84e7332328ddeee22021-10-11Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Stavudine 40V, Negative-QTOFsplash10-0006-9100000000-22b5a0eeff96c030db6a2021-10-11Wishart LabView Spectrum
Biological Properties
Cellular LocationsNot Available
Biospecimen Locations
  • Blood
  • Urine
Tissue LocationsNot Available
Pathways
Normal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
BloodExpected but not QuantifiedNot QuantifiedNot AvailableNot AvailableTaking drug identified by DrugBank entry DB00649 details
UrineExpected but not QuantifiedNot QuantifiedNot AvailableNot AvailableTaking drug identified by DrugBank entry DB00649 details
Abnormal Concentrations
Not Available
Predicted Concentrations
BiospecimenValueOriginal ageOriginal sexOriginal conditionComments
Blood0.000 uMAdult (>18 years old)BothNormalPredicted based on drug qualities
Blood0.000 umol/mmol creatinineAdult (>18 years old)BothNormalPredicted based on drug qualities
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDDB00649
Phenol Explorer Compound IDNot Available
FooDB IDNot Available
KNApSAcK IDNot Available
Chemspider ID17270
KEGG Compound IDC07312
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkStavudine
METLIN IDNot Available
PubChem Compound18283
PDB IDNot Available
ChEBI ID63581
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

Transporters

General function:
Involved in ion transmembrane transporter activity
Specific function:
Involved in the renal elimination of endogenous and exogenous organic anions. Functions as organic anion exchanger when the uptake of one molecule of organic anion is coupled with an efflux of one molecule of endogenous dicarboxylic acid (glutarate, ketoglutarate, etc). Mediates the sodium-independent uptake of 2,3-dimercapto-1-propanesulfonic acid (DMPS). Mediates the sodium-independent uptake of p- aminohippurate (PAH), ochratoxin (OTA), acyclovir (ACV), 3'-azido- 3-'deoxythymidine (AZT), cimetidine (CMD), 2,4-dichloro- phenoxyacetate (2,4-D), hippurate (HA), indoleacetate (IA), indoxyl sulfate (IS) and 3-carboxy-4-methyl-5-propyl-2- furanpropionate (CMPF), cidofovir, adefovir, 9-(2- phosphonylmethoxyethyl) guanine (PMEG), 9-(2- phosphonylmethoxyethyl) diaminopurine (PMEDAP) and edaravone sulfate. PAH uptake is inhibited by p- chloromercuribenzenesulphonate (PCMBS), diethyl pyrocarbonate (DEPC), sulindac, diclofenac, carprofen, glutarate and okadaic acid. PAH uptake is inhibited by benzothiazolylcysteine (BTC), S-chlorotrifluoroethylcysteine (CTFC), cysteine S-conjugates S-dichlorovinylcysteine (DCVC), furosemide, steviol, phorbol 12-myristate 13-acetate (PMA), calcium ionophore A23187, benzylpenicillin, furosemide, indomethacin, bumetamide, losartan, probenecid, phenol red, urate, and alpha-ketoglutarate
Gene Name:
SLC22A6
Uniprot ID:
Q4U2R8
Molecular weight:
61815.8
References
  1. Wada S, Tsuda M, Sekine T, Cha SH, Kimura M, Kanai Y, Endou H: Rat multispecific organic anion transporter 1 (rOAT1) transports zidovudine, acyclovir, and other antiviral nucleoside analogs. J Pharmacol Exp Ther. 2000 Sep;294(3):844-9. [PubMed:10945832 ]