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Record Information
Creation Date2009-07-21 20:27:15 UTC
Update Date2014-12-24 20:25:52 UTC
Accession NumberT3D2838
Common NameRifabutin
ClassSmall Molecule
DescriptionRifabutin is only found in individuals that have used or taken this drug. It is a broad-spectrum antibiotic that is being used as prophylaxis against disseminated Mycobacterium avium complex infection in HIV-positive patients. [PubChem]Rifabutin acts via the inhibition of DNA-dependent RNA polymerase in gram-positive and some gram-negative bacteria, leading to a suppression of RNA synthesis and cell death.
Compound Type
  • Amide
  • Amine
  • Anti-Bacterial Agent
  • Antibiotic, Antitubercular
  • Drug
  • Ester
  • Ether
  • Metabolite
  • Organic Compound
  • Synthetic Compound
Chemical Structure
4-Deoxo-3,4-(2-spiro(N-isobutyl-4-piperidyl)-2,5-dihydro-1H-imidazo)-rifamycin S
4-N-Isobutylspiropiperidylrifamycin S
Antibiotic LM 427
Chemical FormulaC46H62N4O11
Average Molecular Mass847.005 g/mol
Monoisotopic Mass846.442 g/mol
CAS Registry Number72559-06-9
IUPAC Name(7S,9Z,11S,12R,13S,14R,15R,16R,17S,18S,19Z,21Z)-2,15,17,23-tetrahydroxy-11-methoxy-3,7,12,14,16,18,22-heptamethyl-1'-(2-methylpropyl)-6,32-dioxo-8,33-dioxa-24,27,29-triazaspiro[pentacyclo[^{4,7}.0^{5,31}.0^{26,30}]tritriacontane-28,4'-piperidine]-1(31),2,4,9,19,21,23,25,29-nonaen-13-yl acetate
Traditional Name(7S,9Z,11S,12R,13S,14R,15R,16R,17S,18S,19Z,21Z)-2,15,17,23-tetrahydroxy-11-methoxy-3,7,12,14,16,18,22-heptamethyl-1'-(2-methylpropyl)-6,32-dioxo-8,33-dioxa-24,27,29-triazaspiro[pentacyclo[^{4,7}.0^{5,31}.0^{26,30}]tritriacontane-28,4'-piperidine]-1(31),2,4,9,19,21,23,25,29-nonaen-13-yl acetate
InChI IdentifierInChI=1S/C46H62N4O11/c1-22(2)21-50-18-16-46(17-19-50)48-34-31-32-39(54)28(8)42-33(31)43(56)45(10,61-42)59-20-15-30(58-11)25(5)41(60-29(9)51)27(7)38(53)26(6)37(52)23(3)13-12-14-24(4)44(57)47-36(40(32)55)35(34)49-46/h12-15,20,22-23,25-27,30,37-38,41,49,52-54H,16-19,21H2,1-11H3,(H,47,57)/b13-12-,20-15-,24-14-/t23-,25+,26+,27+,30-,37-,38+,41+,45-/m0/s1
Chemical Taxonomy
Description belongs to the class of organic compounds known as macrolactams. These are cyclic amides of amino carboxylic acids, having a 1-azacycloalkan-2-one structure, or analogues having unsaturation or heteroatoms replacing one or more carbon atoms of the ring. They are nitrogen analogues (the a nitrogen atom replacing the o atom of the cyclic carboxylic acid group ) of the naturally occurring macrolides.
KingdomOrganic compounds
Super ClassPhenylpropanoids and polyketides
Sub ClassNot Available
Direct ParentMacrolactams
Alternative Parents
  • Naphthofuran
  • Macrolactam
  • Azaspirodecane
  • Naphthalene
  • Benzofuran
  • Coumaran
  • Aryl ketone
  • Aryl alkyl ketone
  • Ketal
  • Piperidine
  • Benzenoid
  • 3-imidazoline
  • Vinylogous amide
  • Vinylogous acid
  • Lactam
  • Ketimine
  • Amino acid or derivatives
  • Tertiary aliphatic amine
  • Tertiary amine
  • Secondary carboxylic acid amide
  • Carboxylic acid ester
  • Ketone
  • Carboxamide group
  • Secondary alcohol
  • Acetal
  • Carboxylic acid derivative
  • Dialkyl ether
  • Secondary aliphatic amine
  • Enamine
  • Ether
  • Oxacycle
  • Azacycle
  • Organoheterocyclic compound
  • Organic 1,3-dipolar compound
  • Propargyl-type 1,3-dipolar organic compound
  • Monocarboxylic acid or derivatives
  • Polyol
  • Secondary amine
  • Organic oxygen compound
  • Organopnictogen compound
  • Imine
  • Carbonyl group
  • Organic oxide
  • Alcohol
  • Hydrocarbon derivative
  • Amine
  • Organic nitrogen compound
  • Organonitrogen compound
  • Organooxygen compound
  • Aromatic heteropolycyclic compound
Molecular FrameworkAromatic heteropolycyclic compounds
External DescriptorsNot Available
Biological Properties
StatusDetected and Not Quantified
Cellular Locations
  • Cytoplasm
  • Membrane
Biofluid LocationsNot Available
Tissue LocationsNot Available
PathwaysNot Available
Biological Roles
Chemical RolesNot Available
Physical Properties
AppearanceWhite powder.
Experimental Properties
Melting PointNot Available
Boiling PointNot Available
SolubilityMinimally soluble (0.19 mg/mL)
Predicted Properties
Water Solubility0.0091 g/LALOGPS
pKa (Strongest Acidic)5.29ChemAxon
pKa (Strongest Basic)7.9ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count14ChemAxon
Hydrogen Donor Count5ChemAxon
Polar Surface Area209.04 ŲChemAxon
Rotatable Bond Count5ChemAxon
Refractivity233.17 m³·mol⁻¹ChemAxon
Polarizability91.1 ųChemAxon
Number of Rings6ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Spectrum TypeDescriptionSplash KeyDeposition DateView
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-06vi-2000000290-b6c2e05a4e08c21c80092016-08-03View Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-0a4i-8000002970-8db040b5d2c5d1c7f8702016-08-03View Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-0a4i-9000003500-61568975d849f4e014902016-08-03View Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-0002-1000000390-013052b1c695816767092016-08-04View Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-0kbs-2000000790-222783e8f7fc477df8552016-08-04View Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-000m-3000001910-593444223c16d943f93e2016-08-04View Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-05pa-0000000970-2dfaa272c475120f19972021-10-11View Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-00kr-0000000930-3f004468a35f4bfc7d812021-10-11View Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-00kk-0000000950-e0fa551433e76d0694bb2021-10-11View Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-0002-1000000290-6b79ec41174e5c65892f2021-10-11View Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-0a4i-6000000930-138088289c4e164844b32021-10-11View Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-000l-2000000940-3d9bc441c2d70d5471512021-10-11View Spectrum
Toxicity Profile
Route of ExposureRifabutin is readily absorbed from the gastrointestinal tract, with an absolute bioavailability averaging 20%.
Mechanism of ToxicityRifabutin acts via the inhibition of DNA-dependent RNA polymerase in gram-positive and some gram-negative bacteria, leading to a suppression of RNA synthesis and cell death.
MetabolismHepatic. Of the five metabolites that have been identified, 25-O-desacetyl and 31-hydroxy are the most predominant. The former metabolite has an activity equal to the parent drug and contributes up to 10% to the total antimicrobial activity. Route of Elimination: A mass-balance study in three healthy adult volunteers with 14C-labeled rifabutin showed that 53% of the oral dose was excreted in the urine, primarily as metabolites. About 30% of the dose is excreted in the feces. Half Life: 45 (± 17) hours
Toxicity ValuesLD50: 4.8 g/kg (male mouse)
Lethal DoseNot Available
Carcinogenicity (IARC Classification)No indication of carcinogenicity to humans (not listed by IARC).
Uses/SourcesFor the prevention of disseminated Mycobacterium avium complex (MAC) disease in patients with advanced HIV infection. Used in the treatment of tuberculosis. It has also found to be useful in the treatment of (Chlamydia) Chlamydophila pneumoniae (Cpn) Infection.[Wikipedia]
Minimum Risk LevelNot Available
Health EffectsNot Available
SymptomsSymptoms include diarrhea, eructation, abdominal pain, vomitting, nausea, and insomnia.
TreatmentClinical experience with rifamycins suggests that gastric lavage to evacuate gastric contents (within a few hours of overdose), followed by instillation of an activated charcoal slurry into the stomach, may help absorb any remaining drug from the gastrointestinal tract. (2)
Normal Concentrations
Not Available
Abnormal Concentrations
Not Available
DrugBank IDDB00615
PubChem Compound ID6323490
ChemSpider ID4883445
UniProt IDNot Available
ChEBI ID8857
BioCyc IDNot Available
CTD IDNot Available
Stitch IDRifabutin
ACToR IDNot Available
Wikipedia LinkRifabutin
Synthesis ReferenceNot Available
General References
  1. [Link]
  2. RxList: The Internet Drug Index (2009). [Link]
Gene Regulation
Up-Regulated Genes
GeneGene SymbolGene IDInteractionChromosomeDetails
Down-Regulated GenesNot Available


General Function:
Tpr domain binding
Specific Function:
Molecular chaperone that promotes the maturation, structural maintenance and proper regulation of specific target proteins involved for instance in cell cycle control and signal transduction. Undergoes a functional cycle that is linked to its ATPase activity. This cycle probably induces conformational changes in the client proteins, thereby causing their activation. Interacts dynamically with various co-chaperones that modulate its substrate recognition, ATPase cycle and chaperone function. Binds bacterial lipopolysaccharide (LPS) et mediates LPS-induced inflammatory response, including TNF secretion by monocytes.
Gene Name:
Uniprot ID:
Molecular Weight:
84659.015 Da
  1. Schnaider T, Somogyi J, Csermely P, Szamel M: The Hsp90-specific inhibitor geldanamycin selectively disrupts kinase-mediated signaling events of T-lymphocyte activation. Cell Stress Chaperones. 2000 Jan;5(1):52-61. [10701840 ]
  2. Neckers L, Schulte TW, Mimnaugh E: Geldanamycin as a potential anti-cancer agent: its molecular target and biochemical activity. Invest New Drugs. 1999;17(4):361-73. [10759403 ]
  3. Srethapakdi M, Liu F, Tavorath R, Rosen N: Inhibition of Hsp90 function by ansamycins causes retinoblastoma gene product-dependent G1 arrest. Cancer Res. 2000 Jul 15;60(14):3940-6. [10919672 ]
  4. Munster PN, Srethapakdi M, Moasser MM, Rosen N: Inhibition of heat shock protein 90 function by ansamycins causes the morphological and functional differentiation of breast cancer cells. Cancer Res. 2001 Apr 1;61(7):2945-52. [11306472 ]
  5. Yang J, Yang JM, Iannone M, Shih WJ, Lin Y, Hait WN: Disruption of the EF-2 kinase/Hsp90 protein complex: a possible mechanism to inhibit glioblastoma by geldanamycin. Cancer Res. 2001 May 15;61(10):4010-6. [11358819 ]
General Function:
Virion binding
Specific Function:
Molecular chaperone that functions in the processing and transport of secreted proteins. When associated with CNPY3, required for proper folding of Toll-like receptors (By similarity). Functions in endoplasmic reticulum associated degradation (ERAD). Has ATPase activity.
Gene Name:
Uniprot ID:
Molecular Weight:
92468.06 Da
  1. Barzilay E, Ben-Califa N, Supino-Rosin L, Kashman Y, Hirschberg K, Elazar Z, Neumann D: Geldanamycin-associated inhibition of intracellular trafficking is attributed to a co-purified activity. J Biol Chem. 2004 Feb 20;279(8):6847-52. Epub 2003 Dec 1. [14660597 ]
  2. Chavany C, Mimnaugh E, Miller P, Bitton R, Nguyen P, Trepel J, Whitesell L, Schnur R, Moyer J, Neckers L: p185erbB2 binds to GRP94 in vivo. Dissociation of the p185erbB2/GRP94 heterocomplex by benzoquinone ansamycins precedes depletion of p185erbB2. J Biol Chem. 1996 Mar 1;271(9):4974-7. [8617772 ]
  3. Lawson B, Brewer JW, Hendershot LM: Geldanamycin, an hsp90/GRP94-binding drug, induces increased transcription of endoplasmic reticulum (ER) chaperones via the ER stress pathway. J Cell Physiol. 1998 Feb;174(2):170-8. [9428803 ]