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Showing drug card for Novobiocin (DB01051)

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Version 2.5
Creation Date 2005-06-13 13:24:05
Update Date 2009-06-23 18:06:53
Primary Accession Number DB01051
Secondary Accession Number
  • APRD00694
Name Novobiocin
Drug Type
  • Approved
  • Small Molecule
Description An antibiotic compound derived from Streptomyces niveus. It has a chemical structure similar to coumarin. Novobiocin binds to DNA gyrase, and blocks adenosine triphosphatase (ATPase) activity. (From Reynolds, Martindale The Extra Pharmacopoeia, 30th ed, p189) [PubChem]
Synonyms
  1. Antibiotic Pa-93
  2. Crystallinic Acid
  3. NOV
  4. Novobiocina [INN-Spanish]
  5. Novobiocine [INN-French]
  6. Novobiocinum [INN-Latin]
Brand Names
  1. Albamix
  2. Albamycin
  3. Cardelmycin
  4. Cathocin
  5. Cathomycin
  6. Inamycin
  7. Novo-R
  8. Robiocina
  9. Sirbiocina
  10. Spheromycin
  11. Stilbiocina
  12. Streptonivicin
Brand Mixtures
  1. Albacillin Suspension (Novobiocin (Novobiocin Sodium) + Penicillin G Procaine)
  2. Delta-Albaplex Tablets (Novobiocin (Novobiocin Sodium) + Prednisolone + Tetracycline Hydrochloride)
  3. Novodry Plus Suspension (Novobiocin (Novobiocin Sodium) + Penicillin G Procaine)
  4. Special Formula 17900-Forte Suspension (Dihydrostreptomycin (Dihydrostreptomycin Sulfate) + Hydrocortisone Acetate + Hydrocortisone Sodium Succinate + Novobiocin (Novobiocin Sodium) + Penicillin G Procaine + Polymyxin B Sulfate)
Chemical IUPAC Name [(3R,4S,5R,6R)-5-hydroxy-6-[2-hydroxy-3-[[4-hydroxy-3-(3-methylbut-2-enyl)benzoyl]amino]-8-methyl-4-oxochromen-7-yl]oxy-3-methoxy-2,2-dimethyloxan-4-yl] carbamate
Chemical Formula C31H36N2O11
Chemical Structure Structure
CAS Registry Number 303-81-1
InChI Identifier InChI=1/C31H36N2O11/c1-14(2)7-8-16-13-17(9-11-19(16)34)27(37)33-21-22(35)18-10-12-20(15(3)24(18)42-28(21)38)41-29-23(36)25(43-30(32)39)26(40-6)31(4,5)44-29/h7,9-13,23,25-26,29,34,36,38H,8H2,1-6H3,(H2,32,39)(H,33,37)/t23-,25+,26-,29-/m1/s1/f/h33H,32H2
InChI Key DYYIUCVAQGRACE-QAVRQHGKDQ
KEGG Drug Not Available
KEGG Compound C05080 Link Image
PubChem Compound 9346 Link Image
PubChem Substance 7526 Link Image
ChEBI ID Not Available
PharmGKB ID Not Available
HET ID NOV Link Image
GenBank ID Not Available
Drug ID Number [DIN] Not Available
RxList Link Not Available
PDRhealth Link Not Available
Wikipedia Link http://en.wikipedia.org/wiki/Novobiocin Link Image
FDA Label Not Available
Material Safety Data Sheet (MSDS)
Synthesis Reference Not Available
Average Molecular Weight 612.6243
Monoisotopic Molecular Weight 612.2319
State Solid
Melting Point Not Available
Experimental Water Solubility Insoluble Source: PhysProp
Predicted Water Solubility 9.79e-03 mg/mL Calculated using ALOGPS
Experimental LogP/Hydrophobicity 4.1 Source: PhysProp
Predicted LogP 3.03 Calculated using ALOGPS
Experimental LogS Not Available
Predicted LogS -4.80 Calculated using ALOGPS
Experimental Caco2 Permeability Not Available
pKa/Isoelectric Point 4.3
Mass Spectrum Not Available
MOL File Show Link Image | Download Link Image
SDF File Show Link Image | Download Link Image
PDB File Show Link Image | Download Link Image
2D Structure
3D Structure
Experimental PDB ID Not Available
Isomeric SMILES CO[C@@H]1[C@@H](OC(N)=O)[C@@H](O)[C@H](OC2=C(C)C3=C(C=C2)C(=O)C(NC(=O)C2=CC(C\C=C(\C)C)=C(O)C=C2)=C(O)O3)OC1(C)C
Canonical SMILES COC1C(OC(N)=O)C(O)C(OC2=C(C)C3=C(C=C2)C(=O)C(NC(=O)C2=CC(CC=C(C)C)=C(O)C=C2)=C(O)O3)OC1(C)C
Drug Category
  • Anti-Bacterial Agents
  • Enzyme Inhibitors
  • Nucleic Acid Synthesis Inhibitors
ATC Codes Not Available
AHFS Codes Not Available
Indication For the treatment of infections due to staphylococci and other susceptible organisms
Pharmacology Novobiocin is an aminocoumarin antibiotic that was produced by the actinomycete Streptomyces niveus. Novobiocin binds to DNA gyrase, and blocks adenosine triphosphatase (ATPase) activity. Other antibiotics in the aminocoumarin class include coumermycin A1 and clorobiocin.
Mechanism of Action Novobiocin is an aminocoumarin. Aminocoumarins are very potent inhibitors of bacterial DNA gyrase and work by targeting the GyrB subunit of the enzyme involved in energy tranduction. Novobiocin as well as the other aminocoumarin antibiotics act as competitive inhibitors of the ATPase reaction catalysed by GyrB.
Absorption Oral bioavailability is negligible.
Toxicity Not Available
Protein Binding 95%
Biotransformation Not Available
Half Life 6 hours
Dosage Forms
Form Route
Injection, powder, for solution Intravenous
Patient Information Not Available
Contraindications Not Available
Interactions Not Available
Drug Interactions Not Available
Food Interactions Not Available
Pathways Not Available
General References
  1. DAVID NA, BURGNER PR: Clinical effectiveness and safety of novobiocin. Antibiotic Med Clin Ther. 1956 Apr;2(4):219-29. [PubMed Link Image]
  2. CORBIN EE, PRIGOT A: Novobiocin; absorption, diffusion, and excretion studies. Antibiot Annu. 1956-1957;:392-5. [PubMed Link Image]
  3. Singh G, Jayanarayan KG, Dey CS: Novobiocin induces apoptosis-like cell death in topoisomerase II over-expressing arsenite resistant Leishmania donovani. Mol Biochem Parasitol. 2005 May;141(1):57-69. [PubMed Link Image]
  4. Burlison JA, Neckers L, Smith AB, Maxwell A, Blagg BS: Novobiocin: redesigning a DNA gyrase inhibitor for selective inhibition of hsp90. J Am Chem Soc. 2006 Dec 6;128(48):15529-36. [PubMed Link Image]
  5. Vickers AA, Chopra I, O'neill AJ: Intrinsic novobiocin resistance in Staphylococcus saprophyticus. Antimicrob Agents Chemother. 2007 Sep 17;. [PubMed Link Image]
  6. Wikipedia Link Image
Organisms Affected
  • Enteric bacteria and other eubacteria
Targets
  1. DNA gyrase subunit B
Drug Target 1 [top]
Target 1 ID 4150
Target 1 Name DNA gyrase subunit B
Target 1 Synonyms
  1. EC 5.99.1.3
Target 1 Gene Name gyrB
Target 1 Protein Sequence >DNA gyrase subunit B 
MVTALSDVNNTDNYGAGQIQVLEGLEAVRKRPGMYIGSTSERGLHHLVWEIVDNSIDEAL
AGYANQIEVVIEKDNWIKVTDNGRGIPVDIQEKMGRPAVEVILTVLHAGGKFGGGGYKVS
GGLHGVGSSVVNALSQDLEVYVHRNETIYHQAYKKGVPQFDLKEVGTTDKTGTVIRFKAD
GEIFTETTVYNYETLQQRIRELAFLNKGIQITLRDERDEENVREDSYHYEGGIKSYVELL
NENKEPIHDEPIYIHQSKDDIEVEIAIQYNSGYATNLLTYANNIHTYEGGTHEDGFKRAL
TRVLNSYGLSSKIMKEEKDRLSGEDTREGMTAIISIKHGDPQFEGQTKTKLGNSEVRQVV
DKLFSEHFERFLYENPQVARTVVEKGIMAARARVAAKKAREVTRRKSALDVASLPGKLAD
CSSKSPEECEIFLVEGDSAGGSTKSGRDSRTQAILPLRGKILNVEKARLDRILNNNEIRQ
MITAFGTGIGGDFDLAKARYHKIVIMTDADVDGAHIRTLLLTFFYRFMRPLIEAGYVYIA
QPPLYKLTQGKQKYYVYNDRELDKLKSELNPTPKWSIARYKGLGEMNADQLWETTMNPEH
RALLQVKLEDAIEADQTFEMLMGDVVENRRQFIEDNAVYANLDF
Target 1 Number of Residues 654
Target 1 Molecular Weight 72541
Target 1 Theoretical pI 5.68
Target 1 GO Classification
Function
DNA topoisomerase (ATP-hydrolyzing) activity
DNA topoisomerase (ATP-hydrolyzing) activity
DNA topoisomerase (ATP-hydrolyzing) activity
DNA topoisomerase activity
DNA topoisomerase (ATP-hydrolyzing) activity
nucleic acid binding
DNA binding
binding
nucleotide binding
purine nucleotide binding
adenyl nucleotide binding
ATP binding
Process
DNA modification
DNA topological change
physiological process
metabolism
cellular metabolism
nucleobase, nucleoside, nucleotide and nucleic acid metabolism
DNA metabolism
Component
Not Available
Target 1 General Function Involved in ATP binding
Target 1 Specific Function DNA gyrase negatively supercoils closed circular double- stranded DNA in an ATP-dependent manner and also catalyzes the interconversion of other topological isomers of double-stranded DNA rings, including catenanes and knotted rings
Target 1 Pathways Not Available
Target 1 Reactions Not Available
Target 1 Pfam Domain Function
Target 1 Signals
  • None
Target 1 Transmembrane Regions
  • None
Target 1 Essentiality Essential
Target 1 GenBank ID Protein Not Available
Target 1 UniProtKB/Swiss-Prot ID P0A0K8 Link Image
Target 1 UniProtKB/Swiss-Prot Entry Name GYRB_STAAU Link Image
Target 1 PDB ID Not Available
Target 1 Cellular Location
  • Cytoplasmic
Target 1 Gene Sequence >1935 bp 
ATGGTGACTGCATTGTCAGATGTAAACAACACGGATAATTATGGTGCTGGGCAAATACAA
GTATTAGAAGGTTTAGAAGCAGTACGTAAAAGACCAGGTATGTATATAGGATCGACTTCA
GAGAGAGGTTTGCACCATTTAGTGTGGGAAATTGTCGATAATAGTATCGATGAAGCATTA
GCTGGTTATGCAAATCAAATTGAAGTTGTTATTGAAAAAGATAACTGGATTAAAGTAACG
GATAACGGACGTGGTATCCCAGTTGATATTCAAGAAAAAATGGGACGTCCAGCTGTCGAA
GTTATTTTAACTGTTTTACATGCTGGTGGTAAATTCGGCGGTGGCGGATACAAAGTATCT
GGTGGTTTACATGGTGTTGGTTCATCAGTTGTAAACGCATTGTCACAAGACTTAGAAGTA
TATGTACACAGAAATGAGACTATATATCATCAAGCATATAAAAAAGGTGTACCTCAATTT
GACTTAAAAGAAGTTGGCACAACTGATAAGACAGGTACTGTCATTCGTTTTAAAGCAGAT
GGAGAAATCTTCACAGAGACAACTGTATACAACTATGAAACATTACAGCAACGTATTAGA
GAGCTTGCTTTCTTAAACAAAGGAATTCAAATCACATTAAGAGATGAACGTGATGAAGAA
AACGTTAGAGAAGACTCCTATCACTATGAGGGCGGTATTAAATCTTATGTTGAGTTATTG
AACGAAAATAAAGAACCTATTCATGATGAGCCAATTTATATTCATCAATCTAAAGATGAT
ATTGAAGTAGAAATTGCGATTCAATATAACTCAGGATATGCCACAAATCTTTTAACTTAC
GCAAATAACATTCATACGTACGAAGGTGGTACGCATGAAGACGGATTTAAACGTGCATTA
ACGCGTGTCTTAAATAGTTATGGTTTAAGTAGCAAGATTATGAAAGAAGAAAAAGATAGA
CTTTCTGGTGAAGATACACGTGAAGGTATGACAGCAATTATATCTATCAAACATGGTGAT
CCTCAATTCGAAGGTCAAACGAAGACAAAATTAGGTAATTCTGAAGTGCGTCAAGTTGTA
GATAAATTATTCTCAGAGCACTTTGAACGATTTTTATATGAAAATCCACAAGTCGCACGT
ACAGTGGTTGAAAAAGGTATTATGGCGGCACGTGCACGTGTTGCTGCGAAAAAAGCGCGT
GAAGTTACACGTCGTAAATCAGCGTTAGATGTAGCAAGTCTTCCAGGTAAATTAGCCGAT
TGCTCTAGTAAAAGTCCTGAAGAATGTGAGATATTCTTAGTCGAAGGGGACTCTGCTGGG
GGGTCTACAAAATCTGGTCGTGACTCTAGAACGCAGGCGATTTTACCATTACGAGGTAAG
ATATTAAATGTTGAAAAAGCACGATTAGATAGAATTTTGAATAACAATGAAATTCGTCAA
ATGATCACAGCATTTGGTACAGGAATTGGTGGCGACTTTGATCTAGCGAAAGCAAGATAT
CACAAAATCGTCATTATGACTGATGCCGATGTGGATGGAGCGCATATTAGAACATTGTTA
TTAACATTCTTCTATCGATTTATGAGACCGTTAATTGAAGCAGGCTATGTGTATATTGCA
CAGCCACCGTTGTATAAACTGACACAAGGTAAACAAAAGTATTATGTATACAATGATAGG
GAACTTGATAAACTTAAATCTGAATTGAATCCAACACCAAAATGGTCTATTGCACGATAC
AAAGGTCTTGGAGAAATGAATGCAGATCAATTATGGGAAACAACAATGAACCCTGAGCAC
CGTGCTCTTTTACAAGTAAAACTTGAAGATGCGATTGAAGCGGACCAAACATTTGAAATG
TTAATGGGTGACGTTGTAGAAAACCGTAGACAATTTATAGAAGATAATGCAGTTTATGCA
AACTTAGACTTCTAA
Target 1 GenBank Gene ID
Target 1 GeneCard ID Not Available
Target 1 GenAtlas ID Not Available
Target 1 HGNC ID Not Available
Target 1 Chromosome Location Not Available
Target 1 Locus Not Available
Target 1 SNPs SNPJam Report Link Image
Target 1 General References
  1. Margerrison EE, Hopewell R, Fisher LM: Nucleotide sequence of the Staphylococcus aureus gyrB-gyrA locus encoding the DNA gyrase A and B proteins. J Bacteriol. 1992 Mar;174(5):1596-603. [PubMed Link Image]
  2. Hopewell R, Oram M, Briesewitz R, Fisher LM: DNA cloning and organization of the Staphylococcus aureus gyrA and gyrB genes: close homology among gyrase proteins and implications for 4-quinolone action and resistance. J Bacteriol. 1990 Jun;172(6):3481-4. [PubMed Link Image]
  3. Ito H, Yoshida H, Bogaki-Shonai M, Niga T, Hattori H, Nakamura S: Quinolone resistance mutations in the DNA gyrase gyrA and gyrB genes of Staphylococcus aureus. Antimicrob Agents Chemother. 1994 Sep;38(9):2014-23. [PubMed Link Image]
  4. Alonso JC, Fisher LM: Nucleotide sequence of the recF gene cluster from Staphylococcus aureus and complementation analysis in Bacillus subtilis recF mutants. Mol Gen Genet. 1995 Mar 20;246(6):680-6. [PubMed Link Image]
  5. Brockbank SM, Barth PT: Cloning, sequencing, and expression of the DNA gyrase genes from Staphylococcus aureus. J Bacteriol. 1993 Jun;175(11):3269-77. [PubMed Link Image]
Target 1 Drug References
  1. Maxwell A: The interaction between coumarin drugs and DNA gyrase. Mol Microbiol. 1993 Aug;9(4):681-6. [PubMed Link Image]
  2. Gormley NA, Orphanides G, Meyer A, Cullis PM, Maxwell A: The interaction of coumarin antibiotics with fragments of DNA gyrase B protein. Biochemistry. 1996 Apr 16;35(15):5083-92. [PubMed Link Image]

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