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Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2012-09-06 15:16:51 UTC
Update Date2022-03-07 02:51:53 UTC
HMDB IDHMDB0015185
Secondary Accession Numbers
  • HMDB15185
Metabolite Identification
Common NameNovobiocin
DescriptionNovobiocin is only found in individuals that have used or taken this drug. It is 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]Novobiocin is an aminocoumarin. Aminocoumarins are very potent inhibitors of bacterial DNA gyrase and work by inhibiting 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.
Structure
Data?1582753268
Synonyms
ValueSource
N-{7-[(3-O-carbamoyl-6-deoxy-5-methyl-4-O-methyl-beta-D-gulopyranosyl)oxy]-4-hydroxy-8-methyl-2-oxo-2H-chromen-3-yl}-4-hydroxy-3-(3-methylbut-2-en-1-yl)benzamideChEBI
NovobiocinaChEBI
NovobiocineChEBI
NovobiocinumChEBI
N-{7-[(3-O-carbamoyl-6-deoxy-5-methyl-4-O-methyl-b-D-gulopyranosyl)oxy]-4-hydroxy-8-methyl-2-oxo-2H-chromen-3-yl}-4-hydroxy-3-(3-methylbut-2-en-1-yl)benzamideGenerator
N-{7-[(3-O-carbamoyl-6-deoxy-5-methyl-4-O-methyl-β-D-gulopyranosyl)oxy]-4-hydroxy-8-methyl-2-oxo-2H-chromen-3-yl}-4-hydroxy-3-(3-methylbut-2-en-1-yl)benzamideGenerator
Antibiotic pa-93HMDB
Crystallinic acidHMDB
NOVHMDB
Sodium, novobiocinHMDB
StreptonivicinHMDB
Calcium, novobiocinHMDB
Monosodium salt novobiocinHMDB
Novobiocin, monosodium saltHMDB
Novobiocin calciumHMDB
Novobiocin sodiumHMDB
Chemical FormulaC31H36N2O11
Average Molecular Weight612.6243
Monoisotopic Molecular Weight612.231910004
IUPAC Name(3R,4S,5R,6R)-5-hydroxy-6-({4-hydroxy-3-[4-hydroxy-3-(3-methylbut-2-en-1-yl)benzamido]-8-methyl-2-oxo-2H-chromen-7-yl}oxy)-3-methoxy-2,2-dimethyloxan-4-yl carbamate
Traditional Namenovobiocin
CAS Registry Number303-81-1
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(O)C(CC=C(C)C)=C2)C(=O)O3)OC1(C)C
InChI Identifier
InChI=1S/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/h7,9-13,23,25-26,29,34-36H,8H2,1-6H3,(H2,32,39)(H,33,37)/t23-,25+,26-,29-/m1/s1
InChI KeyYJQPYGGHQPGBLI-KGSXXDOSSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as coumarin glycosides. These are aromatic compounds containing a carbohydrate moiety glycosidically bound to a coumarin moiety.
KingdomOrganic compounds
Super ClassPhenylpropanoids and polyketides
ClassCoumarins and derivatives
Sub ClassCoumarin glycosides
Direct ParentCoumarin glycosides
Alternative Parents
Substituents
  • Coumarin-7-o-glycoside
  • Coumarin o-glycoside
  • Phenolic glycoside
  • 4-hydroxycoumarin
  • Hydroxycoumarin
  • Hexose monosaccharide
  • O-glycosyl compound
  • Glycosyl compound
  • Benzopyran
  • 1-benzopyran
  • Benzamide
  • Benzoic acid or derivatives
  • Benzoyl
  • 1-hydroxy-2-unsubstituted benzenoid
  • Phenol
  • Pyranone
  • Pyran
  • Monocyclic benzene moiety
  • Monosaccharide
  • Oxane
  • Benzenoid
  • Heteroaromatic compound
  • Vinylogous acid
  • Carbamic acid ester
  • Carboxamide group
  • Secondary carboxylic acid amide
  • Secondary alcohol
  • Lactone
  • Carbonic acid derivative
  • Ether
  • Dialkyl ether
  • Acetal
  • Organoheterocyclic compound
  • Carboxylic acid derivative
  • Oxacycle
  • Organic nitrogen compound
  • Carbonyl group
  • Hydrocarbon derivative
  • Organic oxide
  • Organopnictogen compound
  • Alcohol
  • Organooxygen compound
  • Organonitrogen compound
  • Organic oxygen compound
  • Aromatic heteropolycyclic compound
Molecular FrameworkAromatic heteropolycyclic compounds
External Descriptors
Ontology
Disposition

Biological location

Physical Properties
StateSolid
Experimental Molecular Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water Solubility0.0097 g/LNot Available
LogP4.1Not Available
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
PropertyValueSource
Water Solubility0.0097 g/LALOGPS
logP3.07ALOGPS
logP3.26ChemAxon
logS-4.8ALOGPS
pKa (Strongest Acidic)6.96ChemAxon
pKa (Strongest Basic)-3.9ChemAxon
Physiological Charge-1ChemAxon
Hydrogen Acceptor Count9ChemAxon
Hydrogen Donor Count5ChemAxon
Polar Surface Area196.1 ŲChemAxon
Rotatable Bond Count9ChemAxon
Refractivity158.24 m³·mol⁻¹ChemAxon
Polarizability63.97 ųChemAxon
Number of Rings4ChemAxon
BioavailabilityYesChemAxon
Rule of FiveNoChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleYesChemAxon
Predicted Chromatographic Properties

Predicted Collision Cross Sections

PredictorAdduct TypeCCS Value (Å2)Reference
DarkChem[M+H]+241.67231661259
DarkChem[M-H]-230.23131661259
DeepCCS[M+H]+238.84930932474
DeepCCS[M-H]-237.00430932474
DeepCCS[M-2H]-271.03830932474
DeepCCS[M+Na]+245.04230932474
AllCCS[M+H]+240.232859911
AllCCS[M+H-H2O]+239.232859911
AllCCS[M+NH4]+241.232859911
AllCCS[M+Na]+241.432859911
AllCCS[M-H]-238.132859911
AllCCS[M+Na-2H]-240.432859911
AllCCS[M+HCOO]-243.132859911

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
NovobiocinCO[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(O)C(CC=C(C)C)=C2)C(=O)O3)OC1(C)C5582.7Standard polar33892256
NovobiocinCO[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(O)C(CC=C(C)C)=C2)C(=O)O3)OC1(C)C4483.4Standard non polar33892256
NovobiocinCO[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(O)C(CC=C(C)C)=C2)C(=O)O3)OC1(C)C5105.3Semi standard non polar33892256

Derivatized

Derivative Name / StructureSMILESKovats RI ValueColumn TypeReference
Novobiocin,1TMS,isomer #1CO[C@@H]1[C@@H](OC(N)=O)[C@@H](O[Si](C)(C)C)[C@H](OC2=CC=C3C(O)=C(NC(=O)C4=CC=C(O)C(CC=C(C)C)=C4)C(=O)OC3=C2C)OC1(C)C4788.5Semi standard non polar33892256
Novobiocin,1TMS,isomer #2CO[C@@H]1[C@@H](OC(N)=O)[C@@H](O)[C@H](OC2=CC=C3C(O[Si](C)(C)C)=C(NC(=O)C4=CC=C(O)C(CC=C(C)C)=C4)C(=O)OC3=C2C)OC1(C)C4779.2Semi standard non polar33892256
Novobiocin,1TMS,isomer #3CO[C@@H]1[C@@H](OC(N)=O)[C@@H](O)[C@H](OC2=CC=C3C(O)=C(NC(=O)C4=CC=C(O[Si](C)(C)C)C(CC=C(C)C)=C4)C(=O)OC3=C2C)OC1(C)C4768.0Semi standard non polar33892256
Novobiocin,1TMS,isomer #4CO[C@@H]1[C@@H](OC(=O)N[Si](C)(C)C)[C@@H](O)[C@H](OC2=CC=C3C(O)=C(NC(=O)C4=CC=C(O)C(CC=C(C)C)=C4)C(=O)OC3=C2C)OC1(C)C4831.0Semi standard non polar33892256
Novobiocin,1TMS,isomer #5CO[C@@H]1[C@@H](OC(N)=O)[C@@H](O)[C@H](OC2=CC=C3C(O)=C(N(C(=O)C4=CC=C(O)C(CC=C(C)C)=C4)[Si](C)(C)C)C(=O)OC3=C2C)OC1(C)C4620.3Semi standard non polar33892256
Novobiocin,2TMS,isomer #1CO[C@@H]1[C@@H](OC(N)=O)[C@@H](O[Si](C)(C)C)[C@H](OC2=CC=C3C(O[Si](C)(C)C)=C(NC(=O)C4=CC=C(O)C(CC=C(C)C)=C4)C(=O)OC3=C2C)OC1(C)C4693.2Semi standard non polar33892256
Novobiocin,2TMS,isomer #10CO[C@@H]1[C@@H](OC(=O)N([Si](C)(C)C)[Si](C)(C)C)[C@@H](O)[C@H](OC2=CC=C3C(O)=C(NC(=O)C4=CC=C(O)C(CC=C(C)C)=C4)C(=O)OC3=C2C)OC1(C)C4752.0Semi standard non polar33892256
Novobiocin,2TMS,isomer #11CO[C@@H]1[C@@H](OC(=O)N[Si](C)(C)C)[C@@H](O)[C@H](OC2=CC=C3C(O)=C(N(C(=O)C4=CC=C(O)C(CC=C(C)C)=C4)[Si](C)(C)C)C(=O)OC3=C2C)OC1(C)C4559.4Semi standard non polar33892256
Novobiocin,2TMS,isomer #2CO[C@@H]1[C@@H](OC(N)=O)[C@@H](O[Si](C)(C)C)[C@H](OC2=CC=C3C(O)=C(NC(=O)C4=CC=C(O[Si](C)(C)C)C(CC=C(C)C)=C4)C(=O)OC3=C2C)OC1(C)C4680.6Semi standard non polar33892256
Novobiocin,2TMS,isomer #3CO[C@@H]1[C@@H](OC(=O)N[Si](C)(C)C)[C@@H](O[Si](C)(C)C)[C@H](OC2=CC=C3C(O)=C(NC(=O)C4=CC=C(O)C(CC=C(C)C)=C4)C(=O)OC3=C2C)OC1(C)C4757.0Semi standard non polar33892256
Novobiocin,2TMS,isomer #4CO[C@@H]1[C@@H](OC(N)=O)[C@@H](O[Si](C)(C)C)[C@H](OC2=CC=C3C(O)=C(N(C(=O)C4=CC=C(O)C(CC=C(C)C)=C4)[Si](C)(C)C)C(=O)OC3=C2C)OC1(C)C4532.4Semi standard non polar33892256
Novobiocin,2TMS,isomer #5CO[C@@H]1[C@@H](OC(N)=O)[C@@H](O)[C@H](OC2=CC=C3C(O[Si](C)(C)C)=C(NC(=O)C4=CC=C(O[Si](C)(C)C)C(CC=C(C)C)=C4)C(=O)OC3=C2C)OC1(C)C4700.3Semi standard non polar33892256
Novobiocin,2TMS,isomer #6CO[C@@H]1[C@@H](OC(=O)N[Si](C)(C)C)[C@@H](O)[C@H](OC2=CC=C3C(O[Si](C)(C)C)=C(NC(=O)C4=CC=C(O)C(CC=C(C)C)=C4)C(=O)OC3=C2C)OC1(C)C4744.8Semi standard non polar33892256
Novobiocin,2TMS,isomer #7CO[C@@H]1[C@@H](OC(N)=O)[C@@H](O)[C@H](OC2=CC=C3C(O[Si](C)(C)C)=C(N(C(=O)C4=CC=C(O)C(CC=C(C)C)=C4)[Si](C)(C)C)C(=O)OC3=C2C)OC1(C)C4499.7Semi standard non polar33892256
Novobiocin,2TMS,isomer #8CO[C@@H]1[C@@H](OC(=O)N[Si](C)(C)C)[C@@H](O)[C@H](OC2=CC=C3C(O)=C(NC(=O)C4=CC=C(O[Si](C)(C)C)C(CC=C(C)C)=C4)C(=O)OC3=C2C)OC1(C)C4737.4Semi standard non polar33892256
Novobiocin,2TMS,isomer #9CO[C@@H]1[C@@H](OC(N)=O)[C@@H](O)[C@H](OC2=CC=C3C(O)=C(N(C(=O)C4=CC=C(O[Si](C)(C)C)C(CC=C(C)C)=C4)[Si](C)(C)C)C(=O)OC3=C2C)OC1(C)C4503.7Semi standard non polar33892256
Novobiocin,3TMS,isomer #1CO[C@@H]1[C@@H](OC(N)=O)[C@@H](O[Si](C)(C)C)[C@H](OC2=CC=C3C(O[Si](C)(C)C)=C(NC(=O)C4=CC=C(O[Si](C)(C)C)C(CC=C(C)C)=C4)C(=O)OC3=C2C)OC1(C)C4643.0Semi standard non polar33892256
Novobiocin,3TMS,isomer #10CO[C@@H]1[C@@H](OC(=O)N([Si](C)(C)C)[Si](C)(C)C)[C@@H](O)[C@H](OC2=CC=C3C(O[Si](C)(C)C)=C(NC(=O)C4=CC=C(O)C(CC=C(C)C)=C4)C(=O)OC3=C2C)OC1(C)C4706.0Semi standard non polar33892256
Novobiocin,3TMS,isomer #11CO[C@@H]1[C@@H](OC(=O)N[Si](C)(C)C)[C@@H](O)[C@H](OC2=CC=C3C(O[Si](C)(C)C)=C(N(C(=O)C4=CC=C(O)C(CC=C(C)C)=C4)[Si](C)(C)C)C(=O)OC3=C2C)OC1(C)C4506.8Semi standard non polar33892256
Novobiocin,3TMS,isomer #12CO[C@@H]1[C@@H](OC(=O)N([Si](C)(C)C)[Si](C)(C)C)[C@@H](O)[C@H](OC2=CC=C3C(O)=C(NC(=O)C4=CC=C(O[Si](C)(C)C)C(CC=C(C)C)=C4)C(=O)OC3=C2C)OC1(C)C4689.7Semi standard non polar33892256
Novobiocin,3TMS,isomer #13CO[C@@H]1[C@@H](OC(=O)N[Si](C)(C)C)[C@@H](O)[C@H](OC2=CC=C3C(O)=C(N(C(=O)C4=CC=C(O[Si](C)(C)C)C(CC=C(C)C)=C4)[Si](C)(C)C)C(=O)OC3=C2C)OC1(C)C4510.9Semi standard non polar33892256
Novobiocin,3TMS,isomer #14CO[C@@H]1[C@@H](OC(=O)N([Si](C)(C)C)[Si](C)(C)C)[C@@H](O)[C@H](OC2=CC=C3C(O)=C(N(C(=O)C4=CC=C(O)C(CC=C(C)C)=C4)[Si](C)(C)C)C(=O)OC3=C2C)OC1(C)C4511.6Semi standard non polar33892256
Novobiocin,3TMS,isomer #2CO[C@@H]1[C@@H](OC(=O)N[Si](C)(C)C)[C@@H](O[Si](C)(C)C)[C@H](OC2=CC=C3C(O[Si](C)(C)C)=C(NC(=O)C4=CC=C(O)C(CC=C(C)C)=C4)C(=O)OC3=C2C)OC1(C)C4698.4Semi standard non polar33892256
Novobiocin,3TMS,isomer #3CO[C@@H]1[C@@H](OC(N)=O)[C@@H](O[Si](C)(C)C)[C@H](OC2=CC=C3C(O[Si](C)(C)C)=C(N(C(=O)C4=CC=C(O)C(CC=C(C)C)=C4)[Si](C)(C)C)C(=O)OC3=C2C)OC1(C)C4446.9Semi standard non polar33892256
Novobiocin,3TMS,isomer #4CO[C@@H]1[C@@H](OC(=O)N[Si](C)(C)C)[C@@H](O[Si](C)(C)C)[C@H](OC2=CC=C3C(O)=C(NC(=O)C4=CC=C(O[Si](C)(C)C)C(CC=C(C)C)=C4)C(=O)OC3=C2C)OC1(C)C4695.7Semi standard non polar33892256
Novobiocin,3TMS,isomer #5CO[C@@H]1[C@@H](OC(N)=O)[C@@H](O[Si](C)(C)C)[C@H](OC2=CC=C3C(O)=C(N(C(=O)C4=CC=C(O[Si](C)(C)C)C(CC=C(C)C)=C4)[Si](C)(C)C)C(=O)OC3=C2C)OC1(C)C4450.0Semi standard non polar33892256
Novobiocin,3TMS,isomer #6CO[C@@H]1[C@@H](OC(=O)N([Si](C)(C)C)[Si](C)(C)C)[C@@H](O[Si](C)(C)C)[C@H](OC2=CC=C3C(O)=C(NC(=O)C4=CC=C(O)C(CC=C(C)C)=C4)C(=O)OC3=C2C)OC1(C)C4696.2Semi standard non polar33892256
Novobiocin,3TMS,isomer #7CO[C@@H]1[C@@H](OC(=O)N[Si](C)(C)C)[C@@H](O[Si](C)(C)C)[C@H](OC2=CC=C3C(O)=C(N(C(=O)C4=CC=C(O)C(CC=C(C)C)=C4)[Si](C)(C)C)C(=O)OC3=C2C)OC1(C)C4527.4Semi standard non polar33892256
Novobiocin,3TMS,isomer #8CO[C@@H]1[C@@H](OC(=O)N[Si](C)(C)C)[C@@H](O)[C@H](OC2=CC=C3C(O[Si](C)(C)C)=C(NC(=O)C4=CC=C(O[Si](C)(C)C)C(CC=C(C)C)=C4)C(=O)OC3=C2C)OC1(C)C4708.2Semi standard non polar33892256
Novobiocin,3TMS,isomer #9CO[C@@H]1[C@@H](OC(N)=O)[C@@H](O)[C@H](OC2=CC=C3C(O[Si](C)(C)C)=C(N(C(=O)C4=CC=C(O[Si](C)(C)C)C(CC=C(C)C)=C4)[Si](C)(C)C)C(=O)OC3=C2C)OC1(C)C4465.4Semi standard non polar33892256
Novobiocin,1TBDMS,isomer #1CO[C@@H]1[C@@H](OC(N)=O)[C@@H](O[Si](C)(C)C(C)(C)C)[C@H](OC2=CC=C3C(O)=C(NC(=O)C4=CC=C(O)C(CC=C(C)C)=C4)C(=O)OC3=C2C)OC1(C)C4976.1Semi standard non polar33892256
Novobiocin,1TBDMS,isomer #2CO[C@@H]1[C@@H](OC(N)=O)[C@@H](O)[C@H](OC2=CC=C3C(O[Si](C)(C)C(C)(C)C)=C(NC(=O)C4=CC=C(O)C(CC=C(C)C)=C4)C(=O)OC3=C2C)OC1(C)C4968.9Semi standard non polar33892256
Novobiocin,1TBDMS,isomer #3CO[C@@H]1[C@@H](OC(N)=O)[C@@H](O)[C@H](OC2=CC=C3C(O)=C(NC(=O)C4=CC=C(O[Si](C)(C)C(C)(C)C)C(CC=C(C)C)=C4)C(=O)OC3=C2C)OC1(C)C4970.2Semi standard non polar33892256
Novobiocin,1TBDMS,isomer #4CO[C@@H]1[C@@H](OC(=O)N[Si](C)(C)C(C)(C)C)[C@@H](O)[C@H](OC2=CC=C3C(O)=C(NC(=O)C4=CC=C(O)C(CC=C(C)C)=C4)C(=O)OC3=C2C)OC1(C)C5047.5Semi standard non polar33892256
Novobiocin,1TBDMS,isomer #5CO[C@@H]1[C@@H](OC(N)=O)[C@@H](O)[C@H](OC2=CC=C3C(O)=C(N(C(=O)C4=CC=C(O)C(CC=C(C)C)=C4)[Si](C)(C)C(C)(C)C)C(=O)OC3=C2C)OC1(C)C4836.2Semi standard non polar33892256
Novobiocin,2TBDMS,isomer #1CO[C@@H]1[C@@H](OC(N)=O)[C@@H](O[Si](C)(C)C(C)(C)C)[C@H](OC2=CC=C3C(O[Si](C)(C)C(C)(C)C)=C(NC(=O)C4=CC=C(O)C(CC=C(C)C)=C4)C(=O)OC3=C2C)OC1(C)C5057.9Semi standard non polar33892256
Novobiocin,2TBDMS,isomer #10CO[C@@H]1[C@@H](OC(=O)N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C)[C@@H](O)[C@H](OC2=CC=C3C(O)=C(NC(=O)C4=CC=C(O)C(CC=C(C)C)=C4)C(=O)OC3=C2C)OC1(C)C5197.9Semi standard non polar33892256
Novobiocin,2TBDMS,isomer #11CO[C@@H]1[C@@H](OC(=O)N[Si](C)(C)C(C)(C)C)[C@@H](O)[C@H](OC2=CC=C3C(O)=C(N(C(=O)C4=CC=C(O)C(CC=C(C)C)=C4)[Si](C)(C)C(C)(C)C)C(=O)OC3=C2C)OC1(C)C4964.1Semi standard non polar33892256
Novobiocin,2TBDMS,isomer #2CO[C@@H]1[C@@H](OC(N)=O)[C@@H](O[Si](C)(C)C(C)(C)C)[C@H](OC2=CC=C3C(O)=C(NC(=O)C4=CC=C(O[Si](C)(C)C(C)(C)C)C(CC=C(C)C)=C4)C(=O)OC3=C2C)OC1(C)C5060.9Semi standard non polar33892256
Novobiocin,2TBDMS,isomer #3CO[C@@H]1[C@@H](OC(=O)N[Si](C)(C)C(C)(C)C)[C@@H](O[Si](C)(C)C(C)(C)C)[C@H](OC2=CC=C3C(O)=C(NC(=O)C4=CC=C(O)C(CC=C(C)C)=C4)C(=O)OC3=C2C)OC1(C)C5109.2Semi standard non polar33892256
Novobiocin,2TBDMS,isomer #4CO[C@@H]1[C@@H](OC(N)=O)[C@@H](O[Si](C)(C)C(C)(C)C)[C@H](OC2=CC=C3C(O)=C(N(C(=O)C4=CC=C(O)C(CC=C(C)C)=C4)[Si](C)(C)C(C)(C)C)C(=O)OC3=C2C)OC1(C)C4914.0Semi standard non polar33892256
Novobiocin,2TBDMS,isomer #5CO[C@@H]1[C@@H](OC(N)=O)[C@@H](O)[C@H](OC2=CC=C3C(O[Si](C)(C)C(C)(C)C)=C(NC(=O)C4=CC=C(O[Si](C)(C)C(C)(C)C)C(CC=C(C)C)=C4)C(=O)OC3=C2C)OC1(C)C5089.2Semi standard non polar33892256
Novobiocin,2TBDMS,isomer #6CO[C@@H]1[C@@H](OC(=O)N[Si](C)(C)C(C)(C)C)[C@@H](O)[C@H](OC2=CC=C3C(O[Si](C)(C)C(C)(C)C)=C(NC(=O)C4=CC=C(O)C(CC=C(C)C)=C4)C(=O)OC3=C2C)OC1(C)C5123.1Semi standard non polar33892256
Novobiocin,2TBDMS,isomer #7CO[C@@H]1[C@@H](OC(N)=O)[C@@H](O)[C@H](OC2=CC=C3C(O[Si](C)(C)C(C)(C)C)=C(N(C(=O)C4=CC=C(O)C(CC=C(C)C)=C4)[Si](C)(C)C(C)(C)C)C(=O)OC3=C2C)OC1(C)C4899.7Semi standard non polar33892256
Novobiocin,2TBDMS,isomer #8CO[C@@H]1[C@@H](OC(=O)N[Si](C)(C)C(C)(C)C)[C@@H](O)[C@H](OC2=CC=C3C(O)=C(NC(=O)C4=CC=C(O[Si](C)(C)C(C)(C)C)C(CC=C(C)C)=C4)C(=O)OC3=C2C)OC1(C)C5125.7Semi standard non polar33892256
Novobiocin,2TBDMS,isomer #9CO[C@@H]1[C@@H](OC(N)=O)[C@@H](O)[C@H](OC2=CC=C3C(O)=C(N(C(=O)C4=CC=C(O[Si](C)(C)C(C)(C)C)C(CC=C(C)C)=C4)[Si](C)(C)C(C)(C)C)C(=O)OC3=C2C)OC1(C)C4919.9Semi standard non polar33892256
Spectra

GC-MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted GC-MSPredicted GC-MS Spectrum - Novobiocin GC-MS (Non-derivatized) - 70eV, Positivesplash10-000i-9501040000-ea711ce6f17080b821c22017-09-01Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Novobiocin GC-MS (1 TMS) - 70eV, Positivesplash10-000i-9531007000-845ccc25b7b9a4ba819d2017-10-06Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Novobiocin GC-MS (TMS_1_2) - 70eV, PositiveNot Available2021-10-16Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Novobiocin GC-MS (TMS_1_3) - 70eV, PositiveNot Available2021-10-16Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Novobiocin GC-MS (TMS_1_4) - 70eV, PositiveNot Available2021-10-16Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Novobiocin GC-MS (TMS_1_5) - 70eV, PositiveNot Available2021-10-16Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Novobiocin GC-MS (TMS_2_1) - 70eV, PositiveNot Available2021-10-16Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Novobiocin GC-MS (TMS_2_2) - 70eV, PositiveNot Available2021-10-16Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Novobiocin GC-MS (TMS_2_3) - 70eV, PositiveNot Available2021-10-16Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Novobiocin GC-MS (TMS_2_4) - 70eV, PositiveNot Available2021-10-16Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Novobiocin GC-MS (TMS_2_5) - 70eV, PositiveNot Available2021-10-16Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Novobiocin GC-MS (TMS_2_6) - 70eV, PositiveNot Available2021-10-16Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Novobiocin GC-MS (TMS_2_7) - 70eV, PositiveNot Available2021-10-16Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Novobiocin GC-MS (TMS_2_8) - 70eV, PositiveNot Available2021-10-16Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Novobiocin GC-MS (TMS_2_9) - 70eV, PositiveNot Available2021-10-16Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Novobiocin GC-MS (TMS_2_10) - 70eV, PositiveNot Available2021-10-16Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Novobiocin GC-MS (TMS_2_11) - 70eV, PositiveNot Available2021-10-16Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Novobiocin GC-MS (TMS_3_1) - 70eV, PositiveNot Available2021-10-16Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Novobiocin GC-MS (TMS_3_2) - 70eV, PositiveNot Available2021-10-16Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Novobiocin GC-MS (TMS_3_3) - 70eV, PositiveNot Available2021-10-16Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Novobiocin GC-MS (TMS_3_4) - 70eV, PositiveNot Available2021-10-16Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Novobiocin GC-MS (TMS_3_5) - 70eV, PositiveNot Available2021-10-16Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Novobiocin GC-MS (TMS_3_6) - 70eV, PositiveNot Available2021-10-16Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Novobiocin GC-MS (TMS_3_7) - 70eV, PositiveNot Available2021-10-16Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Novobiocin GC-MS (TMS_3_8) - 70eV, PositiveNot Available2021-10-16Wishart LabView Spectrum

MS/MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Experimental LC-MS/MSLC-MS/MS Spectrum - Novobiocin LC-ESI-QTOF , negative-QTOFsplash10-03di-0000009000-b1cde524a6fa9a8469fb2017-09-14HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Novobiocin LC-ESI-QTOF , negative-QTOFsplash10-03di-0000449000-4b6598caa7dcff199d3c2017-09-14HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Novobiocin LC-ESI-QTOF , negative-QTOFsplash10-0230-0005904000-5fe18777e8a9abd4250a2017-09-14HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Novobiocin LC-ESI-QTOF , negative-QTOFsplash10-0a59-0096200000-4ea433cdc759c03b554d2017-09-14HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Novobiocin LC-ESI-QTOF , negative-QTOFsplash10-0a4i-0091000000-912d33bd49e7c2686b5b2017-09-14HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Novobiocin LC-ESI-QTOF , positive-QTOFsplash10-03di-0141009000-46efbf9ab2bd123e33292017-09-14HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Novobiocin LC-ESI-QTOF , positive-QTOFsplash10-000i-0900000000-e321cd21925818d2156a2017-09-14HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Novobiocin LC-ESI-QTOF , positive-QTOFsplash10-000i-0900000000-6425ec6e8bbb44075cf42017-09-14HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Novobiocin LC-ESI-QTOF , positive-QTOFsplash10-000i-0900000000-32fb8ff4ec7fde30b5132017-09-14HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Novobiocin LC-ESI-QTOF , positive-QTOFsplash10-000i-0900000000-004f89ab3d920e8c59362017-09-14HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Novobiocin LC-ESI-QTOF , positive-QTOFsplash10-000j-0933000000-cd71bb412108d603ba2d2017-09-14HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Novobiocin 50V, Negative-QTOFsplash10-0a4i-0091000000-912d33bd49e7c2686b5b2021-09-20HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Novobiocin 40V, Negative-QTOFsplash10-0a59-0096200000-4ea433cdc759c03b554d2021-09-20HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Novobiocin 40V, Positive-QTOFsplash10-0a59-0096200000-11dbab50d0282c78d5d32021-09-20HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Novobiocin 50V, Positive-QTOFsplash10-000i-0900000000-7e8f1b6857305a58cdd62021-09-20HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Novobiocin -1V, Positive-QTOFsplash10-000i-0900000000-fa445cda52f068430dd92021-09-20HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Novobiocin 40V, Positive-QTOFsplash10-000i-0900000000-659dbda5f820b7b4b5a92021-09-20HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Novobiocin 10V, Positive-QTOFsplash10-03di-0141009000-46efbf9ab2bd123e33292021-09-20HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Novobiocin 30V, Positive-QTOFsplash10-000i-0900000000-ba6e55c3d22bd781820c2021-09-20HMDB team, MONAView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Novobiocin 10V, Positive-QTOFsplash10-01ot-2319062000-88f8c273adda497b18db2016-06-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Novobiocin 20V, Positive-QTOFsplash10-000j-1619010000-8f36ccee24f46649d2fa2016-06-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Novobiocin 40V, Positive-QTOFsplash10-029i-4902000000-251ff87ab1779a3c93ee2016-06-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Novobiocin 10V, Negative-QTOFsplash10-0006-8092031000-b1e5ad67b96535763fdf2016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Novobiocin 20V, Negative-QTOFsplash10-0006-9003030000-1010bbb42c15ce8156a52016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Novobiocin 40V, Negative-QTOFsplash10-0006-9322000000-7884d3b71b2733b2e74f2016-08-03Wishart 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 DB01051 details
UrineExpected but not QuantifiedNot QuantifiedNot AvailableNot AvailableTaking drug identified by DrugBank entry DB01051 details
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDDB01051
Phenol Explorer Compound IDNot Available
FooDB IDNot Available
KNApSAcK IDC00002487
Chemspider ID10226117
KEGG Compound IDC05080
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNovobiocin
METLIN IDNot Available
PubChem Compound54675769
PDB IDNOV
ChEBI ID28368
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. DAVID NA, BURGNER PR: Clinical effectiveness and safety of novobiocin. Antibiotic Med Clin Ther (New York). 1956 Apr;2(4):219-29. [PubMed:13303117 ]
  2. CORBIN EE, PRIGOT A: Novobiocin; absorption, diffusion, and excretion studies. Antibiot Annu. 1956-1957:392-5. [PubMed:13425410 ]
  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:15811527 ]
  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:17132020 ]
  5. Vickers AA, Chopra I, O'Neill AJ: Intrinsic novobiocin resistance in Staphylococcus saprophyticus. Antimicrob Agents Chemother. 2007 Dec;51(12):4484-5. Epub 2007 Sep 17. [PubMed:17876001 ]

Transporters

General function:
Involved in ATP binding
Specific function:
Involved in the ATP-dependent secretion of bile salts into the canaliculus of hepatocytes
Gene Name:
ABCB11
Uniprot ID:
O95342
Molecular weight:
146405.8
References
  1. Saito H, Osumi M, Hirano H, Shin W, Nakamura R, Ishikawa T: Technical pitfalls and improvements for high-speed screening and QSAR analysis to predict inhibitors of the human bile salt export pump (ABCB11/BSEP). AAPS J. 2009 Sep;11(3):581-9. doi: 10.1208/s12248-009-9137-9. Epub 2009 Aug 18. [PubMed:19688600 ]
General function:
Involved in ATP binding
Specific function:
Xenobiotic transporter that may play an important role in the exclusion of xenobiotics from the brain. May be involved in brain-to-blood efflux. Appears to play a major role in the multidrug resistance phenotype of several cancer cell lines. When overexpressed, the transfected cells become resistant to mitoxantrone, daunorubicin and doxorubicin, display diminished intracellular accumulation of daunorubicin, and manifest an ATP- dependent increase in the efflux of rhodamine 123
Gene Name:
ABCG2
Uniprot ID:
Q9UNQ0
Molecular weight:
72313.5
References
  1. Gedeon C, Behravan J, Koren G, Piquette-Miller M: Transport of glyburide by placental ABC transporters: implications in fetal drug exposure. Placenta. 2006 Nov-Dec;27(11-12):1096-102. Epub 2006 Feb 3. [PubMed:16460798 ]
  2. Shiozawa K, Oka M, Soda H, Yoshikawa M, Ikegami Y, Tsurutani J, Nakatomi K, Nakamura Y, Doi S, Kitazaki T, Mizuta Y, Murase K, Yoshida H, Ross DD, Kohno S: Reversal of breast cancer resistance protein (BCRP/ABCG2)-mediated drug resistance by novobiocin, a coumermycin antibiotic. Int J Cancer. 2004 Jan 1;108(1):146-51. [PubMed:14618629 ]
  3. Elahian F, Kalalinia F, Behravan J: Evaluation of indomethacin and dexamethasone effects on BCRP-mediated drug resistance in MCF-7 parental and resistant cell lines. Drug Chem Toxicol. 2010 Apr;33(2):113-9. doi: 10.3109/01480540903390000. [PubMed:20307139 ]
General function:
Involved in transporter activity
Specific function:
Mediates saturable uptake of estrone sulfate, dehydroepiandrosterone sulfate and related compounds
Gene Name:
SLC22A11
Uniprot ID:
Q9NSA0
Molecular weight:
59970.9
References
  1. Duan P, You G: Novobiocin is a potent inhibitor for human organic anion transporters. Drug Metab Dispos. 2009 Jun;37(6):1203-10. doi: 10.1124/dmd.109.026880. Epub 2009 Mar 12. [PubMed:19282394 ]
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. Duan P, You G: Novobiocin is a potent inhibitor for human organic anion transporters. Drug Metab Dispos. 2009 Jun;37(6):1203-10. doi: 10.1124/dmd.109.026880. Epub 2009 Mar 12. [PubMed:19282394 ]