ContaminantDB: Novobiocin

Identification Taxonomy Biological Properties Physical Properties Toxicity Profile Spectra Concentrations Links References XML

Record Information

Version

1.0

Creation Date

2016-05-25 18:24:33 UTC

Update Date

2016-11-09 01:17:27 UTC

Accession Number

CHEM022222

Identification

Common Name

Novobiocin

Class

Small Molecule

Description

Novobiocin 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)

Contaminant Sources

HMDB Contaminants - Urine
STOFF IDENT Compounds

Contaminant Type

Not Available

Chemical Structure

MOL SDF 3D-SDF PDB SMILES InChI View 3D Structure

Synonyms

Value	Source
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)benzamide	ChEBI
Novobiocina	ChEBI
Novobiocine	ChEBI
Novobiocinum	ChEBI
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)benzamide	Generator
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)benzamide	Generator
Antibiotic pa-93	HMDB
Crystallinic acid	HMDB
NOV	HMDB
Sodium, novobiocin	HMDB
Streptonivicin	HMDB
Calcium, novobiocin	HMDB
Monosodium salt novobiocin	HMDB
Novobiocin, monosodium salt	HMDB
Novobiocin calcium	HMDB
Novobiocin sodium	HMDB

Chemical Formula

C₃₁H₃₆N₂O₁₁

Average Molecular Mass

612.624 g/mol

Monoisotopic Mass

612.232 g/mol

CAS Registry Number

303-81-1

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 Name

novobiocin

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 Key

YJQPYGGHQPGBLI-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.

Kingdom

Organic compounds

Super Class

Phenylpropanoids and polyketides

Class

Coumarins and derivatives

Sub Class

Coumarin glycosides

Direct Parent

Coumarin 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 Framework

Aromatic heteropolycyclic compounds

External Descriptors

monocarboxylic acid amide (CHEBI:28368 )
monosaccharide derivative (CHEBI:28368 )
hexoside (CHEBI:28368 )
hydroxycoumarin (CHEBI:28368 )
Aromatic compounds (C05080 )

Biological Properties

Status

Detected and Not Quantified

Origin

Not Available

Cellular Locations

Not Available

Biofluid Locations

Not Available

Tissue Locations

Not Available

Pathways

Not Available

Applications

Not Available

Biological Roles

Not Available

Chemical Roles

Not Available

Physical Properties

State

Not Available

Appearance

Not Available

Experimental Properties

Property	Value
Melting Point	Not Available
Boiling Point	Not Available
Solubility	Not Available

Predicted Properties

Property	Value	Source
Water Solubility	0.0097 g/L	ALOGPS
logP	3.07	ALOGPS
logP	3.26	ChemAxon
logS	-4.8	ALOGPS
pKa (Strongest Acidic)	6.96	ChemAxon
pKa (Strongest Basic)	-3.9	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	9	ChemAxon
Hydrogen Donor Count	5	ChemAxon
Polar Surface Area	196.1 Å²	ChemAxon
Rotatable Bond Count	9	ChemAxon
Refractivity	158.24 m³·mol⁻¹	ChemAxon
Polarizability	63.97 Å³	ChemAxon
Number of Rings	4	ChemAxon
Bioavailability	1	ChemAxon
Rule of Five	No	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	Yes	ChemAxon

Spectra

Spectrum Type	Description	Splash Key	View
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	splash10-000i-9501040000-ea711ce6f17080b821c2	Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (1 TMS) - 70eV, Positive	splash10-000i-9531007000-845ccc25b7b9a4ba819d	Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_1_2) - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_1_3) - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_1_4) - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_1_5) - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_1) - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_2) - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_3) - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_4) - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_5) - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_6) - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_7) - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_8) - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_9) - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_10) - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_11) - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_3_1) - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_3_2) - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_3_3) - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_3_4) - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_3_5) - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_3_6) - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_3_7) - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_3_8) - 70eV, Positive	Not Available	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QTOF , negative	splash10-03di-0000009000-b1cde524a6fa9a8469fb	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QTOF , negative	splash10-03di-0000449000-4b6598caa7dcff199d3c	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QTOF , negative	splash10-0230-0005904000-5fe18777e8a9abd4250a	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QTOF , negative	splash10-0a59-0096200000-4ea433cdc759c03b554d	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QTOF , negative	splash10-0a4i-0091000000-912d33bd49e7c2686b5b	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QTOF , positive	splash10-03di-0141009000-46efbf9ab2bd123e3329	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QTOF , positive	splash10-000i-0900000000-e321cd21925818d2156a	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QTOF , positive	splash10-000i-0900000000-6425ec6e8bbb44075cf4	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QTOF , positive	splash10-000i-0900000000-32fb8ff4ec7fde30b513	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QTOF , positive	splash10-000i-0900000000-004f89ab3d920e8c5936	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QTOF , positive	splash10-000j-0933000000-cd71bb412108d603ba2d	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - 50V, Negative	splash10-0a4i-0091000000-912d33bd49e7c2686b5b	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - 40V, Negative	splash10-0a59-0096200000-4ea433cdc759c03b554d	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - 40V, Positive	splash10-0a59-0096200000-11dbab50d0282c78d5d3	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - 50V, Positive	splash10-000i-0900000000-7e8f1b6857305a58cdd6	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - -1V, Positive	splash10-000i-0900000000-fa445cda52f068430dd9	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - 40V, Positive	splash10-000i-0900000000-659dbda5f820b7b4b5a9	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - 10V, Positive	splash10-03di-0141009000-46efbf9ab2bd123e3329	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - 30V, Positive	splash10-000i-0900000000-ba6e55c3d22bd781820c	Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-01ot-2319062000-88f8c273adda497b18db	Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-000j-1619010000-8f36ccee24f46649d2fa	Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-029i-4902000000-251ff87ab1779a3c93ee	Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-0006-8092031000-b1e5ad67b96535763fdf	Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-0006-9003030000-1010bbb42c15ce8156a5	Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-0006-9322000000-7884d3b71b2733b2e74f	Spectrum