Novobiocin (CED0003004)

Record Information

Version

1.0

Creation Date

2016-05-25 18:24:33 UTC

Update Date

2026-08-22 10:37:11 UTC

Accession Number

CHEM022222

Identification

Common Name

Novobiocin

Class

Small Molecule

Description

Novobiocin is a chemical compound with the molecular formula C31H36N2O11. Novobiocin belongs to the coumarin glycosides, a subclass of coumarins and derivatives within the organic compounds. With an average molecular weight of 612.62 g/mol, Novobiocin is a heavy molecule. This substance is categorized under the superclass of phenylpropanoids and polyketides. The compound is found in or released from two recorded sources: healthcare, pharmaceuticals & veterinary products (specifically antibiotics), and food, food processing & cookware (specifically agglomerated sugar products). Recorded exposure routes for Novobiocin include inhalation and oral administration. In terms of biological activity, the compound interacts with four recorded protein targets. It functions as an inhibitor of DNA gyrase subunit B (gyrB), DNA topoisomerase 1 (topA), DNA topoisomerase 2-alpha (TOP2A), and DNA topoisomerase 2-beta (TOP2B).

Contaminant Type

Not Available

Chemical Structure

MOL SDF PDB SMILES InChI

Synonyms

Not Available

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

Classification

Not classified

Biological Properties

Status

Detected and Not Quantified

Origin

Not Available

Cellular Locations

Not Available

Biofluid Locations

Not Available

Tissue Locations

Not Available

Applications

Not Available

Biological Roles

Not Available

Chemical Roles

Not Available

Organoleptic Effects

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	Yes	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	Deposition Date	View
Predicted GC-MS	Predicted GC-MS Spectrum	splash10-000i-9501040000-ea711ce6f17080b821c2	Not Available	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum	splash10-000i-9531007000-845ccc25b7b9a4ba819d	Not Available	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum	Not Available	Not Available	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum	Not Available	Not Available	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum	Not Available	Not Available	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum	Not Available	Not Available	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum	Not Available	Not Available	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum	Not Available	Not Available	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum	Not Available	Not Available	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum	Not Available	Not Available	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum	Not Available	Not Available	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum	Not Available	Not Available	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum	Not Available	Not Available	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum	Not Available	Not Available	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum	Not Available	Not Available	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum	Not Available	Not Available	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum	Not Available	Not Available	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum	Not Available	Not Available	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum	Not Available	Not Available	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum	Not Available	Not Available	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum	Not Available	Not Available	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum	Not Available	Not Available	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum	Not Available	Not Available	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum	Not Available	Not Available	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum	Not Available	Not Available	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum	Not Available	Not Available	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum	Not Available	Not Available	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum	Not Available	Not Available	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum	Not Available	Not Available	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum	Not Available	Not Available	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum	Not Available	Not Available	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum	Not Available	Not Available	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum	Not Available	Not Available	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum	Not Available	Not Available	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum	Not Available	Not Available	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum	Not Available	Not Available	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum	Not Available	Not Available	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum	Not Available	Not Available	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum	Not Available	Not Available	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum	Not Available	Not Available	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum	Not Available	Not Available	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum	Not Available	Not Available	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum	Not Available	Not Available	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum	Not Available	Not Available	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum	Not Available	Not Available	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum	Not Available	Not Available	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum	Not Available	Not Available	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum	Not Available	Not Available	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum	splash10-03di-0000009000-b1cde524a6fa9a8469fb	Not Available	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum	splash10-03di-0000449000-4b6598caa7dcff199d3c	Not Available	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum	splash10-0230-0005904000-5fe18777e8a9abd4250a	Not Available	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum	splash10-0a59-0096200000-4ea433cdc759c03b554d	Not Available	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum	splash10-0a4i-0091000000-912d33bd49e7c2686b5b	Not Available	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum	splash10-03di-0141009000-46efbf9ab2bd123e3329	Not Available	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum	splash10-000i-0900000000-e321cd21925818d2156a	Not Available	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum	splash10-000i-0900000000-6425ec6e8bbb44075cf4	Not Available	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum	splash10-000i-0900000000-32fb8ff4ec7fde30b513	Not Available	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum	splash10-000i-0900000000-004f89ab3d920e8c5936	Not Available	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum	splash10-000j-0933000000-cd71bb412108d603ba2d	Not Available	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum	splash10-0a4i-0091000000-912d33bd49e7c2686b5b	Not Available	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum	splash10-0a59-0096200000-4ea433cdc759c03b554d	Not Available	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum	splash10-0a59-0096200000-11dbab50d0282c78d5d3	Not Available	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum	splash10-000i-0900000000-7e8f1b6857305a58cdd6	Not Available	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum	splash10-000i-0900000000-fa445cda52f068430dd9	Not Available	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum	splash10-000i-0900000000-659dbda5f820b7b4b5a9	Not Available	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum	splash10-03di-0141009000-46efbf9ab2bd123e3329	Not Available	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum	splash10-000i-0900000000-ba6e55c3d22bd781820c	Not Available	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum	splash10-03di-0000009000-b1cde524a6fa9a8469fb	Not Available	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum	splash10-000j-0933000000-cd71bb412108d603ba2d	Not Available	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum	splash10-03di-0000449000-4b6598caa7dcff199d3c	Not Available	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum	splash10-0230-0005904000-5fe18777e8a9abd4250a	Not Available	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum	splash10-01ot-2319062000-88f8c273adda497b18db	Not Available	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum	splash10-000j-1619010000-8f36ccee24f46649d2fa	Not Available	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum	splash10-029i-4902000000-251ff87ab1779a3c93ee	Not Available	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum	splash10-0006-8092031000-b1e5ad67b96535763fdf	Not Available	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum	splash10-0006-9003030000-1010bbb42c15ce8156a5	Not Available	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum	splash10-0006-9322000000-7884d3b71b2733b2e74f	Not Available	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum	splash10-03di-0000139000-34cefc73c8b2785442cf	Not Available	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum	splash10-01ox-9102251000-376d3be428a729410374	Not Available	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum	splash10-0006-9314230000-58e008f3358c766f20a4	Not Available	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum	splash10-014s-0965122000-7e93699463a097548260	Not Available	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum	splash10-000g-1709030000-762a038e543d787c308f	Not Available	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum	splash10-000f-5900000000-b7c7ed20246758c4094b	Not Available	View Spectrum

Toxicity Profile

Mechanism of Toxicity

Not Available

Carcinogenicity (IARC Classification)

Not Available

Minimum Risk Level

Not Available

Symptoms

Not Available

Treatment

Not Available

Toxicity Values

Toxicity Value	Unit	Value Range	Organism	Dose Descriptor	Route of Exposure	Predicted or Experimental	Reference
1165.0	Log mg/kg	[660:2100]	Rat	LD50	oral	predicted	Not Available

Health Effects

Health Effect	Relationship	Direction	Reference

Exposure Sources

Source ID	Source	Sector	Reference
306	Antibiotics	Healthcare, pharmaceuticals & veterinary products	Not Available
541	Agglomerated Sugar Products	Food, food processing & cookware	Not Available

Pathways

2 pathways

Novobiocin Drug Metabolism Action Pathway

Novobiocin Predicted Metabolism Pathway

Targets

Structure	Protein	UniProt ID	Organism	Relationship	Details
Click to view 3D structure	DNA gyrase subunit B	P0C559	Mycobacterium smegmatis	Predicted (SEA)	0.0778492
Click to view 3D structure	DNA gyrase subunit B	P0A4L9	Streptococcus pneumoniae serotype 4 (strain ATCC BAA-334 / TIGR4)	Predicted (SEA)	0.0778492
Click to view 3D structure	ParE	Q7X1P7	Streptococcus pneumoniae	Predicted (SEA)	0.0778492
Click to view 3D structure	DNA gyrase subunit B	A0QNE0	Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155)	Predicted (SEA)	0.0778492
Click to view 3D structure	Microtubule-associated protein 1 light chain 3 alpha	Q9H492	Humans	Predicted (SEA)	0.233548
Click to view 3D structure	DNA topoisomerase 4 subunit B	P0C1S7	Staphylococcus aureus	Predicted (SEA)	0.0778492
Click to view 3D structure	DNA gyrase subunit B	P0AES6	Escherichia coli (strain K12)	Predicted (SEA)	1.08989
Click to view 3D structure	DNA gyrase subunit B	P0A0K8	Staphylococcus aureus	Predicted (SEA)	0.0778492
Click to view 3D structure	Probable nicotinate-nucleotide adenylyltransferase	P65502	Staphylococcus aureus (strain N315)	Predicted (SEA)	40.8708
Click to view 3D structure	UDP-glucose 4-epimerase	Q8T8E9	Trypanosoma brucei	Predicted (SEA)	8.09632
Click to view 3D structure	Bis(5'-adenosyl)-triphosphatase	P49789	Humans	Predicted (SEA)	11.8331
Click to view 3D structure	Sialidase	P10481	Clostridium perfringens	Predicted (SEA)	22.8877
Click to view 3D structure	3',5'-cyclic-AMP phosphodiesterase 4D	Q08499	Humans	Predicted (SEA)	841.628
Click to view 3D structure	Streptokinase A	P10520	Streptococcus pyogenes serotype M1	Predicted (SEA)	1864.8
Click to view 3D structure	Tyrosine-protein phosphatase non-receptor type 1	P18031	Humans	Predicted (SEA)	773.043
Click to view 3D structure	Phosphotyrosine protein phosphatase	A0A045ISB3	Mycobacterium tuberculosis	Predicted (SEA)	64.537
Click to view 3D structure	Low molecular weight protein-tyrosine phosphatase A	P9WIA1	Mycobacterium tuberculosis	Predicted (SEA)	71.232
Click to view 3D structure	Phosphodiesterase 4A	O77823	Sus scrofa	Predicted (SEA)	182.167
Click to view 3D structure	Replicative DNA helicase	A0A6L8Q2B7	Bacillus anthracis	Predicted (SEA)	117.786
Click to view 3D structure	Acetylcholinesterase	P22303	Humans	Predicted (SEA)	3161.46
Click to view 3D structure	Urokinase-type plasminogen activator	P00749	Humans	Predicted (SEA)	1518.92
Click to view 3D structure	Chloride anion exchanger	P40879	Humans	Predicted (SEA)	85.7898
Click to view 3D structure	Amine oxidase [flavin-containing] B	P27338	Humans	Predicted (SEA)	2849.44
Click to view 3D structure	Fatty acid synthase	P49327	Humans	Predicted (SEA)	1557.14
Click to view 3D structure	Polyunsaturated fatty acid lipoxygenase ALOX15	P16050	Humans	Predicted (SEA)	306.57