Novobiocin

A summary of the most common chemical descriptors (InChI Key and SMILES codes) for Novobiocin are summarized together with 3D and 2D structures and relevant physico-chemical properties.

What is the Novobiocin?

The molecule Novobiocin presents a molecular formula of C31H36N2O11 and its IUPAC name is [(3R,4S,5R,6R)-5-hydroxy-6-[4-hydroxy-3-[[4-hydroxy-3-(3-methylbut-2-enyl)benzoyl]amino]-8-methyl-2-oxochromen-7-yl]oxy-3-methoxy-2,2-dimethyloxan-4-yl] carbamate.

Novobiocin is a naphthoquinone antibiotic produced by Streptomyces niveus. It was first isolated in 1953 by W.C. Rose and E.L. Tatum. Novobiocin inhibits bacterial DNA gyrase, an enzyme that is essential for the replication, transcription, and repair of double-stranded DNA. Novobiocin is active against a wide range of Gram-positive and Gram-negative bacteria, with the exception of Pseudomonas aeruginosa. Novobiocin is used clinically to treat infections caused by susceptible bacteria, such as staphylococcal infections. It is also used to treat MRSA infections..

3D structure

Cartesian coordinates

Geometry of Novobiocin in x, y and z coordinates (Å units) to copy/paste elsewhere. Generated with Open Babel software.

2D drawing

 

Novobiocin YJQPYGGHQPGBLI-KGSXXDOSSA-N chemical compound 2D structure molecule svg
Novobiocin

 

Molecule descriptors

 
IUPAC name[(3R,4S,5R,6R)-5-hydroxy-6-[4-hydroxy-3-[[4-hydroxy-3-(3-methylbut-2-enyl)benzoyl]amino]-8-methyl-2-oxochromen-7-yl]oxy-3-methoxy-2,2-dimethyloxan-4-yl] carbamate
InChI codeInChI=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
SMILESCO[C@@H]1[C@@H](OC(N)=O)[C@@H](O)[C@H](Oc2ccc3c(O)c(NC(=O)c4ccc(O)c(CC=C(C)C)c4)c(=O)oc3c2C)OC1(C)C

Other names (synonyms)

IUPAC nomenclature provides a standardized method for naming chemical compounds. Although this system is widely used in chemistry, many chemical compounds have also other names commonly used in different contexts. These synonyms can come from a variety of sources and are used for a variety of purposes.

One common source of synonyms for chemical compounds is the common or trivial names, assigned on the basis of appearance, properties, or origin of the molecule.

Another source of synonyms are historical or obsolete names employed in the past, however replaced nowadays by more modern or standardized names.

In addition to common and historical names, chemical compounds may also have synonyms that are specific to a particular field or industry.

  • (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-dimethyltetrahydro-2H-pyran-4-yl carbamate
  • (3R,4S,5R,6R)-5-hydroxy-6-(4-hydroxy-3-(4-hydroxy-3-(3-methylbut-2-enyl)benzamido)-2-oxo-2H-chromen-7-yloxy)-3-methoxy-2,2-dimethyl-tetrahydro-2H-pyran-4-yl carbamate
  • (3R,4S,5R,6R)-5-hydroxy-6-(4-hydroxy-3-(4-hydroxy-3-(3-methylbut-2-enyl)benzamido)-8-methyl-2-oxo-2H-chromen-7-yloxy)-3-methoxy-2,2-dimethyl-tetrahydro-2H-pyran-4-yl carbamate
  • (3R,4S,5R,6R)-5-hydroxy-6-(4-hydroxy-3-(4-hydroxy-3-(3-methylbut-2-enyl)benzamido)-8-methyl-2-oxo-2H-chromen-7-yloxy)-3-methoxy-2,2-dimethyltetrahydro-2H-pyran-4-yl carbamate
  • (3R,4S,5R,6R)-5-hydroxy-6-[(2-hydroxy-3-{[4-hydroxy-3-(3-methylbut-2-en-1-yl)benzene]amido}-8-methyl-4-oxo-4H-chromen-7-yl)oxy]-3-methoxy-2,2-dimethyloxan-4-yl carbamate
  • (3R,4S,5R,6R)-5-hydroxy-6-[(4-hydroxy-3-{[4-hydroxy-3-(3-methylbut-2-en-1-yl)benzene]amido}-8-methyl-2-oxo-2H-chromen-7-yl)oxy]-3-methoxy-2,2-dimethyloxan-4-yl carbamate
  • (3R,4S,5R,6R)-5-hydroxy-6-{[4-hydroxy-3-({[4-hydroxy-3-(3-methylbut-2-en-1-yl)phenyl]carbonyl}amino)-8-methyl-2-oxo-2H-chromen-7-yl]oxy}-3-methoxy-2,2-dimethyltetrahydro-2H-pyran-4-yl carbamate
  • 1476-53-5
  • 17EC19951N
  • 1aj6
  • 303-81-1
  • 4urn
  • 4uro
  • 7-(3-(O-Carbamoyl)-4-(O-methyl)-5,5-dimethyl-alpha-L-lyxopyranosyloxy)-4-hydroxy-3-(4-hydroxy-3-(3-methyl-2-butenyl)benzamidol)-8-methylcumarin
  • 7-(Carbamoyltetrahydro-3-hydroxy-5-methoxy-6,6-dimethylpyran-2-yloxy)-4-hydroxy-3-(4-hydroxy-3-(3-methylbut-2-enyl)benzamide)-8-methyl-2H-chromen-2-one
  • A-256
  • ACon0_000808
  • ACon1_001693
  • AI3-50148
  • Albamix
  • Albamycin
  • Antibiotic PA-93
  • BDBM282
  • BDBM50226181
  • BENZAMIDE, N-(7-((3-O-(AMINOCARBONYL)-6-DEOXY-5-C-METHYL-4-O-METHYL-.ALPHA.-L-LYXO-HEXOPYRANOSYL)OXY)-4-HYDROXY-8-METHYL-2-OXO-2H-1-BENZOPYRAN-3-YL)-4-HYDROXY-3-(3-METHYL-2-BUTEN-1-YL)-
  • BENZAMIDE, N-(7-((3-O-(AMINOCARBONYL)-6-DEOXY-5-C-METHYL-4-O-METHYL-.BETA.-L-LYXO-HEXOPYRANOSYL)OXY)-4-HYDROXY-8-METHYL-2-OXO-2H-1-BENZOPYRAN-3-YL)-4-HYDROXY-3-(3-METHYL-2-BUTENYL)-
  • BSPBio_002115
  • Benzamide, N-(7-((3-O-(aminocarbonyl)-6-deoxy-5-C-methyl-4-O-methyl-beta-L-lyxo-hexopyranosyl)oxy)-4-hydroxy-8-methyl-2-oxo-2H-1-benzopyran-3-yl)-4-hydroxy-3-(3-methyl-2-butenyl)-
  • C05080
  • C31H36N2O11
  • CS-0082991
  • Carbamic acid (3R,4S,5R,6R)-5-hydroxy-6-{4-hydroxy-3-[4-hydroxy-3-(3-methyl-but-2-enyl)-benzoylamino]-8-methyl-2-oxo-2H-chromen-7-yloxy}-3-methoxy-2,2-dimethyl-tetrahydro-pyran-4-yl ester
  • Carbamic acid (3R,4S,5R,6R)-5-hydroxy-6-{4-hydroxy-3-[4-hydroxy-3-(4-methyl-pent-3-enyl)-benzoylamino]-8-methyl-2-oxo-2H-chromen-7-yloxy}-3-methoxy-2,2-dimethyl-tetrahydro-pyran-4-yl ester
  • Carbamic acid 5-hydroxy-6-{4-hydroxy-3-[4-hydroxy-3-(3-methyl-but-2-enyl)-benzoylamino]-8-methyl-2-oxo-2H-chromen-7-yloxy}-3-methoxy-2,2-dimethyl-tetrahydro-pyran-4-yl ester
  • Carbamic acid 5-hydroxy-6-{4-hydroxy-3-[4-hydroxy-3-(3-methyl-but-2-enyl)-benzoylamino]-8-methyl-2-oxo-2H-chromen-7-yloxy}-3-methoxy-2,2-dimethyl-tetrahydro-pyran-4-yl ester(Novobiocin)
  • Cardelmycin
  • Cathocin
  • Cathomycin
  • Coumarin, 7-(4-(carbamoyloxy)tetrahydro-3-hydroxy-5-methoxy-6,6-dimethylpyran-2-yloxy)-4-hydroxy-3-(4-hydroxy-3-(4-hydroxy-3-(3-methyl-2-butenyl)benzamido)-8-methyl-
  • Crystallinic acid
  • DB01051
  • DivK1c_000260
  • GTPL12021
  • HSDB 7443
  • HY-B0425
  • IDI1_000260
  • Inamycin
  • KBio1_000260
  • KBio2_001481
  • KBio2_002402
  • KBio2_004049
  • KBio2_004970
  • KBio2_006617
  • KBio2_007538
  • KBio3_001615
  • KBio3_002881
  • KBioGR_000874
  • KBioGR_002402
  • KBioSS_001481
  • KBioSS_002407
  • MEGxm0_000273
  • MLS001032086
  • N-[7-[[3-O-(Aminocarbonyl)-6-deoxy-5-C-methyl-4-O-methyl-.beta.-L-lyxo-hexopyranosyl]oxy]-4-hydroxy-8-methyl-2-oxo-2H-1-benzopyran-3-yl]-4-hydroxy-3-(3-methyl-2-butenyl)
  • 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
  • NCGC00188981-01
  • NINDS_000260
  • NOV
  • Novo-R
  • Novobiocin
  • Novobiocin, Antibiotic for Culture Media Use Only
  • Novobiocina
  • Novobiocine
  • Novobiocinum
  • PA 93
  • Q1639291
  • Robiocina
  • SMR000718617
  • STL564718
  • Sirbiocina
  • Spheromycin
  • Stilbiocina
  • Streptonivicin
  • Streptonivicin (*Sodium salt*)
  • U-6391
  • W-204218
  • [(3R,4S,5R,6R)-5-hydroxy-6-[4-hydroxy-3-[[4-hydroxy-3-(3-methylbut-2-enyl)benzoyl]amino]-8-methyl-2-oxo-chromen-7-yl]oxy-3-methoxy-2,2-dimethyl-tetrahydropyran-4-yl] carbamate
  • [(3R,4S,5R,6R)-5-hydroxy-6-[4-hydroxy-3-[[4-hydroxy-3-(3-methylbut-2-enyl)benzoyl]amino]-8-methyl-2-oxochromen-7-yl]oxy-3-methoxy-2,2-dimethyloxan-4-yl] carbamate
  • cMAP_000043
  • novobiocin

Reference codes for other databases

There exist several different chemical codes commonly used in orded to identify molecules:
  • ZINC14879999
  • UNII-17EC19951N
  • AKOS027295139
  • BRD-K85307935-236-02-0
  • DTXSID3041083
  • CHEMBL36506
  • CHEBI:28368
  • EINECS 206-146-3
  • SPBio_001013
  • SCHEMBL24805
  • SCHEMBL238345
  • Spectrum_001001
  • Spectrum2_000977
  • Spectrum3_000528
  • Spectrum4_000457
  • Spectrum5_001274

Physico-Chemical properties

IUPAC name[(3R,4S,5R,6R)-5-hydroxy-6-[4-hydroxy-3-[[4-hydroxy-3-(3-methylbut-2-enyl)benzoyl]amino]-8-methyl-2-oxochromen-7-yl]oxy-3-methoxy-2,2-dimethyloxan-4-yl] carbamate
Molecular formulaC31H36N2O11
Molecular weight612.624
Melting point (ºC)
Boiling point (ºC)
Density (g/cm3)
Molar refractivity160.02
LogP4.4
Topological polar surface area200.0

LogP and topological polar surface area (TPSA) values were estimated using Open Babel software.

The n-octanol/water partition coeficient (Kow) data is applied in toxicology and drug research. Kow values are used, to guess the environmental fate of persistent organic pollutants. High partition coefficients values, tend to accumulate in the fatty tissue of organisms. Molecules with a log(Kow) (or LogP) greater than 5 are considered to bioaccumulate.

TPSA values are the sum of the surface area over all polar atoms or molecules, mainly oxygen and nitrogen, also including hydrogen atoms.

In medicinal chemistry, TPSA is used to assess the ability of a drug to permeabilise cells.

For molecules to penetrate the blood-brain barrier (and act on receptors in the central nervous system), TPSA values below 90 Å2 are required. Thus, molecules with a polar surface area greater than 140 Å2 tend to be poorly permeable to cell membranes.