Virginiamycin S1

Identification

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Name
Virginiamycin S1
Accession Number
DB04805
Type
Small Molecule
Groups
Experimental
Description

One of the components of virginiamycin, a cyclic polypeptide antibiotic complex from streptomyces virginiae, s. Loidensis, s. Mitakaensis, s. Pristina-spiralis, s. Ostreogriseus, and others. It is used to treat infections with gram-positive organisms and as a growth promoter in cattle, swine, and poultry.

Structure
Thumb
Synonyms
  • Staphylomycin S
  • Staphylomycin S1
  • Virginiamycin factor S
  • Virginiamycin factor S1
External IDs
Antibiotic 1754Z3B / NSC-177858
Categories
UNII
J91D5GN5AT
CAS number
23152-29-6
Weight
Average: 823.904
Monoisotopic: 823.354090806
Chemical Formula
C43H49N7O10
InChI Key
FEPMHVLSLDOMQC-IYPFLVAKSA-N
InChI
InChI=1S/C43H49N7O10/c1-4-29-40(56)49-21-12-17-30(49)41(57)48(3)32(23-26-13-7-5-8-14-26)42(58)50-22-19-28(51)24-31(50)37(53)47-35(27-15-9-6-10-16-27)43(59)60-25(2)34(38(54)45-29)46-39(55)36-33(52)18-11-20-44-36/h5-11,13-16,18,20,25,29-32,34-35,52H,4,12,17,19,21-24H2,1-3H3,(H,45,54)(H,46,55)(H,47,53)/t25-,29-,30+,31+,32+,34+,35+/m1/s1
IUPAC Name
N-[(3S,6S,12R,15S,16R,19S,22S)-3-benzyl-12-ethyl-4,16-dimethyl-2,5,11,14,18,21,24-heptaoxo-19-phenyl-17-oxa-1,4,10,13,20-pentaazatricyclo[20.4.0.0⁶,¹⁰]hexacosan-15-yl]-3-hydroxypyridine-2-carboxamide
SMILES
[H][C@@]12CCCN1C(=O)[C@@H](CC)NC(=O)[C@@H](NC(=O)C1=NC=CC=C1O)[C@@H](C)OC(=O)[C@@H](NC(=O)[C@]1([H])CC(=O)CCN1C(=O)[C@]([H])(CC1=CC=CC=C1)N(C)C2=O)C1=CC=CC=C1

Pharmacology

Indication
Not Available
Pharmacodynamics
Not Available
Mechanism of action
TargetActionsOrganism
U60S ribosomal protein L37Not AvailableHumans
Absorption
Not Available
Volume of distribution
Not Available
Protein binding
Not Available
Metabolism
Not Available
Route of elimination
Not Available
Half life
Not Available
Clearance
Not Available
Toxicity
Not Available
Affected organisms
  • Humans and other mammals
Pathways
Not Available
Pharmacogenomic Effects/ADRs
Not Available

Interactions

Drug Interactions
Not Available
Food Interactions
Not Available

References

General References
Not Available
External Links
KEGG Compound
C11269
PubChem Compound
5388936
PubChem Substance
46507514
ChemSpider
4534976
ChEBI
46416
ChEMBL
CHEMBL1236684
Wikipedia
Virginiamycin_S1

Clinical Trials

Clinical Trials
Not Available

Pharmacoeconomics

Manufacturers
Not Available
Packagers
Not Available
Dosage forms
Not Available
Prices
Not Available
Patents
Not Available

Properties

State
Solid
Experimental Properties
Not Available
Predicted Properties
PropertyValueSource
Water Solubility0.139 mg/mLALOGPS
logP2.25ALOGPS
logP1.85ChemAxon
logS-3.8ALOGPS
pKa (Strongest Acidic)7.53ChemAxon
pKa (Strongest Basic)1.57ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count10ChemAxon
Hydrogen Donor Count4ChemAxon
Polar Surface Area224.72 Å2ChemAxon
Rotatable Bond Count6ChemAxon
Refractivity213.24 m3·mol-1ChemAxon
Polarizability82.42 Å3ChemAxon
Number of Rings6ChemAxon
Bioavailability0ChemAxon
Rule of FiveNoChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleYesChemAxon
Predicted ADMET features
PropertyValueProbability
Human Intestinal Absorption-0.6797
Blood Brain Barrier-0.9962
Caco-2 permeable-0.733
P-glycoprotein substrateSubstrate0.8305
P-glycoprotein inhibitor INon-inhibitor0.7713
P-glycoprotein inhibitor IINon-inhibitor0.6866
Renal organic cation transporterNon-inhibitor0.8908
CYP450 2C9 substrateNon-substrate0.8155
CYP450 2D6 substrateNon-substrate0.897
CYP450 3A4 substrateSubstrate0.6366
CYP450 1A2 substrateNon-inhibitor0.9179
CYP450 2C9 inhibitorNon-inhibitor0.8335
CYP450 2D6 inhibitorNon-inhibitor0.823
CYP450 2C19 inhibitorNon-inhibitor0.8524
CYP450 3A4 inhibitorNon-inhibitor0.882
CYP450 inhibitory promiscuityLow CYP Inhibitory Promiscuity0.9079
Ames testNon AMES toxic0.8103
CarcinogenicityNon-carcinogens0.8855
BiodegradationNot ready biodegradable0.966
Rat acute toxicity3.0523 LD50, mol/kg Not applicable
hERG inhibition (predictor I)Weak inhibitor0.9287
hERG inhibition (predictor II)Inhibitor0.6534
ADMET data is predicted using admetSAR, a free tool for evaluating chemical ADMET properties. (23092397)

Spectra

Mass Spec (NIST)
Not Available
Spectra
SpectrumSpectrum TypeSplash Key
Predicted MS/MS Spectrum - 10V, Positive (Annotated)Predicted LC-MS/MSNot Available
Predicted MS/MS Spectrum - 20V, Positive (Annotated)Predicted LC-MS/MSNot Available
Predicted MS/MS Spectrum - 40V, Positive (Annotated)Predicted LC-MS/MSNot Available
Predicted MS/MS Spectrum - 10V, Negative (Annotated)Predicted LC-MS/MSNot Available
Predicted MS/MS Spectrum - 20V, Negative (Annotated)Predicted LC-MS/MSNot Available
Predicted MS/MS Spectrum - 40V, Negative (Annotated)Predicted LC-MS/MSNot Available

Taxonomy

Description
This compound belongs to the class of organic compounds known as cyclic depsipeptides. These are natural or synthetic compounds having sequences of amino and hydroxy carboxylic acid residues (usually α-amino and α-hydroxy acids) connected in a ring. The residues are commonly but not necessarily regularly alternating.
Kingdom
Organic compounds
Super Class
Organic acids and derivatives
Class
Peptidomimetics
Sub Class
Depsipeptides
Direct Parent
Cyclic depsipeptides
Alternative Parents
Macrolide lactams / Alpha amino acid esters / Macrolactams / N-acyl-alpha amino acids and derivatives / Pyridinecarboxamides / 2-heteroaryl carboxamides / Hydroxypyridines / Piperidinones / Benzene and substituted derivatives / Vinylogous acids
show 15 more
Substituents
Cyclic depsipeptide / Macrolide lactam / Alpha-amino acid ester / Macrolactam / N-acyl-alpha amino acid or derivatives / Alpha-amino acid or derivatives / Pyridine carboxylic acid or derivatives / Pyridinecarboxamide / 2-heteroaryl carboxamide / Hydroxypyridine
show 30 more
Molecular Framework
Aromatic heteropolycyclic compounds
External Descriptors
macrolide antibiotic, cyclodepsipeptide (CHEBI:46416)

Targets

Kind
Protein
Organism
Humans
Pharmacological action
Unknown
General Function
Structural constituent of ribosome
Specific Function
Binds to the 23S rRNA.
Gene Name
RPL37
Uniprot ID
P61927
Uniprot Name
60S ribosomal protein L37
Molecular Weight
11077.81 Da
References
  1. Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, Shindyalov IN, Bourne PE: The Protein Data Bank. Nucleic Acids Res. 2000 Jan 1;28(1):235-42. [PubMed:10592235]

Drug created on September 11, 2007 11:49 / Updated on June 04, 2019 06:11