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Record Information
Version1.0
Created at2020-12-09 03:03:42 UTC
Updated at2021-07-15 16:53:27 UTC
NP-MRD IDNP0005958
Secondary Accession NumbersNone
Natural Product Identification
Common Name(-)-Caprazamycin F
Provided ByNPAtlasNPAtlas Logo
Description(-)-Caprazamycin F belongs to the class of organic compounds known as dipeptides. These are organic compounds containing a sequence of exactly two alpha-amino acids joined by a peptide bond. (-)-Caprazamycin F is found in Streptomyces sp. It was first documented in 2005 (PMID: 16060385). Based on a literature review very few articles have been published on (-)-Caprazamycin F (PMID: 34383398) (PMID: 34383397) (PMID: 34383396) (PMID: 34384147).
Structure
Thumb
Synonyms
ValueSource
(2S,5S,6S)-2-({[(2S,3R,4S,5R)-5-(aminomethyl)-3,4-dihydroxyoxolan-2-yl]oxy}[(2S,3S,4R,5R)-3,4-dihydroxy-5-(4-hydroxy-2-oxo-1,2-dihydropyrimidin-1-yl)oxolan-2-yl]methyl)-1,4-dimethyl-6-{[(3S)-12-methyl-3-{[(3S)-3-methyl-5-oxo-5-{[(2S,3R,4R,5R,6R)-3,4,5-trimethoxy-6-methyloxan-2-yl]oxy}pentanoyl]oxy}tridecanoyl]oxy}-3-oxo-1,4-diazepane-5-carboxylateGenerator
Chemical FormulaC51H83N5O22
Average Mass1118.2380 Da
Monoisotopic Mass1117.55297 Da
IUPAC Name(2S,5S,6S)-2-[(S)-{[(2S,3R,4S,5R)-5-(aminomethyl)-3,4-dihydroxyoxolan-2-yl]oxy}[(2S,3S,4R,5R)-5-(2,4-dioxo-1,2,3,4-tetrahydropyrimidin-1-yl)-3,4-dihydroxyoxolan-2-yl]methyl]-1,4-dimethyl-6-{[(3S)-12-methyl-3-{[(3S)-3-methyl-5-oxo-5-{[(2S,3R,4R,5R,6R)-3,4,5-trimethoxy-6-methyloxan-2-yl]oxy}pentanoyl]oxy}tridecanoyl]oxy}-3-oxo-1,4-diazepane-5-carboxylic acid
Traditional Name(2S,5S,6S)-2-[(S)-{[(2S,3R,4S,5R)-5-(aminomethyl)-3,4-dihydroxyoxolan-2-yl]oxy}[(2S,3S,4R,5R)-5-(2,4-dioxo-3H-pyrimidin-1-yl)-3,4-dihydroxyoxolan-2-yl]methyl]-1,4-dimethyl-6-{[(3S)-12-methyl-3-{[(3S)-3-methyl-5-oxo-5-{[(2S,3R,4R,5R,6R)-3,4,5-trimethoxy-6-methyloxan-2-yl]oxy}pentanoyl]oxy}tridecanoyl]oxy}-3-oxo-1,4-diazepane-5-carboxylic acid
CAS Registry NumberNot Available
SMILES
CO[C@@H]1[C@@H](C)O[C@@H](OC(=O)C[C@@H](C)CC(=O)O[C@@H](CCCCCCCCC(C)C)CC(=O)O[C@H]2CN(C)[C@@H](C(O[C@@H]3O[C@H](CN)[C@@H](O)[C@H]3O)[C@H]3O[C@H]([C@H](O)[C@@H]3O)N3C=CC(=O)NC3=O)C(=O)N(C)[C@@H]2C(O)=O)[C@H](OC)[C@@H]1OC
InChI Identifier
InChI=1S/C51H83N5O22/c1-25(2)16-14-12-10-11-13-15-17-28(73-32(58)20-26(3)21-33(59)76-50-45(71-9)44(70-8)41(69-7)27(4)72-50)22-34(60)74-30-24-54(5)36(46(65)55(6)35(30)48(66)67)42(78-49-40(64)37(61)29(23-52)75-49)43-38(62)39(63)47(77-43)56-19-18-31(57)53-51(56)68/h18-19,25-30,35-45,47,49-50,61-64H,10-17,20-24,52H2,1-9H3,(H,66,67)(H,53,57,68)/t26-,27+,28-,29+,30-,35-,36-,37+,38-,39+,40+,41+,42?,43-,44+,45+,47+,49-,50-/m0/s1
InChI KeyPKWIDCLNQMPNGI-PVRDQFSGSA-N
Experimental Spectra
Not Available
Predicted Spectra
Spectrum TypeDescriptionDepositor IDDepositor OrganizationDepositorDeposition DateView
1D NMR13C NMR Spectrum (1D, 25 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 100 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 252 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 1000 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 50 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 200 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 75 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 300 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 101 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 400 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 126 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 500 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 151 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 600 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 176 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 700 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 201 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 800 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 226 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 900 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
Chemical Shift Submissions
Not Available
Species
Species of Origin
Species NameSourceReference
Streptomyces sp.NPAtlas
Chemical Taxonomy
Description Belongs to the class of organic compounds known as dipeptides. These are organic compounds containing a sequence of exactly two alpha-amino acids joined by a peptide bond.
KingdomOrganic compounds
Super ClassOrganic acids and derivatives
ClassCarboxylic acids and derivatives
Sub ClassAmino acids, peptides, and analogues
Direct ParentDipeptides
Alternative Parents
Substituents
  • Alpha-dipeptide
  • Tetracarboxylic acid or derivatives
  • Disaccharide
  • Glycosyl compound
  • N-glycosyl compound
  • O-glycosyl compound
  • Alpha-amino acid or derivatives
  • 1,4-diazepane
  • Diazepane
  • Fatty acid ester
  • Pyrimidone
  • Hydropyrimidine
  • Oxane
  • Pyrimidine
  • Fatty acyl
  • Tetrahydrofuran
  • Vinylogous amide
  • Tertiary carboxylic acid amide
  • Heteroaromatic compound
  • Tertiary amine
  • Secondary alcohol
  • Urea
  • Tertiary aliphatic amine
  • Amino acid or derivatives
  • Carboxamide group
  • Carboxylic acid ester
  • Amino acid
  • Lactam
  • Organoheterocyclic compound
  • Azacycle
  • Acetal
  • Carboxylic acid
  • Dialkyl ether
  • Ether
  • Oxacycle
  • Organopnictogen compound
  • Amine
  • Alcohol
  • Organooxygen compound
  • Organic oxygen compound
  • Carbonyl group
  • Organic oxide
  • Primary amine
  • Organonitrogen compound
  • Hydrocarbon derivative
  • Organic nitrogen compound
  • Primary aliphatic amine
  • Aromatic heteromonocyclic compound
Molecular FrameworkAromatic heteromonocyclic compounds
External DescriptorsNot Available
Physical Properties
StateNot Available
Experimental Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Predicted Properties
PropertyValueSource
logP0.55ALOGPS
logP-1.4ChemAxon
logS-3.8ALOGPS
pKa (Strongest Acidic)2.72ChemAxon
pKa (Strongest Basic)8.75ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count21ChemAxon
Hydrogen Donor Count7ChemAxon
Polar Surface Area360.71 ŲChemAxon
Rotatable Bond Count31ChemAxon
Refractivity265.82 m³·mol⁻¹ChemAxon
Polarizability113.73 ųChemAxon
Number of Rings5ChemAxon
BioavailabilityNoChemAxon
Rule of FiveNoChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleYesChemAxon
NPAtlas IDNPA017541
HMDB IDNot Available
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FoodDB IDNot Available
KNApSAcK IDNot Available
Chemspider ID78438373
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound139587968
PDB IDNot Available
ChEBI IDNot Available
Good Scents IDNot Available
References
General References
  1. Igarashi M, Takahashi Y, Shitara T, Nakamura H, Naganawa H, Miyake T, Akamatsu Y: Caprazamycins, novel lipo-nucleoside antibiotics, from Streptomyces sp. II. Structure elucidation of caprazamycins. J Antibiot (Tokyo). 2005 May;58(5):327-37. doi: 10.1038/ja.2005.41. [PubMed:16060385 ]
  2. Mitchell PM: The cost-effectiveness of what in health and care?. 2021 Feb. [PubMed:34383398 ]
  3. Authors unspecified: Ozanimod. 2012. [PubMed:34383397 ]
  4. Authors unspecified: Ponesimod. 2012. [PubMed:34383396 ]
  5. Lee J, Cho Y, Choi KH, Hwang I, Oh YL: Metastatic leiomyosarcoma of the thyroid gland: cytologic findings and differential diagnosis. J Pathol Transl Med. 2021 Aug 13. pii: jptm.2021.06.23. doi: 10.4132/jptm.2021.06.23. [PubMed:34384147 ]