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Record Information
Version1.0
Created at2021-01-05 20:08:17 UTC
Updated at2021-07-15 17:06:52 UTC
NP-MRD IDNP0010712
Secondary Accession NumbersNone
Natural Product Identification
Common NameDidemnin Y
Provided ByNPAtlasNPAtlas Logo
DescriptionDidemnin Y 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. Didemnin Y is found in Tistrella mobilis and Trididemnum solidum. It was first documented in 2012 (PMID: 22458477). Based on a literature review very few articles have been published on didemnin Y.
Structure
Thumb
Synonyms
ValueSource
(4S)-5-{[(2S)-1-[(2S)-2-{[(1R)-1-{[(3S,6S,7S,10S,11S,15S,17R,20S,25as)-10-[(2S)-butan-2-yl]-8,11,18-trihydroxy-3-[(4-methoxyphenyl)methyl]-2,6,17-trimethyl-20-(2-methylpropyl)-1,4,13,16,21-pentaoxo-15-(propan-2-yl)-1H,2H,3H,4H,6H,7H,10H,11H,12H,13H,15H,16H,17H,20H,21H,23H,24H,25H,25ah-pyrrolo[2,1-F]1,15-dioxa-4,7,10,20-tetraazacyclotricosan-7-yl]-C-hydroxycarbonimidoyl}-3-methylbutyl](methyl)carbamoyl}pyrrolidin-1-yl]-1-oxopropan-2-yl]oxy}-4-{[(2S)-2-{[(2S)-2-{[(2S)-2-{[(3R)-1,3-dihydroxydecylidene]amino}-1-hydroxy-4-(C-hydroxycarbonimidoyl)butylidene]amino}-1-hydroxy-4-(C-hydroxycarbonimidoyl)butylidene]amino}-1-hydroxy-4-(C-hydroxycarbonimidoyl)butylidene]amino}-5-oxopentanoateGenerator
Chemical FormulaC87H138N14O26
Average Mass1796.1330 Da
Monoisotopic Mass1794.99067 Da
IUPAC Name(4S)-5-{[(2S)-1-[(2S)-2-{[(1R)-1-{[(3S,6S,7S,10S,11S,15S,17S,20S,25aS)-10-[(2S)-butan-2-yl]-11-hydroxy-3-[(4-methoxyphenyl)methyl]-2,6,17-trimethyl-20-(2-methylpropyl)-1,4,8,13,16,18,21-heptaoxo-15-(propan-2-yl)-docosahydro-1H-pyrrolo[2,1-f]1,15-dioxa-4,7,10,20-tetraazacyclotricosan-7-yl]carbamoyl}-3-methylbutyl](methyl)carbamoyl}pyrrolidin-1-yl]-1-oxopropan-2-yl]oxy}-4-[(2S)-4-carbamoyl-2-[(2S)-4-carbamoyl-2-[(2S)-4-carbamoyl-2-[(3R)-3-hydroxydecanamido]butanamido]butanamido]butanamido]-5-oxopentanoic acid
Traditional Name(4S)-5-{[(2S)-1-[(2S)-2-{[(1R)-1-{[(3S,6S,7S,10S,11S,15S,17S,20S,25aS)-10-[(2S)-butan-2-yl]-11-hydroxy-15-isopropyl-3-[(4-methoxyphenyl)methyl]-2,6,17-trimethyl-20-(2-methylpropyl)-1,4,8,13,16,18,21-heptaoxo-tetradecahydro-3H-pyrrolo[2,1-f]1,15-dioxa-4,7,10,20-tetraazacyclotricosan-7-yl]carbamoyl}-3-methylbutyl](methyl)carbamoyl}pyrrolidin-1-yl]-1-oxopropan-2-yl]oxy}-4-[(2S)-4-carbamoyl-2-[(2S)-4-carbamoyl-2-[(2S)-4-carbamoyl-2-[(3R)-3-hydroxydecanamido]butanamido]butanamido]butanamido]-5-oxopentanoic acid
CAS Registry NumberNot Available
SMILES
CCCCCCC[C@@H](O)CC(=O)N[C@@H](CCC(N)=O)C(=O)N[C@@H](CCC(N)=O)C(=O)N[C@@H](CCC(N)=O)C(=O)N[C@@H](CCC(O)=O)C(=O)O[C@@H](C)C(=O)N1CCC[C@H]1C(=O)N(C)[C@H](CC(C)C)C(=O)N[C@H]1[C@H](C)OC(=O)[C@H](CC2=CC=C(OC)C=C2)N(C)C(=O)[C@@H]2CCCN2C(=O)[C@H](CC(C)C)NC(=O)[C@@H](C)C(=O)[C@@H](OC(=O)C[C@H](O)[C@@H](NC1=O)[C@@H](C)CC)C(C)C
InChI Identifier
InChI=1S/C87H138N14O26/c1-16-18-19-20-21-24-54(102)44-69(107)91-56(31-35-66(88)104)77(113)92-57(32-36-67(89)105)78(114)93-58(33-37-68(90)106)79(115)94-59(34-38-70(108)109)86(122)126-52(12)82(118)100-39-22-25-61(100)84(120)98(13)63(42-47(5)6)80(116)97-73-51(11)125-87(123)64(43-53-27-29-55(124-15)30-28-53)99(14)85(121)62-26-23-40-101(62)83(119)60(41-46(3)4)95-76(112)50(10)74(111)75(48(7)8)127-71(110)45-65(103)72(49(9)17-2)96-81(73)117/h27-30,46-52,54,56-65,72-73,75,102-103H,16-26,31-45H2,1-15H3,(H2,88,104)(H2,89,105)(H2,90,106)(H,91,107)(H,92,113)(H,93,114)(H,94,115)(H,95,112)(H,96,117)(H,97,116)(H,108,109)/t49-,50-,51-,52-,54+,56-,57-,58-,59-,60-,61-,62-,63+,64-,65-,72-,73-,75-/m0/s1
InChI KeyGXKAOWYTJPGGBI-BHTIDRDUSA-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
Tistrella mobilisNPAtlas
Trididemnum solidumLOTUS Database
Chemical Taxonomy
Description 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.
KingdomOrganic compounds
Super ClassOrganic acids and derivatives
ClassPeptidomimetics
Sub ClassDepsipeptides
Direct ParentCyclic depsipeptides
Alternative Parents
Substituents
  • Cyclic depsipeptide
  • Glutamine or derivatives
  • Glutamic acid or derivatives
  • Leucine or derivatives
  • Macrolide lactam
  • Alpha-amino acid ester
  • Proline or derivatives
  • Macrolactam
  • N-acyl-alpha amino acid or derivatives
  • Tetracarboxylic acid or derivatives
  • Alpha-amino acid amide
  • N-substituted-alpha-amino acid
  • Alpha-amino acid or derivatives
  • Phenoxy compound
  • Anisole
  • N-acylpyrrolidine
  • Phenol ether
  • Pyrrolidine carboxylic acid or derivatives
  • Pyrrolidine-2-carboxamide
  • Methoxybenzene
  • Fatty acid ester
  • Alkyl aryl ether
  • Alpha-acyloxy ketone
  • Monocyclic benzene moiety
  • Fatty amide
  • N-acyl-amine
  • 1,3-dicarbonyl compound
  • Benzenoid
  • Fatty acyl
  • Pyrrolidine
  • Tertiary carboxylic acid amide
  • Cyclic ketone
  • Primary carboxylic acid amide
  • Secondary alcohol
  • Carboxamide group
  • Ketone
  • Lactam
  • Carboxylic acid ester
  • Secondary carboxylic acid amide
  • Lactone
  • Ether
  • Carboxylic acid
  • Carboxylic acid derivative
  • Oxacycle
  • Organoheterocyclic compound
  • Azacycle
  • Organopnictogen compound
  • Carbonyl group
  • Organic oxide
  • Hydrocarbon derivative
  • Organic nitrogen compound
  • Organonitrogen compound
  • Organooxygen compound
  • Alcohol
  • Organic oxygen compound
  • Aromatic heteropolycyclic compound
Molecular FrameworkAromatic heteropolycyclic 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
logP0.48ChemAxon
pKa (Strongest Acidic)3.88ChemAxon
Physiological Charge-1ChemAxon
Hydrogen Acceptor Count23ChemAxon
Hydrogen Donor Count13ChemAxon
Polar Surface Area597.17 ŲChemAxon
Rotatable Bond Count45ChemAxon
Refractivity454.31 m³·mol⁻¹ChemAxon
Polarizability187.31 ųChemAxon
Number of Rings4ChemAxon
BioavailabilityNoChemAxon
Rule of FiveNoChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleYesChemAxon
NPAtlas IDNPA024812
HMDB IDNot Available
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FoodDB IDNot Available
KNApSAcK IDNot Available
Chemspider ID24712842
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound44592546
PDB IDNot Available
ChEBI IDNot Available
Good Scents IDNot Available
References
General References
  1. Xu Y, Kersten RD, Nam SJ, Lu L, Al-Suwailem AM, Zheng H, Fenical W, Dorrestein PC, Moore BS, Qian PY: Bacterial biosynthesis and maturation of the didemnin anti-cancer agents. J Am Chem Soc. 2012 May 23;134(20):8625-32. doi: 10.1021/ja301735a. Epub 2012 Apr 6. [PubMed:22458477 ]