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Record Information
Version1.0
Created at2020-12-09 03:46:37 UTC
Updated at2021-07-15 16:55:59 UTC
NP-MRD IDNP0006858
Secondary Accession NumbersNone
Natural Product Identification
Common NameOrfamide C
Provided ByNPAtlasNPAtlas Logo
DescriptionOrfamide C 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. Orfamide C is found in Pseudomonas and Pseudomonas fluorescens. It was first documented in 2007 (PMID: 17254952). Based on a literature review very few articles have been published on Orfamide C.
Structure
Thumb
Synonyms
ValueSource
4-{[21-(butan-2-yl)-5,8,11,14,17,20,23-heptahydroxy-6,15-bis(hydroxymethyl)-25-methyl-9,12,18-tris(2-methylpropyl)-2-oxo-3-(propan-2-yl)-1-oxa-4,7,10,13,16,19,22-heptaazacyclopentacosa-4,7,10,13,16,19,22-heptaen-24-yl]-C-hydroxycarbonimidoyl}-4-({2-[(1,3-dihydroxydodecylidene)amino]-1-hydroxy-4-methylpentylidene}amino)butanoateGenerator
Chemical FormulaC62H110N10O17
Average Mass1267.6150 Da
Monoisotopic Mass1266.80504 Da
IUPAC Name(4R)-4-{[(3S,6S,15R,18S,21R,24S,25S)-21-[(2S)-butan-2-yl]-6,15-bis(hydroxymethyl)-25-methyl-9,12,18-tris(2-methylpropyl)-2,5,8,11,14,17,20,23-octaoxo-3-(propan-2-yl)-1-oxa-4,7,10,13,16,19,22-heptaazacyclopentacosan-24-yl]carbamoyl}-4-[(2S)-2-[(3S)-3-hydroxydodecanamido]-4-methylpentanamido]butanoic acid
Traditional Name(4R)-4-{[(3S,6S,15R,18S,21R,24S,25S)-21-[(2S)-butan-2-yl]-6,15-bis(hydroxymethyl)-3-isopropyl-25-methyl-9,12,18-tris(2-methylpropyl)-2,5,8,11,14,17,20,23-octaoxo-1-oxa-4,7,10,13,16,19,22-heptaazacyclopentacosan-24-yl]carbamoyl}-4-[(2S)-2-[(3S)-3-hydroxydodecanamido]-4-methylpentanamido]butanoic acid
CAS Registry NumberNot Available
SMILES
CCCCCCCCCC(O)CC(=O)NC(CC(C)C)C(=O)NC(CCC(O)=O)C(=O)NC1C(C)OC(=O)C(NC(=O)C(CO)NC(=O)C(CC(C)C)NC(=O)C(CC(C)C)NC(=O)C(CO)NC(=O)C(CC(C)C)NC(=O)C(NC1=O)C(C)CC)C(C)C
InChI Identifier
InChI=1S/C62H110N10O17/c1-15-17-18-19-20-21-22-23-40(75)30-48(76)63-42(26-33(3)4)54(80)64-41(24-25-49(77)78)53(79)72-52-39(14)89-62(88)50(37(11)12)70-59(85)47(32-74)69-56(82)44(28-35(7)8)65-55(81)43(27-34(5)6)66-58(84)46(31-73)68-57(83)45(29-36(9)10)67-60(86)51(38(13)16-2)71-61(52)87/h33-47,50-52,73-75H,15-32H2,1-14H3,(H,63,76)(H,64,80)(H,65,81)(H,66,84)(H,67,86)(H,68,83)(H,69,82)(H,70,85)(H,71,87)(H,72,79)(H,77,78)
InChI KeySTDTUHSFISWYFO-UHFFFAOYSA-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
PseudomonasNPAtlas
Pseudomonas fluorescensLOTUS 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
  • Alpha-amino acid ester
  • Macrolactam
  • Alpha-amino acid or derivatives
  • Branched fatty acid
  • Heterocyclic fatty acid
  • Hydroxy fatty acid
  • Dicarboxylic acid or derivatives
  • Fatty acyl
  • Fatty acid
  • Cyclic carboximidic acid
  • Carboxylic acid ester
  • Lactone
  • Secondary alcohol
  • Carboximidic acid
  • Carboximidic acid derivative
  • Carboxylic acid derivative
  • Carboxylic acid
  • Oxacycle
  • Azacycle
  • Organoheterocyclic compound
  • Organic 1,3-dipolar compound
  • Propargyl-type 1,3-dipolar organic compound
  • Polyol
  • Organic oxygen compound
  • Hydrocarbon derivative
  • Organopnictogen compound
  • Carbonyl group
  • Alcohol
  • Organic nitrogen compound
  • Organonitrogen compound
  • Organooxygen compound
  • Organic oxide
  • Primary alcohol
  • Aliphatic heteromonocyclic compound
Molecular FrameworkAliphatic 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
logP2.21ALOGPS
logP2.71ChemAxon
logS-4.9ALOGPS
pKa (Strongest Acidic)3.9ChemAxon
Physiological Charge-1ChemAxon
Hydrogen Acceptor Count16ChemAxon
Hydrogen Donor Count14ChemAxon
Polar Surface Area415.29 ŲChemAxon
Rotatable Bond Count31ChemAxon
Refractivity326.8 m³·mol⁻¹ChemAxon
Polarizability140.26 ųChemAxon
Number of Rings1ChemAxon
BioavailabilityNoChemAxon
Rule of FiveNoChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
NPAtlas IDNPA005175
HMDB IDNot Available
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FoodDB IDNot Available
KNApSAcK IDNot Available
Chemspider ID78444488
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound137628537
PDB IDNot Available
ChEBI IDNot Available
Good Scents IDNot Available
References
General References
  1. Gross H, Stockwell VO, Henkels MD, Nowak-Thompson B, Loper JE, Gerwick WH: The genomisotopic approach: a systematic method to isolate products of orphan biosynthetic gene clusters. Chem Biol. 2007 Jan;14(1):53-63. doi: 10.1016/j.chembiol.2006.11.007. [PubMed:17254952 ]