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Record Information
Version1.0
Created at2020-12-09 03:55:08 UTC
Updated at2021-07-15 16:56:23 UTC
NP-MRD IDNP0007005
Secondary Accession NumbersNone
Natural Product Identification
Common NamePahayokolide B
Provided ByNPAtlasNPAtlas Logo
Description3-[(6S,13S,19S,22S,25E,28S,31Z,34S)-34-benzyl-25,31-diethylidene-5,8,9,12,21,24,27,30,33,36-decahydroxy-22-[(1R)-1-hydroxyethyl]-28-(hydroxymethyl)-2,18-dioxo-19-(2-phenylethyl)-10-(2,4,5-trihydroxy-7-methyloctyl)-1,4,7,11,17,20,23,26,29,32,35-undecaazatricyclo[35.3.0.0¹³,¹⁷]Tetraconta-4,7,11,20,23,26,29,32,35-nonaen-6-yl]propanimidic acid belongs to the class of organic compounds known as cyclic peptides. Cyclic peptides are compounds containing a cyclic moiety bearing a peptide backbone. Pahayokolide B is found in Lyngbya and Lyngbya sp.. It was first documented in 2007 (PMID: 17432902). Based on a literature review very few articles have been published on 3-[(6S,13S,19S,22S,25E,28S,31Z,34S)-34-benzyl-25,31-diethylidene-5,8,9,12,21,24,27,30,33,36-decahydroxy-22-[(1R)-1-hydroxyethyl]-28-(hydroxymethyl)-2,18-dioxo-19-(2-phenylethyl)-10-(2,4,5-trihydroxy-7-methyloctyl)-1,4,7,11,17,20,23,26,29,32,35-undecaazatricyclo[35.3.0.0¹³,¹⁷]Tetraconta-4,7,11,20,23,26,29,32,35-nonaen-6-yl]propanimidic acid (PMID: 21650153).
Structure
Thumb
Synonyms
ValueSource
3-[(6S,13S,19S,22S,25E,28S,31Z,34S)-34-Benzyl-25,31-diethylidene-5,8,9,12,21,24,27,30,33,36-decahydroxy-22-[(1R)-1-hydroxyethyl]-28-(hydroxymethyl)-2,18-dioxo-19-(2-phenylethyl)-10-(2,4,5-trihydroxy-7-methyloctyl)-1,4,7,11,17,20,23,26,29,32,35-undecaazatricyclo[35.3.0.0,]tetraconta-4,7,11,20,23,26,29,32,35-nonaen-6-yl]propanimidateGenerator
Chemical FormulaC63H90N12O18
Average Mass1303.4790 Da
Monoisotopic Mass1302.64960 Da
IUPAC Name3-[(6S,9S,10R,13S,19S,22S,25E,28S,31Z,34S,37R)-34-benzyl-25,31-diethylidene-9-hydroxy-22-[(1R)-1-hydroxyethyl]-28-(hydroxymethyl)-2,5,8,12,18,21,24,27,30,33,36-undecaoxo-19-(2-phenylethyl)-10-[(2S,4S,5S)-2,4,5-trihydroxy-7-methyloctyl]-1,4,7,11,17,20,23,26,29,32,35-undecaazatricyclo[35.3.0.0^{13,17}]tetracontan-6-yl]propanamide
Traditional Name3-[(6S,9S,10R,13S,19S,22S,25E,28S,31Z,34S,37R)-34-benzyl-25,31-diethylidene-9-hydroxy-22-[(1R)-1-hydroxyethyl]-28-(hydroxymethyl)-2,5,8,12,18,21,24,27,30,33,36-undecaoxo-19-(2-phenylethyl)-10-[(2S,4S,5S)-2,4,5-trihydroxy-7-methyloctyl]-1,4,7,11,17,20,23,26,29,32,35-undecaazatricyclo[35.3.0.0^{13,17}]tetracontan-6-yl]propanamide
CAS Registry NumberNot Available
SMILES
C\C=C1/NC(=O)[C@H](CC2=CC=CC=C2)NC(=O)C2CCCN2C(=O)CNC(=O)[C@H](CCC(N)=O)NC(=O)C(O)C(CC(O)CC(O)C(O)CC(C)C)NC(=O)[C@@H]2CCCN2C(=O)[C@H](CCC2=CC=CC=C2)NC(=O)[C@@H](NC(=O)\C(NC(=O)[C@H](CO)NC1=O)=C/C)[C@@H](C)O
InChI Identifier
InChI=1S/C63H90N12O18/c1-6-39-55(85)72-45(33-76)58(88)67-40(7-2)56(86)73-52(35(5)77)61(91)69-42(23-22-36-16-10-8-11-17-36)63(93)75-27-15-21-47(75)60(90)70-43(30-38(78)31-49(80)48(79)28-34(3)4)53(83)62(92)68-41(24-25-50(64)81)54(84)65-32-51(82)74-26-14-20-46(74)59(89)71-44(57(87)66-39)29-37-18-12-9-13-19-37/h6-13,16-19,34-35,38,41-49,52-53,76-80,83H,14-15,20-33H2,1-5H3,(H2,64,81)(H,65,84)(H,66,87)(H,67,88)(H,68,92)(H,69,91)(H,70,90)(H,71,89)(H,72,85)(H,73,86)/b39-6-,40-7+/t35-,38?,41+,42+,43?,44+,45+,46?,47+,48?,49?,52+,53?/m1/s1
InChI KeyOIVBMJYHGKIQDX-RELJIIIESA-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
LyngbyaNPAtlas
Lyngbya sp.-
Chemical Taxonomy
Description Belongs to the class of organic compounds known as cyclic peptides. Cyclic peptides are compounds containing a cyclic moiety bearing a peptide backbone.
KingdomOrganic compounds
Super ClassOrganic acids and derivatives
ClassCarboxylic acids and derivatives
Sub ClassAmino acids, peptides, and analogues
Direct ParentCyclic peptides
Alternative Parents
Substituents
  • Cyclic alpha peptide
  • Alpha-amino acid or derivatives
  • Benzenoid
  • Monocyclic benzene moiety
  • Cyclic carboximidic acid
  • Tertiary carboxylic acid amide
  • Pyrrolidine
  • Secondary alcohol
  • Lactam
  • Carboxamide group
  • Azacycle
  • Organoheterocyclic compound
  • Organic 1,3-dipolar compound
  • Propargyl-type 1,3-dipolar organic compound
  • Polyol
  • Carboximidic acid derivative
  • Carboximidic acid
  • Organic nitrogen compound
  • Organic oxygen compound
  • Organopnictogen compound
  • Organic oxide
  • Hydrocarbon derivative
  • Primary alcohol
  • Organooxygen compound
  • Organonitrogen compound
  • Carbonyl group
  • Alcohol
  • 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
logP0.22ALOGPS
logP-5.5ChemAxon
logS-3.9ALOGPS
pKa (Strongest Acidic)11.36ChemAxon
pKa (Strongest Basic)-3.9ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count18ChemAxon
Hydrogen Donor Count16ChemAxon
Polar Surface Area466.99 ŲChemAxon
Rotatable Bond Count17ChemAxon
Refractivity334.55 m³·mol⁻¹ChemAxon
Polarizability135.24 ųChemAxon
Number of Rings5ChemAxon
BioavailabilityNoChemAxon
Rule of FiveNoChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleYesChemAxon
NPAtlas IDNPA006710
HMDB IDNot Available
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FoodDB IDNot Available
KNApSAcK IDNot Available
Chemspider ID78445510
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound139584997
PDB IDNot Available
ChEBI IDNot Available
Good Scents IDNot Available
References
General References
  1. An T, Kumar TK, Wang M, Liu L, Lay JO Jr, Liyanage R, Berry J, Gantar M, Marks V, Gawley RE, Rein KS: Structures of pahayokolides A and B, cyclic peptides from a Lyngbya sp. J Nat Prod. 2007 May;70(5):730-5. doi: 10.1021/np060389p. Epub 2007 Apr 14. [PubMed:17432902 ]
  2. Liu L, Bearden DW, Rein KS: Biosynthetic origin of the 3-amino-2,5,7,8-tetrahydroxy-10-methylundecanoic acid moiety and absolute configuration of pahayokolides A and B. J Nat Prod. 2011 Jun 24;74(6):1535-8. doi: 10.1021/np200362q. Epub 2011 Jun 8. [PubMed:21650153 ]