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Showing NP-Card for ascr#3 (NP0218211)

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Record Information
Version2.0
Created at2022-09-05 18:47:59 UTC
Updated at2024-09-03 04:15:38 UTC
NP-MRD IDNP0218211
Natural Product DOIhttps://doi.org/10.57994/0337
Secondary Accession NumbersNone
Natural Product Identification
Common Nameascr#3
DescriptionAscr#3, also known as ascaroside C9 or daumone-3, belongs to the class of organic compounds known as sugar acids and derivatives. Sugar acids and derivatives are compounds containing a saccharide unit which bears a carboxylic acid group. Thus, ascr#3 is considered to be a fatty acyl glycoside. Ascr#3 is a secondary metabolite. Secondary metabolites are metabolically or physiologically non-essential metabolites that may serve a role as defense or signalling molecules. In some cases they are simply molecules that arise from the incomplete metabolism of other secondary metabolites. ascr#3 is found in Caenorhabditis elegans. ascr#3 was first documented in 2017 (PMID: 28988862). Based on a literature review a significant number of articles have been published on ascr#3 (PMID: 35094091) (PMID: 29480728) (PMID: 35031295) (PMID: 35047764) (PMID: 34437843) (PMID: 33392151).
Structure
Thumb
MOLSDFPDBSMILESInChI

MOL for NP0218211 (ascr#3)


  Mrv1652309052220482D          

 21 21  0  0  1  0            999 V2000
   -4.2868    2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5724    2.0625    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.8579    2.4750    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1434    2.0625    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.4289    2.4750    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145    2.0625    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.7145    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    2.0625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434    2.0625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579    2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724    2.0625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2868    2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0013    2.0625    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.2868    3.3000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1434    1.2375    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.4289    0.8250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8579    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5724    1.2375    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -4.2868    0.8250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  6  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  1  1  0  0  0
  5  6  1  0  0  0  0
  6  7  1  1  0  0  0
  6  8  1  0  0  0  0
  8  9  1  0  0  0  0
  9 10  1  0  0  0  0
 10 11  1  0  0  0  0
 11 12  1  0  0  0  0
 12 13  2  0  0  0  0
 13 14  1  0  0  0  0
 14 15  2  0  0  0  0
 14 16  1  0  0  0  0
  4 17  1  0  0  0  0
 17 18  1  6  0  0  0
 17 19  1  0  0  0  0
 19 20  1  0  0  0  0
  2 20  1  0  0  0  0
 20 21  1  1  0  0  0
M  END
Download

3D MOL for NP0218211 (ascr#3)

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3D SDF for NP0218211 (ascr#3)

  Mrv1652309052220482D          

 21 21  0  0  1  0            999 V2000
   -4.2868    2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5724    2.0625    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.8579    2.4750    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1434    2.0625    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.4289    2.4750    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145    2.0625    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.7145    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    2.0625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434    2.0625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579    2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724    2.0625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2868    2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0013    2.0625    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.2868    3.3000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1434    1.2375    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.4289    0.8250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8579    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5724    1.2375    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -4.2868    0.8250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  6  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  1  1  0  0  0
  5  6  1  0  0  0  0
  6  7  1  1  0  0  0
  6  8  1  0  0  0  0
  8  9  1  0  0  0  0
  9 10  1  0  0  0  0
 10 11  1  0  0  0  0
 11 12  1  0  0  0  0
 12 13  2  0  0  0  0
 13 14  1  0  0  0  0
 14 15  2  0  0  0  0
 14 16  1  0  0  0  0
  4 17  1  0  0  0  0
 17 18  1  6  0  0  0
 17 19  1  0  0  0  0
 19 20  1  0  0  0  0
  2 20  1  0  0  0  0
 20 21  1  1  0  0  0
M  END
> <DATABASE_ID>
NP0218211

> <DATABASE_NAME>
NP-MRD

> <SMILES>
C[C@H](CCCC\C=C\C(O)=O)O[C@@H]1O[C@@H](C)[C@H](O)C[C@H]1O

> <INCHI_IDENTIFIER>
InChI=1S/C15H26O6/c1-10(7-5-3-4-6-8-14(18)19)20-15-13(17)9-12(16)11(2)21-15/h6,8,10-13,15-17H,3-5,7,9H2,1-2H3,(H,18,19)/b8-6+/t10-,11+,12-,13-,15-/m1/s1

> <INCHI_KEY>
MWGRRKDIJLJLMO-OSYKULTDSA-N

> <FORMULA>
C15H26O6

> <MOLECULAR_WEIGHT>
302.367

> <EXACT_MASS>
302.172938557

> <JCHEM_ACCEPTOR_COUNT>
6

> <JCHEM_ATOM_COUNT>
47

> <JCHEM_AVERAGE_POLARIZABILITY>
32.945426469160964

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
(2E,8R)-8-{[(2R,3R,5R,6S)-3,5-dihydroxy-6-methyloxan-2-yl]oxy}non-2-enoic acid

> <JCHEM_LOGP>
1.6441223573333328

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
13.264073046918021

> <JCHEM_PKA_STRONGEST_ACIDIC>
4.785504628610476

> <JCHEM_PKA_STRONGEST_BASIC>
-3.1878253685480455

> <JCHEM_POLAR_SURFACE_AREA>
96.22000000000001

> <JCHEM_REFRACTIVITY>
77.48890000000002

> <JCHEM_ROTATABLE_BOND_COUNT>
8

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
(2E,8R)-8-{[(2R,3R,5R,6S)-3,5-dihydroxy-6-methyloxan-2-yl]oxy}non-2-enoic acid

> <JCHEM_VEBER_RULE>
0

$$$$

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3D-SDF for NP0218211 (ascr#3)
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PDB for NP0218211 (ascr#3)
HEADER    PROTEIN                                 05-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   05-SEP-22         0                                  
HETATM    1  C   UNK     0      -8.002   4.620   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -6.668   3.850   0.000  0.00  0.00           C+0
HETATM    3  O   UNK     0      -5.335   4.620   0.000  0.00  0.00           O+0
HETATM    4  C   UNK     0      -4.001   3.850   0.000  0.00  0.00           C+0
HETATM    5  O   UNK     0      -2.667   4.620   0.000  0.00  0.00           O+0
HETATM    6  C   UNK     0      -1.334   3.850   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      -1.334   2.310   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       0.000   4.620   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       1.334   3.850   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       2.667   4.620   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       4.001   3.850   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       5.335   4.620   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       6.668   3.850   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       8.002   4.620   0.000  0.00  0.00           C+0
HETATM   15  O   UNK     0       9.336   3.850   0.000  0.00  0.00           O+0
HETATM   16  O   UNK     0       8.002   6.160   0.000  0.00  0.00           O+0
HETATM   17  C   UNK     0      -4.001   2.310   0.000  0.00  0.00           C+0
HETATM   18  O   UNK     0      -2.667   1.540   0.000  0.00  0.00           O+0
HETATM   19  C   UNK     0      -5.335   1.540   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0      -6.668   2.310   0.000  0.00  0.00           C+0
HETATM   21  O   UNK     0      -8.002   1.540   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3   20                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5   17                                                  
CONECT    5    4    6                                                       
CONECT    6    5    7    8                                                  
CONECT    7    6                                                            
CONECT    8    6    9                                                       
CONECT    9    8   10                                                       
CONECT   10    9   11                                                       
CONECT   11   10   12                                                       
CONECT   12   11   13                                                       
CONECT   13   12   14                                                       
CONECT   14   13   15   16                                                  
CONECT   15   14                                                            
CONECT   16   14                                                            
CONECT   17    4   18   19                                                  
CONECT   18   17                                                            
CONECT   19   17   20                                                       
CONECT   20   19    2   21                                                  
CONECT   21   20                                                            
MASTER        0    0    0    0    0    0    0    0   21    0   42    0
END

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3D PDB for NP0218211 (ascr#3)
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SMILES for NP0218211 (ascr#3)
C[C@H](CCCC\C=C\C(O)=O)O[C@@H]1O[C@@H](C)[C@H](O)C[C@H]1O
Download
INCHI for NP0218211 (ascr#3)
InChI=1S/C15H26O6/c1-10(7-5-3-4-6-8-14(18)19)20-15-13(17)9-12(16)11(2)21-15/h6,8,10-13,15-17H,3-5,7,9H2,1-2H3,(H,18,19)/b8-6+/t10-,11+,12-,13-,15-/m1/s1
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View in JSmol
Synonyms
ValueSource
(-)-8R-(3'r,5'r-Dihydroxy-6's-methyl-(2H)-tetrahydropyran-2'-yloxy)-2E-nonenoic acidChEBI
Ascaroside C9ChEBI
Daumone-3ChEBI
(-)-8R-(3'r,5'r-Dihydroxy-6's-methyl-(2H)-tetrahydropyran-2'-yloxy)-2E-nonenoateGenerator
Chemical FormulaC15H26O6
Average Mass302.3670 Da
Monoisotopic Mass302.17294 Da
IUPAC Name(2E,8R)-8-{[(2R,3R,5R,6S)-3,5-dihydroxy-6-methyloxan-2-yl]oxy}non-2-enoic acid
Traditional Name(2E,8R)-8-{[(2R,3R,5R,6S)-3,5-dihydroxy-6-methyloxan-2-yl]oxy}non-2-enoic acid
CAS Registry NumberNot Available
SMILES
C[C@H](CCCC\C=C\C(O)=O)O[C@@H]1O[C@@H](C)[C@H](O)C[C@H]1O
InChI Identifier
InChI=1S/C15H26O6/c1-10(7-5-3-4-6-8-14(18)19)20-15-13(17)9-12(16)11(2)21-15/h6,8,10-13,15-17H,3-5,7,9H2,1-2H3,(H,18,19)/b8-6+/t10-,11+,12-,13-,15-/m1/s1
InChI KeyMWGRRKDIJLJLMO-OSYKULTDSA-N
Experimental Spectra
Spectrum TypeDescriptionDepositor EmailDepositor OrganizationDepositorDeposition DateView
COSY NMR[1H, 1H] NMR Spectrum (2D, 600 MHz, CD3OD, experimental)fs31@cornell.eduNot AvailableNot Available2022-12-23View Spectrum
HMQC NMR[1H, 13C] NMR Spectrum (2D, 600 MHz, C3D6O, experimental)fs31@cornell.eduNot AvailableNot Available2022-12-23View Spectrum
1D NMR1H NMR Spectrum (1D, 600 MHz, CD3OD, experimental)fs31@cornell.eduNot AvailableNot Available2022-12-23View Spectrum
HMBC NMR[1H, 13C] NMR Spectrum (2D, 600 MHz, C3D6O, experimental)fs31@cornell.eduNot AvailableNot Available2022-12-23View Spectrum
Predicted Spectra
Not Available
Chemical Shift Submissions
Not Available
Species
Species of Origin
Species NameSourceReference
Caenorhabditis elegansLOTUS Database
Chemical Taxonomy
Description Belongs to the class of organic compounds known as sugar acids and derivatives. Sugar acids and derivatives are compounds containing a saccharide unit which bears a carboxylic acid group.
KingdomOrganic compounds  
Super ClassOrganic oxygen compounds  
ClassOrganooxygen compounds  
Sub ClassCarbohydrates and carbohydrate conjugates  
Direct ParentSugar acids and derivatives  
Alternative Parents
Substituents
  • Hexose monosaccharide
    • 

  • Medium-chain fatty acid
    • 

  • Branched fatty acid
    • 

  • Heterocyclic fatty acid
    • 

  • Hydroxy fatty acid
    • 

  • Methyl-branched fatty acid
    • 

  • Sugar acid
    • 

  • Fatty acyl
    • 

  • Fatty acid
    • 

  • Unsaturated fatty acid
    • 

  • Oxane
    • 

  • Monosaccharide
    • 

  • Secondary alcohol
    • 

  • Acetal
    • 

  • Carboxylic acid derivative
    • 

  • Carboxylic acid
    • 

  • Oxacycle
    • 

  • Organoheterocyclic compound
    • 

  • Monocarboxylic acid or derivatives
    • 

  • Hydrocarbon derivative
    • 

  • Organic oxide
    • 

  • Carbonyl group
    • 

  • Alcohol
    • 

  • Aliphatic heteromonocyclic compound
Molecular FrameworkAliphatic heteromonocyclic compounds
External Descriptors
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
logP1.64ChemAxon
pKa (Strongest Acidic)4.79ChemAxon
pKa (Strongest Basic)-3.2ChemAxon
Physiological Charge-1ChemAxon
Hydrogen Acceptor Count6ChemAxon
Hydrogen Donor Count3ChemAxon
Polar Surface Area96.22 ŲChemAxon
Rotatable Bond Count8ChemAxon
Refractivity77.49 m³·mol⁻¹ChemAxon
Polarizability32.95 ųChemAxon
Number of Rings1ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
HMDB IDNot Available
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FoodDB IDNot Available
KNApSAcK IDC00045627  
Chemspider ID17226059  
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound16066476  
PDB IDNot Available
ChEBI ID78821  
Good Scents IDNot Available
References
General References
  1. Cohen SM, Wrobel CJJ, Prakash SJ, Schroeder FC, Sternberg PW: Formation and function of dauer ascarosides in the nematodes Caenorhabditis briggsae and Caenorhabditis elegans. G3 (Bethesda). 2022 Mar 4;12(3):jkac014. doi: 10.1093/g3journal/jkac014. [PubMed:35094091  ] 
  2. Dong C, Reilly DK, Bergame C, Dolke F, Srinivasan J, von Reuss SH: Comparative Ascaroside Profiling of Caenorhabditis Exometabolomes Reveals Species-Specific (omega) and (omega - 2)-Hydroxylation Downstream of Peroxisomal beta-Oxidation. J Org Chem. 2018 Jul 6;83(13):7109-7120. doi: 10.1021/acs.joc.8b00094. Epub 2018  Mar 5. [PubMed:29480728  ] 
  3. Wang J, Cao L, Huang Z, Gu X, Cui Y, Li J, Li Y, Xu C, Han R: Influence of the ascarosides on the recovery, yield and dispersal of entomopathogenic nematodes. J Invertebr Pathol. 2022 Feb;188:107717. doi: 10.1016/j.jip.2022.107717. Epub  2022 Jan 11. [PubMed:35031295  ] 
  4. Aprison EZ, Ruvinsky I: ODR-1 acts in AWB neurons to determine the sexual identity of C. elegans pheromone blends. MicroPubl Biol. 2022 Jan 13;2022:10.17912/micropub.biology.000507. doi:  10.17912/micropub.biology.000507. eCollection 2022. [PubMed:35047764  ] 
  5. Luo J, Portman DS: Sex-specific, pdfr-1-dependent modulation of pheromone avoidance by food abundance enables flexibility in C. elegans foraging behavior. Curr Biol. 2021 Oct 25;31(20):4449-4461.e4. doi: 10.1016/j.cub.2021.07.069. Epub  2021 Aug 25. [PubMed:34437843  ] 
  6. El Atab O, Darwiche R, Truax NJ, Schneiter R, Hull KG, Romo D, Asojo OA: Necator americanus Ancylostoma Secreted Protein-2 (Na-ASP-2) Binds an Ascaroside (ascr#3) in Its Fatty Acid Binding Site. Front Chem. 2020 Dec 17;8:608296. doi: 10.3389/fchem.2020.608296. eCollection  2020. [PubMed:33392151  ] 
  7. Ryu L, Cheon Y, Huh YH, Pyo S, Chinta S, Choi H, Butcher RA, Kim K: Feeding state regulates pheromone-mediated avoidance behavior via the insulin signaling pathway in Caenorhabditis elegans. EMBO J. 2018 Aug 1;37(15):e98402. doi: 10.15252/embj.201798402. Epub 2018 Jun 19. [PubMed:29925517  ] 
  8. Fagan KA, Luo J, Lagoy RC, Schroeder FC, Albrecht DR, Portman DS: A Single-Neuron Chemosensory Switch Determines the Valence of a Sexually Dimorphic Sensory Behavior. Curr Biol. 2018 Mar 19;28(6):902-914.e5. doi: 10.1016/j.cub.2018.02.029. Epub  2018 Mar 8. [PubMed:29526590  ] 
  9. Hong M, Ryu L, Ow MC, Kim J, Je AR, Chinta S, Huh YH, Lee KJ, Butcher RA, Choi H, Sengupta P, Hall SE, Kim K: Early Pheromone Experience Modifies a Synaptic Activity to Influence Adult Pheromone Responses of C. elegans. Curr Biol. 2017 Oct 23;27(20):3168-3177.e3. doi: 10.1016/j.cub.2017.08.068. Epub  2017 Oct 5. [PubMed:28988862  ] 
  10. Aprison EZ, Ruvinsky I: Counteracting Ascarosides Act through Distinct Neurons to Determine the Sexual Identity of C. elegans Pheromones. Curr Biol. 2017 Sep 11;27(17):2589-2599.e3. doi: 10.1016/j.cub.2017.07.034. Epub  2017 Aug 30. [PubMed:28844646  ] 
  11. LOTUS database [Link]