NP-MRD: Showing NP-Card for ascr#5 (NP0160808)

Jump To Section:

Identification Spectra BioTaxonomy ChemoTaxonomy Physical properties Links References XML

Record Information

Version

2.0

Created at

2022-09-02 18:50:58 UTC

Updated at

2022-09-02 18:50:58 UTC

NP-MRD ID

NP0160808

Secondary Accession Numbers

None

Natural Product Identification

Common Name

ascr#5

Description

Ascr#5, also known as ascaroside C3, 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#5 is considered to be a fatty acyl glycoside. Ascr#5 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#5 is found in Caenorhabditis elegans. ascr#5 was first documented in 2018 (PMID: 29480728). Based on a literature review a small amount of articles have been published on ascr#5 (PMID: 35031295) (PMID: 34862187) (PMID: 34260587).

Structure

MOL 3D MOL SDF PDB SMILES InChI

     RDKit          3D

 31 31  0  0  0  0  0  0  0  0999 V2000
   -1.8790    2.5302    1.1844 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6115    1.0479    0.9490 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.2852    0.9259    0.6095 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0916   -0.3711    0.2764 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.9700   -0.9198    1.1893 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.2100   -1.2601    0.6892 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9058   -0.0378    0.2101 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2574   -0.3146   -0.3445 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.7702   -1.4415   -0.4101 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.9721    0.7891   -0.8149 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1029   -1.3037    0.2122 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.6316   -2.5219   -0.2901 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1950   -0.7599   -0.6813 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5466    0.6165   -0.1602 C   0  0  1  0  0  0  0  0  0  0  0  0
   -3.8452    0.6276    0.3589 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0525    2.9900    1.7511 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0018    3.0681    0.2124 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8362    2.6656    1.7506 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8080    0.5328    1.8947 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5508   -0.3336   -0.7221 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0341   -2.0099   -0.1273 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.7609   -1.7825    1.5152 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.3242    0.4784   -0.5415 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.0948    0.6041    1.1214 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.0437    1.6334   -0.2559 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4374   -1.4744    1.2490 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3458   -3.0056   -0.7760 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0712   -1.4287   -0.5579 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8054   -0.7452   -1.7094 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5178    1.3520   -0.9837 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0125   -0.1513    0.9451 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  1  0
  4  5  1  0
  5  6  1  0
  6  7  1  0
  7  8  1  0
  8 10  1  0
  8  9  2  0
  4 11  1  0
 11 12  1  0
 11 13  1  0
 13 14  1  0
 14 15  1  0
 14  2  1  0
  1 16  1  0
  1 17  1  0
  1 18  1  0
  2 19  1  1
  4 20  1  6
  6 21  1  0
  6 22  1  0
  7 23  1  0
  7 24  1  0
 10 25  1  0
 11 26  1  1
 12 27  1  0
 13 28  1  0
 13 29  1  0
 14 30  1  6
 15 31  1  0
M  END


  Mrv1652309022220502D          

 15 15  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  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 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    1.2375    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  0  0  0  0
  7  8  1  0  0  0  0
  8  9  2  0  0  0  0
  8 10  1  0  0  0  0
  4 11  1  0  0  0  0
 11 12  1  6  0  0  0
 11 13  1  0  0  0  0
 13 14  1  0  0  0  0
  2 14  1  0  0  0  0
 14 15  1  1  0  0  0
M  END
> <DATABASE_ID>
NP0160808

> <DATABASE_NAME>
NP-MRD

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

> <INCHI_IDENTIFIER>
InChI=1S/C9H16O6/c1-5-6(10)4-7(11)9(15-5)14-3-2-8(12)13/h5-7,9-11H,2-4H2,1H3,(H,12,13)/t5-,6+,7+,9+/m0/s1

> <INCHI_KEY>
RYYMJVGKZLQYPG-YYWONIAYSA-N

> <FORMULA>
C9H16O6

> <MOLECULAR_WEIGHT>
220.221

> <EXACT_MASS>
220.094688235

> <JCHEM_ACCEPTOR_COUNT>
6

> <JCHEM_ATOM_COUNT>
31

> <JCHEM_AVERAGE_POLARIZABILITY>
21.44019532899735

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

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

> <ALOGPS_LOGP>
-1.10

> <JCHEM_LOGP>
-0.8372120220000003

> <ALOGPS_LOGS>
-0.02

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
13.264593259994808

> <JCHEM_PKA_STRONGEST_ACIDIC>
4.147241566968549

> <JCHEM_PKA_STRONGEST_BASIC>
-3.187825138728032

> <JCHEM_POLAR_SURFACE_AREA>
96.22

> <JCHEM_REFRACTIVITY>
48.8178

> <JCHEM_ROTATABLE_BOND_COUNT>
4

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
2.10e+02 g/l

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

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 02-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   02-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       0.000   4.620   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       1.334   3.850   0.000  0.00  0.00           C+0
HETATM    9  O   UNK     0       2.667   4.620   0.000  0.00  0.00           O+0
HETATM   10  O   UNK     0       1.334   2.310   0.000  0.00  0.00           O+0
HETATM   11  C   UNK     0      -4.001   2.310   0.000  0.00  0.00           C+0
HETATM   12  O   UNK     0      -2.667   1.540   0.000  0.00  0.00           O+0
HETATM   13  C   UNK     0      -5.335   1.540   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      -6.668   2.310   0.000  0.00  0.00           C+0
HETATM   15  O   UNK     0      -8.002   1.540   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3   14                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5   11                                                  
CONECT    5    4    6                                                       
CONECT    6    5    7                                                       
CONECT    7    6    8                                                       
CONECT    8    7    9   10                                                  
CONECT    9    8                                                            
CONECT   10    8                                                            
CONECT   11    4   12   13                                                  
CONECT   12   11                                                            
CONECT   13   11   14                                                       
CONECT   14   13    2   15                                                  
CONECT   15   14                                                            
MASTER        0    0    0    0    0    0    0    0   15    0   30    0
END

View in JSmol

Synonyms

Value	Source
(-)-3-(3'r,5'r-Dihydroxy-6's-methyl-(2H)-tetrahydropyran-2'-yloxy)-propanoic acid	ChEBI
3-Hydroxypropanoic acid 3-O-alpha-ascarylopyranoside	ChEBI
Ascaroside C3	ChEBI
(-)-3-(3'r,5'r-Dihydroxy-6's-methyl-(2H)-tetrahydropyran-2'-yloxy)-propanoate	Generator
3-Hydroxypropanoate 3-O-a-ascarylopyranoside	Generator
3-Hydroxypropanoate 3-O-alpha-ascarylopyranoside	Generator
3-Hydroxypropanoate 3-O-α-ascarylopyranoside	Generator
3-Hydroxypropanoic acid 3-O-a-ascarylopyranoside	Generator
3-Hydroxypropanoic acid 3-O-α-ascarylopyranoside	Generator

Chemical Formula

C₉H₁₆O₆

Average Mass

220.2210 Da

Monoisotopic Mass

220.09469 Da

IUPAC Name

3-{[(2R,3R,5R,6S)-3,5-dihydroxy-6-methyloxan-2-yl]oxy}propanoic acid

Traditional Name

3-{[(2R,3R,5R,6S)-3,5-dihydroxy-6-methyloxan-2-yl]oxy}propanoic acid

CAS Registry Number

Not Available

SMILES

C[C@@H]1O[C@@H](OCCC(O)=O)[C@H](O)C[C@H]1O

InChI Identifier

InChI=1S/C9H16O6/c1-5-6(10)4-7(11)9(15-5)14-3-2-8(12)13/h5-7,9-11H,2-4H2,1H3,(H,12,13)/t5-,6+,7+,9+/m0/s1

InChI Key

RYYMJVGKZLQYPG-YYWONIAYSA-N

Experimental Spectra

Not Available

Predicted Spectra

Spectrum Type	Description	Depositor ID	Depositor Organization	Depositor	Deposition Date	View
1D NMR	¹³C NMR Spectrum (1D, 25 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 252 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 50 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 75 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 101 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 126 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 151 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 176 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 201 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 226 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum

Chemical Shift Submissions

Not Available

Species

Species of Origin

Species Name	Source	Reference
Caenorhabditis elegans	LOTUS Database	35616633

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.

Kingdom

Organic compounds

Super Class

Organic oxygen compounds

Class

Organooxygen compounds

Sub Class

Carbohydrates and carbohydrate conjugates

Direct Parent

Sugar acids and derivatives

Alternative Parents

Substituents

Hexose monosaccharide
Sugar acid
Monosaccharide
Oxane
Secondary alcohol
Acetal
Carboxylic acid derivative
Carboxylic acid
Monocarboxylic acid or derivatives
Oxacycle
Organoheterocyclic compound
Organic oxide
Carbonyl group
Hydrocarbon derivative
Alcohol
Aliphatic heteromonocyclic compound

Molecular Framework

Aliphatic heteromonocyclic compounds

External Descriptors

monocarboxylic acid (CHEBI:78829 )
omega-hydroxy fatty acid ascaroside (CHEBI:78829 )

Physical Properties

State

Not Available

Experimental Properties

Property	Value	Reference
Melting Point	Not Available	Not Available
Boiling Point	Not Available	Not Available
Water Solubility	Not Available	Not Available
LogP	Not Available	Not Available

Predicted Properties

Property	Value	Source
logP	-1.1	ALOGPS
logP	-0.84	ChemAxon
logS	-0.02	ALOGPS
pKa (Strongest Acidic)	4.15	ChemAxon
pKa (Strongest Basic)	-3.2	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	6	ChemAxon
Hydrogen Donor Count	3	ChemAxon
Polar Surface Area	96.22 Å²	ChemAxon
Rotatable Bond Count	4	ChemAxon
Refractivity	48.82 m³·mol⁻¹	ChemAxon
Polarizability	21.44 Å³	ChemAxon
Number of Rings	1	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

External Links

HMDB ID

Not Available

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

Not Available

KNApSAcK ID

C00045627

Chemspider ID

26394943

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

44202063

PDB ID

Not Available

ChEBI ID

78829

Good Scents ID

Not Available

References

General References

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 ]
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 ]
Shimizu T, Sugiura K, Sakai Y, Dar AR, Butcher RA, Matsumoto K, Hisamoto N: Chemical Signaling Regulates Axon Regeneration via the GPCR-Gqalpha Pathway in Caenorhabditis elegans. J Neurosci. 2022 Feb 2;42(5):720-730. doi: 10.1523/JNEUROSCI.0929-21.2021. Epub 2021 Dec 3. [PubMed:34862187 ]
Park J, Oh H, Kim DY, Cheon Y, Park YJ, Hwang H, Neal SJ, Dar AR, Butcher RA, Sengupta P, Kim DW, Kim K: CREB mediates the C. elegans dauer polyphenism through direct and cell-autonomous regulation of TGF-beta expression. PLoS Genet. 2021 Jul 14;17(7):e1009678. doi: 10.1371/journal.pgen.1009678. eCollection 2021 Jul. [PubMed:34260587 ]
LOTUS database [Link]

Showing NP-Card for ascr#5 (NP0160808)

MOL for NP0160808 (ascr#5)

3D MOL for NP0160808 (ascr#5)

3D SDF for NP0160808 (ascr#5)

3D-SDF for NP0160808 (ascr#5)

PDB for NP0160808 (ascr#5)

3D PDB for NP0160808 (ascr#5)

SMILES for NP0160808 (ascr#5)

INCHI for NP0160808 (ascr#5)

Structure for NP0160808 (ascr#5)

3D Structure for NP0160808 (ascr#5)