NP-MRD: Showing NP-Card for Arabenoic acid (NP0008005)

Jump To Section:

Identification Spectra BioTaxonomy ChemoTaxonomy Physical properties Links References XML

Record Information

Version

2.0

Created at

2020-12-09 05:37:09 UTC

Updated at

2021-07-15 16:59:09 UTC

NP-MRD ID

NP0008005

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Arabenoic acid

Provided By

NPAtlas

Description

Arabenoic acid, also known as arabenoate, belongs to the class of organic compounds known as hydroxy fatty acids. These are fatty acids in which the chain bears a hydroxyl group. Arabenoic acid is found in Penicillium verrucosum and Unknown-fungus sp. F6286. Arabenoic acid was first documented in 1991 (PMID: 1880069). Based on a literature review very few articles have been published on Arabenoic acid.

Structure

MOL 3D MOL SDF 3D SDF PDB SMILES InChI


  Mrv1652306242106063D          

 20 19  0  0  0  0            999 V2000
    2.5137   -0.3935    0.7417 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8204    0.2918   -0.2812 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.4405    0.5549   -0.1757 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0582    1.4207    0.7284 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2685    1.8577    1.0356 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4791    2.7093    1.9381 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3780    1.3915    0.3864 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5027   -0.1388   -1.0708 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.3962   -1.6197   -0.7462 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.2524   -2.3833   -1.5387 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.5808   -0.4939    0.4597 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.1417   -1.4457    0.8661 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4607    0.0937    1.7173 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8818    1.8644    1.3260 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9284    2.0468   -0.1833 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0286   -0.0536   -2.1156 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4907    0.2450   -1.1851 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6369   -1.8375    0.3150 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6331   -1.9903   -0.9206 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1693   -2.1196   -1.2973 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  3  4  2  0  0  0  0
  4  5  1  0  0  0  0
  5  6  2  0  0  0  0
  5  7  1  0  0  0  0
  3  8  1  0  0  0  0
  8  9  1  0  0  0  0
  9 10  1  0  0  0  0
  1 11  1  0  0  0  0
  1 12  1  0  0  0  0
  1 13  1  0  0  0  0
  4 14  1  0  0  0  0
  7 15  1  0  0  0  0
  8 16  1  0  0  0  0
  8 17  1  0  0  0  0
  9 18  1  0  0  0  0
  9 19  1  0  0  0  0
 10 20  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0008005

> <DATABASE_NAME>
NP-MRD

> <SMILES>
[H]OC(=O)C(\[H])=C(\OC([H])([H])[H])C([H])([H])C([H])([H])O[H]

> <INCHI_IDENTIFIER>
InChI=1S/C6H10O4/c1-10-5(2-3-7)4-6(8)9/h4,7H,2-3H2,1H3,(H,8,9)/b5-4+

> <INCHI_KEY>
RUKBZMQXLNLXDE-SNAWJCMRSA-N

> <FORMULA>
C6H10O4

> <MOLECULAR_WEIGHT>
146.142

> <EXACT_MASS>
146.057908802

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_ATOM_COUNT>
20

> <JCHEM_AVERAGE_POLARIZABILITY>
13.986997890287554

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2E)-5-hydroxy-3-methoxypent-2-enoic acid

> <ALOGPS_LOGP>
0.01

> <JCHEM_LOGP>
-0.8592486399999993

> <ALOGPS_LOGS>
-0.47

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
15.853685794184415

> <JCHEM_PKA_STRONGEST_ACIDIC>
4.765879341239177

> <JCHEM_PKA_STRONGEST_BASIC>
-2.42611666350278

> <JCHEM_POLAR_SURFACE_AREA>
66.76

> <JCHEM_REFRACTIVITY>
36.2485

> <JCHEM_ROTATABLE_BOND_COUNT>
4

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
4.94e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(2E)-5-hydroxy-3-methoxypent-2-enoic acid

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 24-JUN-21   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   24-JUN-21         0                                  
HETATM    1  C   UNK     0       2.514  -0.394   0.742  0.00  0.00           C+0
HETATM    2  O   UNK     0       1.820   0.292  -0.281  0.00  0.00           O+0
HETATM    3  C   UNK     0       0.441   0.555  -0.176  0.00  0.00           C+0
HETATM    4  C   UNK     0       0.058   1.421   0.728  0.00  0.00           C+0
HETATM    5  C   UNK     0      -1.268   1.858   1.036  0.00  0.00           C+0
HETATM    6  O   UNK     0      -1.479   2.709   1.938  0.00  0.00           O+0
HETATM    7  O   UNK     0      -2.378   1.391   0.386  0.00  0.00           O+0
HETATM    8  C   UNK     0      -0.503  -0.139  -1.071  0.00  0.00           C+0
HETATM    9  C   UNK     0      -0.396  -1.620  -0.746  0.00  0.00           C+0
HETATM   10  O   UNK     0      -1.252  -2.383  -1.539  0.00  0.00           O+0
HETATM   11  H   UNK     0       3.581  -0.494   0.460  0.00  0.00           H+0
HETATM   12  H   UNK     0       2.142  -1.446   0.866  0.00  0.00           H+0
HETATM   13  H   UNK     0       2.461   0.094   1.717  0.00  0.00           H+0
HETATM   14  H   UNK     0       0.882   1.864   1.326  0.00  0.00           H+0
HETATM   15  H   UNK     0      -2.928   2.047  -0.183  0.00  0.00           H+0
HETATM   16  H   UNK     0      -0.029  -0.054  -2.116  0.00  0.00           H+0
HETATM   17  H   UNK     0      -1.491   0.245  -1.185  0.00  0.00           H+0
HETATM   18  H   UNK     0      -0.637  -1.837   0.315  0.00  0.00           H+0
HETATM   19  H   UNK     0       0.633  -1.990  -0.921  0.00  0.00           H+0
HETATM   20  H   UNK     0      -2.169  -2.120  -1.297  0.00  0.00           H+0
CONECT    1    2   11   12   13                                             
CONECT    2    1    3                                                       
CONECT    3    2    4    8                                                  
CONECT    4    3    5   14                                                  
CONECT    5    4    6    7                                                  
CONECT    6    5                                                            
CONECT    7    5   15                                                       
CONECT    8    3    9   16   17                                             
CONECT    9    8   10   18   19                                             
CONECT   10    9   20                                                       
CONECT   11    1                                                            
CONECT   12    1                                                            
CONECT   13    1                                                            
CONECT   14    4                                                            
CONECT   15    7                                                            
CONECT   16    8                                                            
CONECT   17    8                                                            
CONECT   18    9                                                            
CONECT   19    9                                                            
CONECT   20   10                                                            
MASTER        0    0    0    0    0    0    0    0   20    0   38    0
END

View in JSmol View NMR Assignments

Synonyms

Value	Source
Arabenoate	Generator
5-Hydroxy-3-methoxy-2-pentenoic acid	MeSH
(2E)-5-Hydroxy-3-methoxypent-2-enoate	Generator

Chemical Formula

C₆H₁₀O₄

Average Mass

146.1420 Da

Monoisotopic Mass

146.05791 Da

IUPAC Name

(2E)-5-hydroxy-3-methoxypent-2-enoic acid

Traditional Name

(2E)-5-hydroxy-3-methoxypent-2-enoic acid

CAS Registry Number

Not Available

SMILES

CO\C(CCO)=C\C(O)=O

InChI Identifier

InChI=1S/C6H10O4/c1-10-5(2-3-7)4-6(8)9/h4,7H,2-3H2,1H3,(H,8,9)/b5-4+

InChI Key

RUKBZMQXLNLXDE-SNAWJCMRSA-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, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 252 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 50 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 75 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 101 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 126 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 151 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 176 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 201 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 226 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, 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
Penicillium verrucosum	LOTUS Database	35616633
Unknown-fungus sp. F6286	NPAtlas	1880069

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as hydroxy fatty acids. These are fatty acids in which the chain bears a hydroxyl group.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Fatty Acyls

Sub Class

Fatty acids and conjugates

Direct Parent

Hydroxy fatty acids

Alternative Parents

Substituents

Hydroxy fatty acid
Unsaturated fatty acid
Vinylogous ester
Monocarboxylic acid or derivatives
Carboxylic acid
Carboxylic acid derivative
Organic oxygen compound
Organic oxide
Hydrocarbon derivative
Primary alcohol
Organooxygen compound
Carbonyl group
Alcohol
Aliphatic acyclic compound

Molecular Framework

Aliphatic acyclic compounds

External Descriptors

Not Available

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	0.01	ALOGPS
logP	-0.86	ChemAxon
logS	-0.47	ALOGPS
pKa (Strongest Acidic)	4.77	ChemAxon
pKa (Strongest Basic)	-2.4	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	4	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	66.76 Å²	ChemAxon
Rotatable Bond Count	4	ChemAxon
Refractivity	36.25 m³·mol⁻¹	ChemAxon
Polarizability	13.99 Å³	ChemAxon
Number of Rings	0	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

NPAtlas ID

NPA020660

HMDB ID

Not Available

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

Not Available

KNApSAcK ID

Not Available

Chemspider ID

4943153

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

6438692

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Isaac BG, Ayer SW, Stonard RJ: Arabenoic acid, a natural product herbicide of fungal origin. J Antibiot (Tokyo). 1991 Jul;44(7):793-4. doi: 10.7164/antibiotics.44.793. [PubMed:1880069 ]

Showing NP-Card for Arabenoic acid (NP0008005)

MOL for NP0008005 (Arabenoic acid)

3D MOL for NP0008005 (Arabenoic acid)

3D SDF for NP0008005 (Arabenoic acid)

3D-SDF for NP0008005 (Arabenoic acid)

PDB for NP0008005 (Arabenoic acid)

3D PDB for NP0008005 (Arabenoic acid)

SMILES for NP0008005 (Arabenoic acid)

INCHI for NP0008005 (Arabenoic acid)

Structure for NP0008005 (Arabenoic acid)

3D Structure for NP0008005 (Arabenoic acid)