NP-MRD: Showing NP-Card for OPC-6:0 (NP0045551)

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Record Information

Version

2.0

Created at

2022-03-17 19:30:22 UTC

Updated at

2022-03-17 19:30:22 UTC

NP-MRD ID

NP0045551

Secondary Accession Numbers

None

Natural Product Identification

Common Name

OPC-6:0

Description

OPC-6:0, Also known as OPC-6, belongs to the class of organic compounds known as prostaglandins and related compounds. These are unsaturated carboxylic acids consisting of a 20 carbon skeleton that also contains a five member ring, and are based upon the fatty acid arachidonic acid. Thus, OPC-6:0 Is considered to be an octadecanoid lipid molecule. OPC-6:0 was first documented in 2008 (PMID: 18267944). OPC-6:0 Is a very hydrophobic molecule, practically insoluble (in water), and relatively neutral (PMID: 21331428).

Structure

MOL SDF PDB SMILES InChI

  Mrv0541 02241221472D          

 19 19  0  0  1  0            999 V2000
   -3.0676    2.6690    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2471    2.7552    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8346    3.4697    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0277    3.2981    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9414    2.4777    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.2269    2.0652    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4875    2.4777    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2020    2.0652    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9165    2.4777    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6309    2.0652    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3454    2.4777    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0599    2.0652    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.3454    3.3027    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6951    2.1421    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.8666    1.3351    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6512    1.0802    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8228    0.2732    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2097   -0.2788    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4250   -0.0239    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  1  0  0  0
  6  7  1  0  0  0  0
  7  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  2  0  0  0  0
 11 13  1  0  0  0  0
  5 14  1  0  0  0  0
  2 14  1  0  0  0  0
 14 15  1  1  0  0  0
 15 16  1  0  0  0  0
 16 17  2  0  0  0  0
 17 18  1  0  0  0  0
 18 19  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0045551

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CC\C=C/C[C@@H]1[C@H](CCCCCC(O)=O)CCC1=O

> <INCHI_IDENTIFIER>
InChI=1S/C16H26O3/c1-2-3-5-9-14-13(11-12-15(14)17)8-6-4-7-10-16(18)19/h3,5,13-14H,2,4,6-12H2,1H3,(H,18,19)/b5-3-/t13-,14-/m1/s1

> <INCHI_KEY>
WIJWBOWLVOOYFR-BDSSXFGHSA-N

> <FORMULA>
C16H26O3

> <MOLECULAR_WEIGHT>
266.3758

> <EXACT_MASS>
266.188194698

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_AVERAGE_POLARIZABILITY>
31.62523774439284

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
6-[(1R,2R)-3-oxo-2-[(2Z)-pent-2-en-1-yl]cyclopentyl]hexanoic acid

> <ALOGPS_LOGP>
4.36

> <JCHEM_LOGP>
4.192585537666666

> <ALOGPS_LOGS>
-4.01

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA_STRONGEST_ACIDIC>
4.649285822780022

> <JCHEM_PKA_STRONGEST_BASIC>
-7.422117548650466

> <JCHEM_POLAR_SURFACE_AREA>
54.370000000000005

> <JCHEM_REFRACTIVITY>
76.9605

> <JCHEM_ROTATABLE_BOND_COUNT>
9

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
2.59e-02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
6-[(1R,2R)-3-oxo-2-[(2Z)-pent-2-en-1-yl]cyclopentyl]hexanoic acid

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 24-FEB-12   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   24-FEB-12         0                                  
HETATM    1  O   UNK     0      -5.726   4.982   0.000  0.00  0.00           O+0
HETATM    2  C   UNK     0      -4.195   5.143   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -3.425   6.477   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -1.918   6.156   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      -1.757   4.625   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      -0.424   3.855   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       0.910   4.625   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       2.244   3.855   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       3.577   4.625   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       4.911   3.855   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       6.245   4.625   0.000  0.00  0.00           C+0
HETATM   12  O   UNK     0       7.578   3.855   0.000  0.00  0.00           O+0
HETATM   13  O   UNK     0       6.245   6.165   0.000  0.00  0.00           O+0
HETATM   14  C   UNK     0      -3.164   3.999   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0      -3.484   2.492   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0      -4.949   2.016   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0      -5.269   0.510   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0      -4.125  -0.520   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0      -2.660  -0.045   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3   14                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4    6   14                                                  
CONECT    6    5    7                                                       
CONECT    7    6    8                                                       
CONECT    8    7    9                                                       
CONECT    9    8   10                                                       
CONECT   10    9   11                                                       
CONECT   11   10   12   13                                                  
CONECT   12   11                                                            
CONECT   13   11                                                            
CONECT   14    5    2   15                                                  
CONECT   15   14   16                                                       
CONECT   16   15   17                                                       
CONECT   17   16   18                                                       
CONECT   18   17   19                                                       
CONECT   19   18                                                            
MASTER        0    0    0    0    0    0    0    0   19    0   38    0
END

View in JSmol

Synonyms

Value	Source
OPC-6	ChEBI

Chemical Formula

C₁₆H₂₆O₃

Average Mass

266.3758 Da

Monoisotopic Mass

266.18819 Da

IUPAC Name

6-[(1R,2R)-3-oxo-2-[(2Z)-pent-2-en-1-yl]cyclopentyl]hexanoic acid

Traditional Name

6-[(1R,2R)-3-oxo-2-[(2Z)-pent-2-en-1-yl]cyclopentyl]hexanoic acid

CAS Registry Number

136768-22-4

SMILES

CC\C=C/C[C@@H]1[C@H](CCCCCC(O)=O)CCC1=O

InChI Identifier

InChI=1S/C16H26O3/c1-2-3-5-9-14-13(11-12-15(14)17)8-6-4-7-10-16(18)19/h3,5,13-14H,2,4,6-12H2,1H3,(H,18,19)/b5-3-/t13-,14-/m1/s1

InChI Key

WIJWBOWLVOOYFR-BDSSXFGHSA-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
Vicia faba	FooDB	KNAPSACK

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as prostaglandins and related compounds. These are unsaturated carboxylic acids consisting of a 20 carbon skeleton that also contains a five member ring, and are based upon the fatty acid arachidonic acid.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Fatty Acyls

Sub Class

Eicosanoids

Direct Parent

Prostaglandins and related compounds

Alternative Parents

Substituents

Prostaglandin skeleton
Medium-chain fatty acid
Cyclic ketone
Ketone
Monocarboxylic acid or derivatives
Carboxylic acid
Carboxylic acid derivative
Organic oxygen compound
Organic oxide
Hydrocarbon derivative
Organooxygen compound
Carbonyl group
Aliphatic homomonocyclic compound

Molecular Framework

Aliphatic homomonocyclic compounds

External Descriptors

12-oxophytodienoic acid metabolites (LMFA02010008 )

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	4.36	ALOGPS
logP	4.19	ChemAxon
logS	-4	ALOGPS
pKa (Strongest Acidic)	4.65	ChemAxon
pKa (Strongest Basic)	-7.4	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	3	ChemAxon
Hydrogen Donor Count	1	ChemAxon
Polar Surface Area	54.37 Å²	ChemAxon
Rotatable Bond Count	9	ChemAxon
Refractivity	76.96 m³·mol⁻¹	ChemAxon
Polarizability	31.63 Å³	ChemAxon
Number of Rings	1	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	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

FDB001429

KNApSAcK ID

Not Available

Chemspider ID

Not Available

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

5716901

PDB ID

Not Available

ChEBI ID

139085

Good Scents ID

Not Available

References

General References

Kienow L, Schneider K, Bartsch M, Stuible HP, Weng H, Miersch O, Wasternack C, Kombrink E: Jasmonates meet fatty acids: functional analysis of a new acyl-coenzyme A synthetase family from Arabidopsis thaliana. J Exp Bot. 2008;59(2):403-19. doi: 10.1093/jxb/erm325. Epub 2008 Feb 10. [PubMed:18267944 ]
Huang YQ, Liu JQ, Gong H, Yang J, Li Y, Feng YQ: Use of isotope mass probes for metabolic analysis of the jasmonate biosynthetic pathway. Analyst. 2011 Apr 7;136(7):1515-22. doi: 10.1039/c0an00736f. Epub 2011 Feb 18. [PubMed:21331428 ]

Showing NP-Card for OPC-6:0 (NP0045551)

MOL for NP0045551 (OPC-6:0)

3D MOL for NP0045551 (OPC-6:0)

3D SDF for NP0045551 (OPC-6:0)

3D-SDF for NP0045551 (OPC-6:0)

PDB for NP0045551 (OPC-6:0)

3D PDB for NP0045551 (OPC-6:0)

SMILES for NP0045551 (OPC-6:0)

INCHI for NP0045551 (OPC-6:0)

Structure for NP0045551 (OPC-6:0)

3D Structure for NP0045551 (OPC-6:0)