NP-MRD: Showing NP-Card for Pseudomonic acid D (NP0061992)

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Record Information

Version

2.0

Created at

2022-04-28 06:41:00 UTC

Updated at

2022-04-28 06:41:00 UTC

NP-MRD ID

NP0061992

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Pseudomonic acid D

Description

Pseudomonic acid D, also known as pseudomonate D, belongs to the class of organic compounds known as medium-chain fatty acids. These are fatty acids with an aliphatic tail that contains between 4 and 12 carbon atoms. Pseudomonic acid D is found in Pseudomonas fluorescens and Pseudomonas fluorescens NCIB 10586. Based on a literature review very few articles have been published on Pseudomonic acid D.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652304282208412D          

 35 36  0  0  1  0            999 V2000
   -1.4289    4.1250    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.4289    4.9500    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.7145    5.3625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0000    4.9500    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0000    4.1250    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.7145    3.7125    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.7145    2.8875    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    3.7125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    4.1250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434    3.7125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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 31 33  1  6  0  0  0
 30 34  1  1  0  0  0
  1 35  1  6  0  0  0
M  END

     RDKit          3D

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M  END


  Mrv1652304282208412D          

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 27 28  1  0  0  0  0
 28 29  1  0  0  0  0
 27 29  1  0  0  0  0
 29 30  1  1  0  0  0
 30 31  1  0  0  0  0
 31 32  1  0  0  0  0
 31 33  1  6  0  0  0
 30 34  1  1  0  0  0
  1 35  1  6  0  0  0
M  END
> <DATABASE_ID>
NP0061992

> <DATABASE_NAME>
NP-MRD

> <SMILES>
C[C@H](O)[C@H](C)[C@@H]1O[C@H]1C[C@H]1CO[C@@H](C\C(C)=C\C(=O)OCCCC\C=C\CCC(O)=O)[C@H](O)[C@@H]1O

> <INCHI_IDENTIFIER>
InChI=1S/C26H42O9/c1-16(13-23(30)33-11-9-7-5-4-6-8-10-22(28)29)12-20-25(32)24(31)19(15-34-20)14-21-26(35-21)17(2)18(3)27/h4,6,13,17-21,24-27,31-32H,5,7-12,14-15H2,1-3H3,(H,28,29)/b6-4+,16-13+/t17-,18-,19-,20-,21-,24+,25-,26-/m0/s1

> <INCHI_KEY>
RJGJFSVDQPCELW-VCXQKUNESA-N

> <FORMULA>
C26H42O9

> <MOLECULAR_WEIGHT>
498.613

> <EXACT_MASS>
498.282882932

> <JCHEM_ACCEPTOR_COUNT>
8

> <JCHEM_ATOM_COUNT>
77

> <JCHEM_AVERAGE_POLARIZABILITY>
54.53451245589885

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(4E)-9-{[(2E)-4-[(2S,3R,4R,5S)-3,4-dihydroxy-5-{[(2S,3S)-3-[(2S,3S)-3-hydroxybutan-2-yl]oxiran-2-yl]methyl}oxan-2-yl]-3-methylbut-2-enoyl]oxy}non-4-enoic acid

> <ALOGPS_LOGP>
2.55

> <JCHEM_LOGP>
2.089404018999999

> <ALOGPS_LOGS>
-4.08

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
13.104769927633853

> <JCHEM_PKA_STRONGEST_ACIDIC>
4.762415996553696

> <JCHEM_PKA_STRONGEST_BASIC>
-2.71476683945935

> <JCHEM_POLAR_SURFACE_AREA>
146.05

> <JCHEM_REFRACTIVITY>
130.51069999999996

> <JCHEM_ROTATABLE_BOND_COUNT>
16

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
4.16e-02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(4E)-9-{[(2E)-4-[(2S,3R,4R,5S)-3,4-dihydroxy-5-{[(2S,3S)-3-[(2S,3S)-3-hydroxybutan-2-yl]oxiran-2-yl]methyl}oxan-2-yl]-3-methylbut-2-enoyl]oxy}non-4-enoic acid

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 28-APR-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   28-APR-22         0                                  
HETATM    1  C   UNK     0      -2.667   7.700   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -2.667   9.240   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -1.334  10.010   0.000  0.00  0.00           C+0
HETATM    4  O   UNK     0      -0.000   9.240   0.000  0.00  0.00           O+0
HETATM    5  C   UNK     0      -0.000   7.700   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      -1.334   6.930   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0      -1.334   5.390   0.000  0.00  0.00           O+0
HETATM    8  C   UNK     0       1.334   6.930   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       2.667   7.700   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       4.001   6.930   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       5.335   7.700   0.000  0.00  0.00           C+0
HETATM   12  O   UNK     0       5.335   9.240   0.000  0.00  0.00           O+0
HETATM   13  O   UNK     0       6.668   6.930   0.000  0.00  0.00           O+0
HETATM   14  C   UNK     0       8.002   7.700   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       9.336   6.930   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0      10.669   7.700   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0      12.003   6.930   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0      13.337   7.700   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0      14.670   6.930   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0      16.004   7.700   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0      17.338   6.930   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0      18.672   7.700   0.000  0.00  0.00           C+0
HETATM   23  O   UNK     0      20.005   6.930   0.000  0.00  0.00           O+0
HETATM   24  O   UNK     0      18.672   9.240   0.000  0.00  0.00           O+0
HETATM   25  C   UNK     0       2.667   9.240   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0      -4.001  10.010   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0      -5.335   9.240   0.000  0.00  0.00           C+0
HETATM   28  O   UNK     0      -6.105   7.906   0.000  0.00  0.00           O+0
HETATM   29  C   UNK     0      -6.875   9.240   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0      -8.208  10.010   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0      -8.208  11.550   0.000  0.00  0.00           C+0
HETATM   32  C   UNK     0      -9.542  12.320   0.000  0.00  0.00           C+0
HETATM   33  O   UNK     0      -6.875  12.320   0.000  0.00  0.00           O+0
HETATM   34  C   UNK     0      -9.542   9.240   0.000  0.00  0.00           C+0
HETATM   35  O   UNK     0      -4.001   6.930   0.000  0.00  0.00           O+0
CONECT    1    2    6   35                                                  
CONECT    2    1    3   26                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4    6    8                                                  
CONECT    6    5    1    7                                                  
CONECT    7    6                                                            
CONECT    8    5    9                                                       
CONECT    9    8   10   25                                                  
CONECT   10    9   11                                                       
CONECT   11   10   12   13                                                  
CONECT   12   11                                                            
CONECT   13   11   14                                                       
CONECT   14   13   15                                                       
CONECT   15   14   16                                                       
CONECT   16   15   17                                                       
CONECT   17   16   18                                                       
CONECT   18   17   19                                                       
CONECT   19   18   20                                                       
CONECT   20   19   21                                                       
CONECT   21   20   22                                                       
CONECT   22   21   23   24                                                  
CONECT   23   22                                                            
CONECT   24   22                                                            
CONECT   25    9                                                            
CONECT   26    2   27                                                       
CONECT   27   26   28   29                                                  
CONECT   28   27   29                                                       
CONECT   29   28   27   30                                                  
CONECT   30   29   31   34                                                  
CONECT   31   30   32   33                                                  
CONECT   32   31                                                            
CONECT   33   31                                                            
CONECT   34   30                                                            
CONECT   35    1                                                            
MASTER        0    0    0    0    0    0    0    0   35    0   72    0
END

View in JSmol

Synonyms

Value	Source
Pseudomonate D	Generator

Chemical Formula

C₂₆H₄₂O₉

Average Mass

498.6130 Da

Monoisotopic Mass

498.28288 Da

IUPAC Name

(4E)-9-{[(2E)-4-[(2S,3R,4R,5S)-3,4-dihydroxy-5-{[(2S,3S)-3-[(2S,3S)-3-hydroxybutan-2-yl]oxiran-2-yl]methyl}oxan-2-yl]-3-methylbut-2-enoyl]oxy}non-4-enoic acid

Traditional Name

(4E)-9-{[(2E)-4-[(2S,3R,4R,5S)-3,4-dihydroxy-5-{[(2S,3S)-3-[(2S,3S)-3-hydroxybutan-2-yl]oxiran-2-yl]methyl}oxan-2-yl]-3-methylbut-2-enoyl]oxy}non-4-enoic acid

CAS Registry Number

Not Available

SMILES

C[C@H](O)[C@H](C)[C@@H]1O[C@H]1C[C@H]1CO[C@@H](C\C(C)=C\C(=O)OCCCC\C=C\CCC(O)=O)[C@H](O)[C@@H]1O

InChI Identifier

InChI=1S/C26H42O9/c1-16(13-23(30)33-11-9-7-5-4-6-8-10-22(28)29)12-20-25(32)24(31)19(15-34-20)14-21-26(35-21)17(2)18(3)27/h4,6,13,17-21,24-27,31-32H,5,7-12,14-15H2,1-3H3,(H,28,29)/b6-4+,16-13+/t17-,18-,19-,20-,21-,24+,25-,26-/m0/s1

InChI Key

RJGJFSVDQPCELW-VCXQKUNESA-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
Pseudomonas fluorescens	LOTUS Database	35616633
Pseudomonas fluorescens NCIB 10586	Bacteria	KNApSAcK

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as medium-chain fatty acids. These are fatty acids with an aliphatic tail that contains between 4 and 12 carbon atoms.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Fatty Acyls

Sub Class

Fatty acids and conjugates

Direct Parent

Medium-chain fatty acids

Alternative Parents

Substituents

Medium-chain fatty acid
Branched fatty acid
Epoxy fatty acid
Fatty acid ester
Heterocyclic fatty acid
Hydroxy fatty acid
Unsaturated fatty acid
Oxane
Monosaccharide
Dicarboxylic acid or derivatives
Enoate ester
Alpha,beta-unsaturated carboxylic ester
Secondary alcohol
Carboxylic acid ester
1,2-diol
Oxacycle
Organoheterocyclic compound
Carboxylic acid derivative
Carboxylic acid
Dialkyl ether
Oxirane
Ether
Hydrocarbon derivative
Organic oxygen compound
Carbonyl group
Organic oxide
Alcohol
Organooxygen compound
Aliphatic heteromonocyclic compound

Molecular Framework

Aliphatic heteromonocyclic 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	2.55	ALOGPS
logP	2.09	ChemAxon
logS	-4.1	ALOGPS
pKa (Strongest Acidic)	4.76	ChemAxon
pKa (Strongest Basic)	-2.7	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	8	ChemAxon
Hydrogen Donor Count	4	ChemAxon
Polar Surface Area	146.05 Å²	ChemAxon
Rotatable Bond Count	16	ChemAxon
Refractivity	130.51 m³·mol⁻¹	ChemAxon
Polarizability	54.53 Å³	ChemAxon
Number of Rings	2	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

C00017911

Chemspider ID

8204442

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

10028871

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Not Available

Showing NP-Card for Pseudomonic acid D (NP0061992)

MOL for NP0061992 (Pseudomonic acid D)

3D MOL for NP0061992 (Pseudomonic acid D)

3D SDF for NP0061992 (Pseudomonic acid D)

3D-SDF for NP0061992 (Pseudomonic acid D)

PDB for NP0061992 (Pseudomonic acid D)

3D PDB for NP0061992 (Pseudomonic acid D)

SMILES for NP0061992 (Pseudomonic acid D)

INCHI for NP0061992 (Pseudomonic acid D)

Structure for NP0061992 (Pseudomonic acid D)

3D Structure for NP0061992 (Pseudomonic acid D)