NP-MRD: Showing NP-Card for S-Glutaryldihydrolipoamide (NP0087652)

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Record Information

Version

2.0

Created at

2022-05-11 16:55:51 UTC

Updated at

2022-05-11 16:55:52 UTC

NP-MRD ID

NP0087652

Secondary Accession Numbers

None

Natural Product Identification

Common Name

S-Glutaryldihydrolipoamide

Description

S-Glutaryldihydrolipoamide belongs to the class of organic compounds known as thia fatty acids. These are fatty acid derivatives obtained by insertion of a sulfur atom at specific positions in the chain. S-Glutaryldihydrolipoamide is an extremely weak basic (essentially neutral) compound (based on its pKa). S-Glutaryldihydrolipoamide can be reversibly created from Glutaryl-CoA by 2-oxoglutarate dehydrogenase E2 component (dihydrolipoamide. Succinyltransferase).

Structure

MOL 3D MOL SDF PDB SMILES InChI

     RDKit          3D

 43 42  0  0  0  0  0  0  0  0999 V2000
   -4.4611    0.1575   -2.9557 N   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4024   -0.7873   -1.9171 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4706   -2.0052   -2.1831 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2588   -0.2839   -0.5133 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1737   -1.3860    0.4728 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0808   -2.3460    0.4068 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6833   -2.0081    0.7483 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0047   -0.8828    0.1204 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.9472   -0.8452   -1.6668 S   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0664    0.4125    0.8405 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3663    0.2679    2.1999 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3368   -0.2380    1.8615 S   0  0  0  0  0  0  0  0  0  0  0  0
    2.1751    1.0918    1.0236 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5782    2.1078    0.7820 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.6223    0.8629    0.6555 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0976    2.0999   -0.0209 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.5036    2.1143   -0.4747 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.8705    1.0857   -1.4532 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.9621    0.2875   -1.8363 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.1124    0.9059   -1.9953 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6049    0.6331   -3.2857 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.3677    0.3830   -3.3976 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.2694    0.2190   -0.3138 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5528    0.5144   -0.5145 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1910   -0.8764    1.4960 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.1906   -1.8990    0.4600 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3718   -3.1920    1.1477 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0864   -2.9361   -0.5755 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5660   -1.9994    1.8837 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0308   -2.9536    0.5069 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1942   -1.1543    0.3341 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3290   -2.1011   -2.1597 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5667    1.2361    0.2528 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0938    0.7192    1.0757 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3673    1.2724    2.7177 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8788   -0.4855    2.7806 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.6001   -0.0397    0.0130 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.1786    0.6551    1.6129 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.9882    2.9349    0.7301 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.3622    2.3556   -0.8186 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.2012    2.1084    0.3918 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.6799    3.1089   -0.9696 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.9194    0.8855   -1.3620 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  2  0
  2  4  1  0
  4  5  1  0
  5  6  1  0
  6  7  1  0
  7  8  1  0
  8  9  1  0
  8 10  1  0
 10 11  1  0
 11 12  1  0
 12 13  1  0
 13 14  2  0
 13 15  1  0
 15 16  1  0
 16 17  1  0
 17 18  1  0
 18 20  1  0
 18 19  2  0
  1 21  1  0
  1 22  1  0
  4 23  1  0
  4 24  1  0
  5 25  1  0
  5 26  1  0
  6 27  1  0
  6 28  1  0
  7 29  1  0
  7 30  1  0
  8 31  1  1
  9 32  1  0
 10 33  1  0
 10 34  1  0
 11 35  1  0
 11 36  1  0
 15 37  1  0
 15 38  1  0
 16 39  1  0
 16 40  1  0
 17 41  1  0
 17 42  1  0
 20 43  1  0
M  END

 
  Mrv0541 02231220532D          
 
 20 19  0  0  0  0            999 V2000
   11.6076  -11.2053    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.3202  -11.6185    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.8915  -11.6185    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
   13.0329  -11.2053    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   13.7454  -11.6185    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   14.4617  -11.2053    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   15.1742  -11.6185    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   15.8834  -11.1984    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   15.1707  -12.4446    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   11.6081  -10.3962    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.8820   -9.9762    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.1710  -10.3862    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
    9.4752   -9.9834    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.7607  -10.3960    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.0461   -9.9834    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.3316  -10.3960    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.6170   -9.9834    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.9025  -10.3960    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    9.4756   -9.1585    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.6170   -9.1586    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  1  3  1  0  0  0  0
  2  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  1  0  0  0  0
  7  8  1  0  0  0  0
  7  9  2  0  0  0  0
  1 10  1  0  0  0  0
 10 11  1  0  0  0  0
 11 12  1  0  0  0  0
 12 13  1  0  0  0  0
 13 14  1  0  0  0  0
 14 15  1  0  0  0  0
 15 16  1  0  0  0  0
 16 17  1  0  0  0  0
 17 18  1  0  0  0  0
 13 19  2  0  0  0  0
 17 20  2  0  0  0  0
M  END
> <DATABASE_ID>
NP0087652

> <DATABASE_NAME>
NP-MRD

> <SMILES>
NC(=O)CCCCC(S)CCSC(=O)CCCC(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C13H23NO4S2/c14-11(15)5-2-1-4-10(19)8-9-20-13(18)7-3-6-12(16)17/h10,19H,1-9H2,(H2,14,15)(H,16,17)

> <INCHI_KEY>
PWTIHZUSTBSVGF-UHFFFAOYSA-N

> <FORMULA>
C13H23NO4S2

> <MOLECULAR_WEIGHT>
321.456

> <EXACT_MASS>
321.106849609

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_AVERAGE_POLARIZABILITY>
35.27170272687727

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
5-[(7-carbamoyl-3-sulfanylheptyl)sulfanyl]-5-oxopentanoic acid

> <ALOGPS_LOGP>
2.36

> <JCHEM_LOGP>
1.5058994909999999

> <ALOGPS_LOGS>
-3.87

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
10.059201348092051

> <JCHEM_PKA_STRONGEST_ACIDIC>
4.141973953441258

> <JCHEM_PKA_STRONGEST_BASIC>
-0.5791181618545472

> <JCHEM_POLAR_SURFACE_AREA>
97.46000000000001

> <JCHEM_REFRACTIVITY>
82.72089999999999

> <JCHEM_ROTATABLE_BOND_COUNT>
13

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
4.29e-02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
S(8)-glutaryldihydrolipoamide

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 23-FEB-12   NONE
TITLE     NULL                                                        
COMPND    MOLECULE:                                                   
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   23-FEB-12         0                                  
HETATM    1  C   UNK     0      21.667 -20.917   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      22.998 -21.688   0.000  0.00  0.00           C+0
HETATM    3  S   UNK     0      20.331 -21.688   0.000  0.00  0.00           S+0
HETATM    4  C   UNK     0      24.328 -20.917   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      25.658 -21.688   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      26.995 -20.917   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      28.325 -21.688   0.000  0.00  0.00           C+0
HETATM    8  N   UNK     0      29.649 -20.904   0.000  0.00  0.00           N+0
HETATM    9  O   UNK     0      28.319 -23.230   0.000  0.00  0.00           O+0
HETATM   10  C   UNK     0      21.668 -19.406   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      20.313 -18.622   0.000  0.00  0.00           C+0
HETATM   12  S   UNK     0      18.986 -19.388   0.000  0.00  0.00           S+0
HETATM   13  C   UNK     0      17.687 -18.636   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      16.353 -19.406   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0      15.019 -18.636   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0      13.686 -19.406   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0      12.352 -18.636   0.000  0.00  0.00           C+0
HETATM   18  O   UNK     0      11.018 -19.406   0.000  0.00  0.00           O+0
HETATM   19  O   UNK     0      17.688 -17.096   0.000  0.00  0.00           O+0
HETATM   20  O   UNK     0      12.352 -17.096   0.000  0.00  0.00           O+0
CONECT    1    2    3   10                                                  
CONECT    2    1    4                                                       
CONECT    3    1                                                            
CONECT    4    2    5                                                       
CONECT    5    4    6                                                       
CONECT    6    5    7                                                       
CONECT    7    6    8    9                                                  
CONECT    8    7                                                            
CONECT    9    7                                                            
CONECT   10    1   11                                                       
CONECT   11   10   12                                                       
CONECT   12   11   13                                                       
CONECT   13   12   14   19                                                  
CONECT   14   13   15                                                       
CONECT   15   14   16                                                       
CONECT   16   15   17                                                       
CONECT   17   16   18   20                                                  
CONECT   18   17                                                            
CONECT   19   13                                                            
CONECT   20   17                                                            
MASTER        0    0    0    0    0    0    0    0   20    0   38    0
END

View in JSmol

Synonyms

Value	Source
S-Glutaryldihydrolipoamide-e	ChEBI
S-Glutaryldihydrolipoamide	ChEBI

Chemical Formula

C₁₃H₂₃NO₄S₂

Average Mass

321.4560 Da

Monoisotopic Mass

321.10685 Da

IUPAC Name

5-[(7-carbamoyl-3-sulfanylheptyl)sulfanyl]-5-oxopentanoic acid

Traditional Name

S(8)-glutaryldihydrolipoamide

CAS Registry Number

Not Available

SMILES

NC(=O)CCCCC(S)CCSC(=O)CCCC(O)=O

InChI Identifier

InChI=1S/C13H23NO4S2/c14-11(15)5-2-1-4-10(19)8-9-20-13(18)7-3-6-12(16)17/h10,19H,1-9H2,(H2,14,15)(H,16,17)

InChI Key

PWTIHZUSTBSVGF-UHFFFAOYSA-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
Anas platyrhynchos	FooDB	FooDB
Anatidae	FooDB	FooDB
Anser anser	FooDB	FooDB
Bison bison	FooDB	FooDB
Bos taurus	FooDB	FooDB
Bos taurus X Bison bison	FooDB	FooDB
Bubalus bubalis	FooDB	FooDB
Capra aegagrus hircus	FooDB	FooDB
Cervidae	FooDB	FooDB
Cervus canadensis	FooDB	FooDB
Columba	FooDB	FooDB
Columbidae	FooDB	FooDB
Dromaius novaehollandiae	FooDB	FooDB
Equus caballus	FooDB	FooDB
Gallus gallus	FooDB	FooDB
Lagopus muta	FooDB	FooDB
Leporidae	FooDB	FooDB
Lepus timidus	FooDB	FooDB
Melanitta fusca	FooDB	FooDB
Meleagris gallopavo	FooDB	FooDB
Numida meleagris	FooDB	FooDB
Odocoileus	FooDB	FooDB
Oryctolagus	FooDB	FooDB
Ovis aries	FooDB	FooDB
Phasianidae	FooDB	FooDB
Phasianus colchicus	FooDB	FooDB
Struthio camelus	FooDB	FooDB
Sus scrofa	FooDB	FooDB
Sus scrofa domestica	FooDB	FooDB

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as thia fatty acids. These are fatty acid derivatives obtained by insertion of a sulfur atom at specific positions in the chain.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Fatty Acyls

Sub Class

Fatty acids and conjugates

Direct Parent

Thia fatty acids

Alternative Parents

Substituents

Thia fatty acid
Fatty acyl thioester
Fatty amide
Carboxamide group
Primary carboxylic acid amide
Thiocarboxylic acid ester
Carbothioic s-ester
Sulfenyl compound
Thiocarboxylic acid or derivatives
Alkylthiol
Monocarboxylic acid or derivatives
Carboxylic acid
Carboxylic acid derivative
Carbonyl group
Organic oxygen compound
Organosulfur compound
Organooxygen compound
Organonitrogen compound
Organic nitrogen compound
Organopnictogen compound
Hydrocarbon derivative
Organic oxide
Aliphatic acyclic compound

Molecular Framework

Aliphatic acyclic compounds

External Descriptors

S-substituted dihydrolipoamide (CHEBI:28391 )

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	2.36	ALOGPS
logP	1.51	ChemAxon
logS	-3.9	ALOGPS
pKa (Strongest Acidic)	4.14	ChemAxon
pKa (Strongest Basic)	-0.58	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	4	ChemAxon
Hydrogen Donor Count	3	ChemAxon
Polar Surface Area	97.46 Å²	ChemAxon
Rotatable Bond Count	13	ChemAxon
Refractivity	82.72 m³·mol⁻¹	ChemAxon
Polarizability	35.27 Å³	ChemAxon
Number of Rings	0	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

HMDB0006832

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

FDB024108

KNApSAcK ID

Not Available

Chemspider ID

10128178

KEGG Compound ID

C06157

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

11953879

PDB ID

Not Available

ChEBI ID

28391

Good Scents ID

Not Available

References

General References

Not Available

Showing NP-Card for S-Glutaryldihydrolipoamide (NP0087652)

MOL for NP0087652 (S-Glutaryldihydrolipoamide)

3D MOL for NP0087652 (S-Glutaryldihydrolipoamide)

3D SDF for NP0087652 (S-Glutaryldihydrolipoamide)

3D-SDF for NP0087652 (S-Glutaryldihydrolipoamide)

PDB for NP0087652 (S-Glutaryldihydrolipoamide)

3D PDB for NP0087652 (S-Glutaryldihydrolipoamide)

SMILES for NP0087652 (S-Glutaryldihydrolipoamide)

INCHI for NP0087652 (S-Glutaryldihydrolipoamide)

Structure for NP0087652 (S-Glutaryldihydrolipoamide)

3D Structure for NP0087652 (S-Glutaryldihydrolipoamide)