MiMeDB: Showing metabocard for (3E,5Z)-dodecadienoyl-CoA (MMDBc0054883)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2022-06-17 19:37:04 UTC

Update Date

2022-08-12 20:09:07 UTC

MiMeDB ID

MMDBc0054883

Metabolite Identification

Common Name

(3E,5Z)-dodecadienoyl-CoA

Description

(3E,5Z)-dodecadienoyl-CoA belongs to the class of organic compounds known as 3-enoyl coas. These are organic compounds containing a coenzyme A substructure linked to a 3-enoyl chain. Based on a literature review very few articles have been published on (3E,5Z)-dodecadienoyl-CoA.

Structure

MOL SDF PDB SMILES InChI


  Mrv1652306172221372D          

 70 72  0  0  1  0            999 V2000
   -8.5061   18.4420    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9090   10.3025    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0840   11.7314    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.7917   18.0295    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.7917   17.2045    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.0772   16.7920    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.0772   15.9670    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.3627   15.5545    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.3627   14.7295    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.6482   14.3170    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9338   14.7295    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2193   14.3170    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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    1.4965   11.0170    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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   -1.3614   14.3170    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
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   11.2253    9.2427    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
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  4  1  1  0  0  0  0
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  6  5  1  0  0  0  0
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  9  8  1  0  0  0  0
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 59 53  1  0  0  0  0
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 60 54  1  0  0  0  0
 60 57  1  0  0  0  0
 61 17  1  0  0  0  0
 61 24  1  0  0  0  0
 62  9  1  0  0  0  0
 63 10  1  0  0  0  0
 64 11  1  0  0  0  0
 65 12  1  0  0  0  0
 22 66  1  6  0  0  0
 26 67  1  1  0  0  0
 27 68  1  1  0  0  0
 28 69  1  6  0  0  0
 32 70  1  6  0  0  0
M  CHG  4  41  -1  45  -1  46  -1  47  -1
M  END


  Mrv1652306172221372D          

 70 72  0  0  1  0            999 V2000
   -8.5061   18.4420    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9090   10.3025    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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 28 69  1  6  0  0  0
 32 70  1  6  0  0  0
M  CHG  4  41  -1  45  -1  46  -1  47  -1
M  END
> <DATABASE_ID>
MMDBc0054883

> <DATABASE_NAME>
MIME

> <SMILES>
[H]\C(CCCCCC)=C(/[H])\C(\[H])=C(/[H])CC(=O)SCCN=C([O-])CCN=C([O-])[C@]([H])(O)C(C)(C)COP(O)(=O)OP(O)(=O)OC[C@@]1([H])O[C@@]([H])(N2C=NC3=C(N)N=CN=C23)[C@]([H])(O)[C@]1([H])OP([O-])([O-])=O

> <INCHI_IDENTIFIER>
InChI=1S/C33H54N7O17P3S/c1-4-5-6-7-8-9-10-11-12-13-24(42)61-17-16-35-23(41)14-15-36-31(45)28(44)33(2,3)19-54-60(51,52)57-59(49,50)53-18-22-27(56-58(46,47)48)26(43)32(55-22)40-21-39-25-29(34)37-20-38-30(25)40/h9-12,20-22,26-28,32,43-44H,4-8,13-19H2,1-3H3,(H,35,41)(H,36,45)(H,49,50)(H,51,52)(H2,34,37,38)(H2,46,47,48)/p-4/b10-9-,12-11+/t22-,26-,27-,28+,32-/m1/s1

> <INCHI_KEY>
ARQUZFJQPYWSSL-IAMYAYMBSA-J

> <FORMULA>
C33H50N7O17P3S

> <MOLECULAR_WEIGHT>
941.78

> <EXACT_MASS>
941.221869666

> <JCHEM_ACCEPTOR_COUNT>
19

> <JCHEM_ATOM_COUNT>
111

> <JCHEM_AVERAGE_POLARIZABILITY>
88.37064908171392

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
5

> <JCHEM_FORMAL_CHARGE>
-4

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2R)-4-({[({[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-4-hydroxy-3-(phosphonooxy)oxolan-2-yl]methoxy}(hydroxy)phosphoryl)oxy](hydroxy)phosphoryl}oxy)-N-[2-({2-[(3E,5Z)-dodeca-3,5-dienoylsulfanyl]ethyl}-C-hydroxycarbonimidoyl)ethyl]-2-hydroxy-3,3-dimethylbutanecarboximidate

> <JCHEM_LOGP>
-0.26786001229661577

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-4

> <JCHEM_PKA>
1.8916934609594889

> <JCHEM_PKA_STRONGEST_ACIDIC>
0.8202003156849478

> <JCHEM_PKA_STRONGEST_BASIC>
4.161302034584584

> <JCHEM_POLAR_SURFACE_AREA>
381.9300000000001

> <JCHEM_REFRACTIVITY>
240.37770000000006

> <JCHEM_ROTATABLE_BOND_COUNT>
28

> <JCHEM_RULE_OF_FIVE>
0

> <JCHEM_TRADITIONAL_IUPAC>
(2R)-4-[({[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-4-hydroxy-3-(phosphonooxy)oxolan-2-yl]methoxy(hydroxy)phosphoryl}oxy(hydroxy)phosphoryl)oxy]-N-[2-({2-[(3E,5Z)-dodeca-3,5-dienoylsulfanyl]ethyl}-C-hydroxycarbonimidoyl)ethyl]-2-hydroxy-3,3-dimethylbutanecarboximidate

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 17-JUN-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   17-JUN-22         0                                  
HETATM    1  C   UNK     0     -15.878  34.425   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       3.563  19.231   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       2.023  21.899   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0     -14.544  33.655   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0     -14.544  32.115   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0     -13.211  31.345   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0     -13.211  29.805   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0     -11.877  29.035   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0     -11.877  27.495   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0     -10.543  26.725   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      -9.210  27.495   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      -7.876  26.725   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      -6.542  27.495   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      -1.208  24.415   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0      -1.208  22.875   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0      -3.875  27.495   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0      -3.875  29.035   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0      12.129  21.335   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       4.127  21.335   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0      19.547  16.627   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0      18.202  21.542   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0      13.463  20.565   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0      -2.541  25.185   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0      -6.542  29.035   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0      19.869  19.690   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0      15.130  18.713   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0      13.624  19.033   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0       1.460  19.795   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0      21.115  18.785   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0      18.462  19.063   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0       0.126  20.565   0.000  0.00  0.00           C+0
HETATM   32  C   UNK     0      15.900  20.047   0.000  0.00  0.00           C+0
HETATM   33  C   UNK     0       2.793  20.565   0.000  0.00  0.00           C+0
HETATM   34  N   UNK     0      22.522  19.411   0.000  0.00  0.00           N+0
HETATM   35  N   UNK     0      -2.541  26.725   0.000  0.00  0.00           N+0
HETATM   36  N   UNK     0       0.126  22.105   0.000  0.00  0.00           N+0
HETATM   37  N   UNK     0      20.954  17.253   0.000  0.00  0.00           N+0
HETATM   38  N   UNK     0      18.301  17.532   0.000  0.00  0.00           N+0
HETATM   39  N   UNK     0      19.708  21.221   0.000  0.00  0.00           N+0
HETATM   40  N   UNK     0      17.432  20.208   0.000  0.00  0.00           N+0
HETATM   41  O   UNK     0      -3.875  24.415   0.000  0.00  0.00           O-1
HETATM   42  O   UNK     0      -7.876  29.805   0.000  0.00  0.00           O+0
HETATM   43  O   UNK     0      15.757  17.306   0.000  0.00  0.00           O+0
HETATM   44  O   UNK     0       1.460  18.255   0.000  0.00  0.00           O+0
HETATM   45  O   UNK     0      -1.208  19.795   0.000  0.00  0.00           O-1
HETATM   46  O   UNK     0      11.491  19.944   0.000  0.00  0.00           O-1
HETATM   47  O   UNK     0      10.539  17.014   0.000  0.00  0.00           O-1
HETATM   48  O   UNK     0       9.550  18.955   0.000  0.00  0.00           O+0
HETATM   49  O   UNK     0       8.692  20.001   0.000  0.00  0.00           O+0
HETATM   50  O   UNK     0      10.232  22.669   0.000  0.00  0.00           O+0
HETATM   51  O   UNK     0       7.564  20.001   0.000  0.00  0.00           O+0
HETATM   52  O   UNK     0       6.024  22.669   0.000  0.00  0.00           O+0
HETATM   53  O   UNK     0      10.795  20.565   0.000  0.00  0.00           O+0
HETATM   54  O   UNK     0       5.461  20.565   0.000  0.00  0.00           O+0
HETATM   55  O   UNK     0      14.870  21.191   0.000  0.00  0.00           O+0
HETATM   56  O   UNK     0      12.479  18.003   0.000  0.00  0.00           O+0
HETATM   57  O   UNK     0       8.128  22.105   0.000  0.00  0.00           O+0
HETATM   58  P   UNK     0      11.015  18.479   0.000  0.00  0.00           P+0
HETATM   59  P   UNK     0       9.462  21.335   0.000  0.00  0.00           P+0
HETATM   60  P   UNK     0       6.794  21.335   0.000  0.00  0.00           P+0
HETATM   61  S   UNK     0      -5.209  29.805   0.000  0.00  0.00           S+0
HETATM   62  H   UNK     0     -13.211  26.725   0.000  0.00  0.00           H+0
HETATM   63  H   UNK     0     -10.543  25.185   0.000  0.00  0.00           H+0
HETATM   64  H   UNK     0      -9.210  29.035   0.000  0.00  0.00           H+0
HETATM   65  H   UNK     0      -7.876  25.185   0.000  0.00  0.00           H+0
HETATM   66  H   UNK     0      12.171  19.726   0.000  0.00  0.00           H+0
HETATM   67  H   UNK     0      14.161  17.516   0.000  0.00  0.00           H+0
HETATM   68  H   UNK     0      14.768  20.064   0.000  0.00  0.00           H+0
HETATM   69  H   UNK     0       1.460  21.335   0.000  0.00  0.00           H+0
HETATM   70  H   UNK     0      16.739  18.755   0.000  0.00  0.00           H+0
CONECT    1    4                                                            
CONECT    2   33                                                            
CONECT    3   33                                                            
CONECT    4    1    5                                                       
CONECT    5    4    6                                                       
CONECT    6    5    7                                                       
CONECT    7    6    8                                                       
CONECT    8    7    9                                                       
CONECT    9    8   10   62                                                  
CONECT   10    9   11   63                                                  
CONECT   11   10   12   64                                                  
CONECT   12   11   13   65                                                  
CONECT   13   12   24                                                       
CONECT   14   15   23                                                       
CONECT   15   14   36                                                       
CONECT   16   17   35                                                       
CONECT   17   16   61                                                       
CONECT   18   22   53                                                       
CONECT   19   33   54                                                       
CONECT   20   37   38                                                       
CONECT   21   39   40                                                       
CONECT   22   18   27   55   66                                             
CONECT   23   14   35   41                                                  
CONECT   24   13   42   61                                                  
CONECT   25   29   30   39                                                  
CONECT   26   27   32   43   67                                             
CONECT   27   22   26   56   68                                             
CONECT   28   31   33   44   69                                             
CONECT   29   25   34   37                                                  
CONECT   30   25   38   40                                                  
CONECT   31   28   36   45                                                  
CONECT   32   26   40   55   70                                             
CONECT   33    2    3   19   28                                             
CONECT   34   29                                                            
CONECT   35   16   23                                                       
CONECT   36   15   31                                                       
CONECT   37   20   29                                                       
CONECT   38   20   30                                                       
CONECT   39   21   25                                                       
CONECT   40   21   30   32                                                  
CONECT   41   23                                                            
CONECT   42   24                                                            
CONECT   43   26                                                            
CONECT   44   28                                                            
CONECT   45   31                                                            
CONECT   46   58                                                            
CONECT   47   58                                                            
CONECT   48   58                                                            
CONECT   49   59                                                            
CONECT   50   59                                                            
CONECT   51   60                                                            
CONECT   52   60                                                            
CONECT   53   18   59                                                       
CONECT   54   19   60                                                       
CONECT   55   22   32                                                       
CONECT   56   27   58                                                       
CONECT   57   59   60                                                       
CONECT   58   46   47   48   56                                             
CONECT   59   49   50   53   57                                             
CONECT   60   51   52   54   57                                             
CONECT   61   17   24                                                       
CONECT   62    9                                                            
CONECT   63   10                                                            
CONECT   64   11                                                            
CONECT   65   12                                                            
CONECT   66   22                                                            
CONECT   67   26                                                            
CONECT   68   27                                                            
CONECT   69   28                                                            
CONECT   70   32                                                            
MASTER        0    0    0    0    0    0    0    0   70    0  144    0
END

Synonyms

Not Available

Chemical Formula

C₃₃H₅₀N₇O₁₇P₃S

Average Molecular Weight

941.78

Monoisotopic Molecular Weight

941.221869666

IUPAC Name

(2R)-4-({[({[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-4-hydroxy-3-(phosphonooxy)oxolan-2-yl]methoxy}(hydroxy)phosphoryl)oxy](hydroxy)phosphoryl}oxy)-N-[2-({2-[(3E,5Z)-dodeca-3,5-dienoylsulfanyl]ethyl}-C-hydroxycarbonimidoyl)ethyl]-2-hydroxy-3,3-dimethylbutanecarboximidate

Traditional Name

(2R)-4-[({[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-4-hydroxy-3-(phosphonooxy)oxolan-2-yl]methoxy(hydroxy)phosphoryl}oxy(hydroxy)phosphoryl)oxy]-N-[2-({2-[(3E,5Z)-dodeca-3,5-dienoylsulfanyl]ethyl}-C-hydroxycarbonimidoyl)ethyl]-2-hydroxy-3,3-dimethylbutanecarboximidate

CAS Registry Number

Not Available

SMILES

[H]\C(CCCCCC)=C(/[H])\C(\[H])=C(/[H])CC(=O)SCCN=C([O-])CCN=C([O-])[C@]([H])(O)C(C)(C)COP(O)(=O)OP(O)(=O)OC[C@@]1([H])O[C@@]([H])(N2C=NC3=C(N)N=CN=C23)[C@]([H])(O)[C@]1([H])OP([O-])([O-])=O

InChI Identifier

InChI=1S/C33H54N7O17P3S/c1-4-5-6-7-8-9-10-11-12-13-24(42)61-17-16-35-23(41)14-15-36-31(45)28(44)33(2,3)19-54-60(51,52)57-59(49,50)53-18-22-27(56-58(46,47)48)26(43)32(55-22)40-21-39-25-29(34)37-20-38-30(25)40/h9-12,20-22,26-28,32,43-44H,4-8,13-19H2,1-3H3,(H,35,41)(H,36,45)(H,49,50)(H,51,52)(H2,34,37,38)(H2,46,47,48)/p-4/b10-9-,12-11+/t22-,26-,27-,28+,32-/m1/s1

InChI Key

ARQUZFJQPYWSSL-IAMYAYMBSA-J

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as 3-enoyl coas. These are organic compounds containing a coenzyme A substructure linked to a 3-enoyl chain.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Fatty Acyls

Sub Class

Fatty acyl thioesters

Direct Parent

3-enoyl CoAs

Alternative Parents

Substituents

Coenzyme a or derivatives
Purine ribonucleoside diphosphate
Purine ribonucleoside bisphosphate
Purine ribonucleoside 3',5'-bisphosphate
Ribonucleoside 3'-phosphate
Pentose-5-phosphate
Pentose phosphate
N-glycosyl compound
Glycosyl compound
Organic pyrophosphate
Monosaccharide phosphate
6-aminopurine
Purine
Imidazopyrimidine
Monoalkyl phosphate
Aminopyrimidine
Imidolactam
Alkyl phosphate
Pyrimidine
Phosphoric acid ester
Organic phosphoric acid derivative
N-substituted imidazole
Monosaccharide
Heteroaromatic compound
Tetrahydrofuran
Imidazole
Azole
Carbothioic s-ester
Thiocarboxylic acid ester
Secondary alcohol
Amino acid or derivatives
Oxacycle
Azacycle
Organoheterocyclic compound
Sulfenyl compound
Thiocarboxylic acid or derivatives
Carboxylic acid derivative
Carboximidic acid derivative
Carboximidic acid
Organic nitrogen compound
Organic oxygen compound
Organopnictogen compound
Organic oxide
Hydrocarbon derivative
Primary amine
Organosulfur compound
Organooxygen compound
Organonitrogen compound
Carbonyl group
Amine
Alcohol
Organic anion
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic heteropolycyclic compounds

External Descriptors

Not Available

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
logP	-0.27	ChemAxon
pKa (Strongest Acidic)	0.82	ChemAxon
pKa (Strongest Basic)	4.16	ChemAxon
Physiological Charge	-4	ChemAxon
Hydrogen Acceptor Count	19	ChemAxon
Hydrogen Donor Count	5	ChemAxon
Polar Surface Area	381.93 Å²	ChemAxon
Rotatable Bond Count	28	ChemAxon
Refractivity	240.38 m³·mol⁻¹	ChemAxon
Polarizability	88.37 Å³	ChemAxon
Number of Rings	3	ChemAxon
Bioavailability	No	ChemAxon
Rule of Five	No	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	Yes	ChemAxon

Spectra

Not Available

Biological Properties

Cellular Locations

Not Available

Biospecimen Locations

Not Available

Tissue Locations

Not Available

Associated OMIM IDs

114500 (Colorectal cancer)
610247 (Eosinophilic esophagitis)

Human Proteins and Enzymes

Proteins

Human Pathways

Pathways

Name	SMPDB/PathBank

Metabolic Reactions

Reaction ID	Precursor	Product	Enzyme	Reaction Type	Data Source	Reference

Health Effects and Bioactivity

Health Outcome/Bioactivity	Metabolite Response/Effect	Related Health Condition	Evidence Type	Measured in Matrix	Data Source	Reference

Microbial Sources

Kingdom	Phylum	Total species	Hosts and Body Sites	Microbial Links
	Proteobacteria	1

Exposure Sources

Source Type	Source Sub-type	Species	Data Source	Reference	Details

Host Biospecimen and Location

Host and Biospecimen	Status	Mean	Std	Min	Max	Units	Age	Sex	Health Condition	Data Source	Reference

External Links

HMDB ID

Not Available

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

Not Available

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

129900405

PDB ID

Not Available

ChEBI ID

138558

Food Biomarker Ontology

Not Available

References

Synthesis Reference

Not Available

General References

Bansal P, Morgat A, Axelsen KB, Muthukrishnan V, Coudert E, Aimo L, Hyka-Nouspikel N, Gasteiger E, Kerhornou A, Neto TB, Pozzato M, Blatter MC, Ignatchenko A, Redaschi N, Bridge A: Rhea, the reaction knowledgebase in 2022. Nucleic Acids Res. 2022 Jan 7;50(D1):D693-D700. doi: 10.1093/nar/gkab1016. [PubMed:34755880 ]

Showing metabocard for (3E,5Z)-dodecadienoyl-CoA (MMDBc0054883)

MOL for #<Metabolite:0x000055b76a509d40>

3D MOL for #<Metabolite:0x000055b76a509d40>

3D SDF for #<Metabolite:0x000055b76a509d40>

3D-SDF for #<Metabolite:0x000055b76a509d40>

PDB for #<Metabolite:0x000055b76a509d40>

3D PDB for #<Metabolite:0x000055b76a509d40>

SMILES for #<Metabolite:0x000055b76a509d40>

INCHI for #<Metabolite:0x000055b76a509d40>

Structure for #<Metabolite:0x000055b76a509d40>

3D Structure for #<Metabolite:0x000055b76a509d40>