Np mrd loader

Showing NP-Card for (4R,8R,12R)-Trimethyl-2E-tridecenoyl-CoA (NP0339009)

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Record Information
Version2.0
Created at2024-09-11 19:13:22 UTC
Updated at2024-09-11 19:13:23 UTC
NP-MRD IDNP0339009
Secondary Accession NumbersNone
Natural Product Identification
Common Name(4R,8R,12R)-Trimethyl-2E-tridecenoyl-CoA
Description(4R,8R,12R)-Trimethyl-2E-tridecenoyl-CoA belongs to the class of organic compounds known as long-chain 2-enoyl coas. These are organic compounds containing a coenzyme A substructure linked to a long-chain 2-enoyl chain of 13 to 21 carbon atoms (4R,8R,12R)-Trimethyl-2E-tridecenoyl-CoA is a strong basic compound (based on its pKa).
Structure
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MOLSDFPDBSMILESInChI

MOL for NP0339009 ((4R,8R,12R)-Trimethyl-2E-tridecenoyl-CoA)


  Mrv0541 02251208052D          

 65 67  0  0  1  0            999 V2000
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M  CHG  4  37  -1  41  -1  53  -1  54  -1
M  END
Download

3D MOL for NP0339009 ((4R,8R,12R)-Trimethyl-2E-tridecenoyl-CoA)

Download
3D SDF for NP0339009 ((4R,8R,12R)-Trimethyl-2E-tridecenoyl-CoA)

  Mrv0541 02251208052D          

 65 67  0  0  1  0            999 V2000
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M  CHG  4  37  -1  41  -1  53  -1  54  -1
M  END
> <DATABASE_ID>
NP0339009

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CC(C)CCC[C@H](C)CCC[C@H](C)\C=C\C(=O)SCCNC(=O)CCNC(=O)C(O)C(C)(C)COP([O-])(=O)OP([O-])(=O)OC[C@H]1O[C@H]([C@@H](O)[C@H]1OP([O-])([O-])=O)N1C=NC2=C1N=CN=C2N

> <INCHI_IDENTIFIER>
InChI=1S/C37H64N7O17P3S/c1-23(2)9-7-10-24(3)11-8-12-25(4)13-14-28(46)65-18-17-39-27(45)15-16-40-35(49)32(48)37(5,6)20-58-64(55,56)61-63(53,54)57-19-26-31(60-62(50,51)52)30(47)36(59-26)44-22-43-29-33(38)41-21-42-34(29)44/h13-14,21-26,30-32,36,47-48H,7-12,15-20H2,1-6H3,(H,39,45)(H,40,49)(H,53,54)(H,55,56)(H2,38,41,42)(H2,50,51,52)/p-4/b14-13+/t24-,25-,26+,30-,31-,32?,36+/m0/s1

> <INCHI_KEY>
XDRCVDXWYZRMDN-BFEXNXLWSA-J

> <FORMULA>
C37H60N7O17P3S

> <MOLECULAR_WEIGHT>
999.895

> <EXACT_MASS>
999.297923755

> <JCHEM_ACCEPTOR_COUNT>
17

> <JCHEM_AVERAGE_POLARIZABILITY>
97.94456029977897

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
5

> <JCHEM_FORMAL_CHARGE>
-4

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
3-hydroxy-2,2-dimethyl-3-({2-[(2-{[(2E,4S,8S)-4,8,12-trimethyltridec-2-enoyl]sulfanyl}ethyl)carbamoyl]ethyl}carbamoyl)propyl ({[(2R,3R,4S,5R)-5-(6-amino-9H-purin-9-yl)-4-hydroxy-3-(phosphonatooxy)oxolan-2-yl]methyl phosphonato}oxy)phosphonate

> <ALOGPS_LOGP>
2.86

> <JCHEM_LOGP>
-0.7367742609663538

> <ALOGPS_LOGS>
-2.80

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-4

> <JCHEM_PKA>
2.67877117985815

> <JCHEM_PKA_STRONGEST_ACIDIC>
0.8252479627216065

> <JCHEM_PKA_STRONGEST_BASIC>
4.946047024039826

> <JCHEM_POLAR_SURFACE_AREA>
374.9499999999999

> <JCHEM_REFRACTIVITY>
233.09720000000002

> <JCHEM_ROTATABLE_BOND_COUNT>
30

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
1.70e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
3-hydroxy-2,2-dimethyl-3-({2-[(2-{[(2E,4S,8S)-4,8,12-trimethyltridec-2-enoyl]sulfanyl}ethyl)carbamoyl]ethyl}carbamoyl)propyl {[(2R,3R,4S,5R)-5-(6-aminopurin-9-yl)-4-hydroxy-3-(phosphonatooxy)oxolan-2-yl]methyl phosphonato}oxyphosphonate

> <JCHEM_VEBER_RULE>
0

$$$$

Download
3D-SDF for NP0339009 ((4R,8R,12R)-Trimethyl-2E-tridecenoyl-CoA)
Download
PDB for NP0339009 ((4R,8R,12R)-Trimethyl-2E-tridecenoyl-CoA)
HEADER    PROTEIN                                 25-FEB-12   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   25-FEB-12         0                                  
HETATM    1  C   UNK     0       6.607 -25.660   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       7.512 -26.906   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       6.886 -28.312   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       9.044 -26.744   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       9.949 -27.990   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      11.481 -27.829   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      12.386 -29.075   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      11.759 -30.482   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      13.917 -28.914   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      14.823 -30.160   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      16.354 -29.999   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      17.259 -31.245   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      16.633 -32.652   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      18.791 -31.084   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0      19.417 -29.677   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0      20.949 -29.516   0.000  0.00  0.00           C+0
HETATM   17  O   UNK     0      21.575 -28.109   0.000  0.00  0.00           O+0
HETATM   18  S   UNK     0      21.854 -30.762   0.000  0.00  0.00           S+0
HETATM   19  C   UNK     0      23.386 -30.601   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0      24.291 -31.847   0.000  0.00  0.00           C+0
HETATM   21  N   UNK     0      25.823 -31.686   0.000  0.00  0.00           N+0
HETATM   22  C   UNK     0      26.728 -32.932   0.000  0.00  0.00           C+0
HETATM   23  O   UNK     0      26.101 -34.339   0.000  0.00  0.00           O+0
HETATM   24  C   UNK     0      28.259 -32.771   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0      29.165 -34.017   0.000  0.00  0.00           C+0
HETATM   26  N   UNK     0      30.696 -33.856   0.000  0.00  0.00           N+0
HETATM   27  C   UNK     0      31.601 -35.102   0.000  0.00  0.00           C+0
HETATM   28  O   UNK     0      30.975 -36.509   0.000  0.00  0.00           O+0
HETATM   29  C   UNK     0      33.133 -34.941   0.000  0.00  0.00           C+0
HETATM   30  O   UNK     0      34.038 -36.187   0.000  0.00  0.00           O+0
HETATM   31  C   UNK     0      33.759 -33.534   0.000  0.00  0.00           C+0
HETATM   32  C   UNK     0      32.353 -32.908   0.000  0.00  0.00           C+0
HETATM   33  C   UNK     0      35.166 -34.161   0.000  0.00  0.00           C+0
HETATM   34  C   UNK     0      34.386 -32.127   0.000  0.00  0.00           C+0
HETATM   35  O   UNK     0      33.481 -30.881   0.000  0.00  0.00           O+0
HETATM   36  P   UNK     0      34.107 -29.474   0.000  0.00  0.00           P+0
HETATM   37  O   UNK     0      32.700 -28.848   0.000  0.00  0.00           O-1
HETATM   38  O   UNK     0      35.514 -30.101   0.000  0.00  0.00           O+0
HETATM   39  O   UNK     0      34.733 -28.068   0.000  0.00  0.00           O+0
HETATM   40  P   UNK     0      33.828 -26.822   0.000  0.00  0.00           P+0
HETATM   41  O   UNK     0      32.582 -27.727   0.000  0.00  0.00           O-1
HETATM   42  O   UNK     0      35.074 -25.916   0.000  0.00  0.00           O+0
HETATM   43  O   UNK     0      32.923 -25.576   0.000  0.00  0.00           O+0
HETATM   44  C   UNK     0      33.549 -24.169   0.000  0.00  0.00           C+0
HETATM   45  C   UNK     0      32.644 -22.923   0.000  0.00  0.00           C+0
HETATM   46  O   UNK     0      31.104 -22.923   0.000  0.00  0.00           O+0
HETATM   47  C   UNK     0      30.628 -21.458   0.000  0.00  0.00           C+0
HETATM   48  C   UNK     0      31.874 -20.553   0.000  0.00  0.00           C+0
HETATM   49  O   UNK     0      31.874 -19.013   0.000  0.00  0.00           O+0
HETATM   50  C   UNK     0      33.120 -21.458   0.000  0.00  0.00           C+0
HETATM   51  O   UNK     0      34.585 -20.982   0.000  0.00  0.00           O+0
HETATM   52  P   UNK     0      35.729 -22.013   0.000  0.00  0.00           P+0
HETATM   53  O   UNK     0      34.699 -23.157   0.000  0.00  0.00           O-1
HETATM   54  O   UNK     0      36.760 -20.868   0.000  0.00  0.00           O-1
HETATM   55  O   UNK     0      36.874 -23.043   0.000  0.00  0.00           O+0
HETATM   56  N   UNK     0      29.163 -20.982   0.000  0.00  0.00           N+0
HETATM   57  C   UNK     0      27.917 -21.888   0.000  0.00  0.00           C+0
HETATM   58  N   UNK     0      26.672 -20.982   0.000  0.00  0.00           N+0
HETATM   59  C   UNK     0      27.148 -19.518   0.000  0.00  0.00           C+0
HETATM   60  C   UNK     0      26.377 -18.184   0.000  0.00  0.00           C+0
HETATM   61  N   UNK     0      24.837 -18.184   0.000  0.00  0.00           N+0
HETATM   62  N   UNK     0      27.148 -16.850   0.000  0.00  0.00           N+0
HETATM   63  C   UNK     0      28.688 -16.850   0.000  0.00  0.00           C+0
HETATM   64  N   UNK     0      29.458 -18.184   0.000  0.00  0.00           N+0
HETATM   65  C   UNK     0      28.688 -19.518   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3    4                                                  
CONECT    3    2                                                            
CONECT    4    2    5                                                       
CONECT    5    4    6                                                       
CONECT    6    5    7                                                       
CONECT    7    6    8    9                                                  
CONECT    8    7                                                            
CONECT    9    7   10                                                       
CONECT   10    9   11                                                       
CONECT   11   10   12                                                       
CONECT   12   11   13   14                                                  
CONECT   13   12                                                            
CONECT   14   12   15                                                       
CONECT   15   14   16                                                       
CONECT   16   15   17   18                                                  
CONECT   17   16                                                            
CONECT   18   16   19                                                       
CONECT   19   18   20                                                       
CONECT   20   19   21                                                       
CONECT   21   20   22                                                       
CONECT   22   21   23   24                                                  
CONECT   23   22                                                            
CONECT   24   22   25                                                       
CONECT   25   24   26                                                       
CONECT   26   25   27                                                       
CONECT   27   26   28   29                                                  
CONECT   28   27                                                            
CONECT   29   27   30   31                                                  
CONECT   30   29                                                            
CONECT   31   29   32   33   34                                             
CONECT   32   31                                                            
CONECT   33   31                                                            
CONECT   34   31   35                                                       
CONECT   35   34   36                                                       
CONECT   36   35   37   38   39                                             
CONECT   37   36                                                            
CONECT   38   36                                                            
CONECT   39   36   40                                                       
CONECT   40   39   41   42   43                                             
CONECT   41   40                                                            
CONECT   42   40                                                            
CONECT   43   40   44                                                       
CONECT   44   43   45                                                       
CONECT   45   44   46   50                                                  
CONECT   46   45   47                                                       
CONECT   47   46   48   56                                                  
CONECT   48   47   49   50                                                  
CONECT   49   48                                                            
CONECT   50   45   48   51                                                  
CONECT   51   50   52                                                       
CONECT   52   51   53   54   55                                             
CONECT   53   52                                                            
CONECT   54   52                                                            
CONECT   55   52                                                            
CONECT   56   47   57   65                                                  
CONECT   57   56   58                                                       
CONECT   58   57   59                                                       
CONECT   59   58   60   65                                                  
CONECT   60   59   61   62                                                  
CONECT   61   60                                                            
CONECT   62   60   63                                                       
CONECT   63   62   64                                                       
CONECT   64   63   65                                                       
CONECT   65   56   59   64                                                  
MASTER        0    0    0    0    0    0    0    0   65    0  134    0
END

Download
3D PDB for NP0339009 ((4R,8R,12R)-Trimethyl-2E-tridecenoyl-CoA)
Download
SMILES for NP0339009 ((4R,8R,12R)-Trimethyl-2E-tridecenoyl-CoA)
CC(C)CCC[C@H](C)CCC[C@H](C)\C=C\C(=O)SCCNC(=O)CCNC(=O)C(O)C(C)(C)COP([O-])(=O)OP([O-])(=O)OC[C@H]1O[C@H]([C@@H](O)[C@H]1OP([O-])([O-])=O)N1C=NC2=C1N=CN=C2N
Download
INCHI for NP0339009 ((4R,8R,12R)-Trimethyl-2E-tridecenoyl-CoA)
InChI=1S/C37H64N7O17P3S/c1-23(2)9-7-10-24(3)11-8-12-25(4)13-14-28(46)65-18-17-39-27(45)15-16-40-35(49)32(48)37(5,6)20-58-64(55,56)61-63(53,54)57-19-26-31(60-62(50,51)52)30(47)36(59-26)44-22-43-29-33(38)41-21-42-34(29)44/h13-14,21-26,30-32,36,47-48H,7-12,15-20H2,1-6H3,(H,39,45)(H,40,49)(H,53,54)(H,55,56)(H2,38,41,42)(H2,50,51,52)/p-4/b14-13+/t24-,25-,26+,30-,31-,32?,36+/m0/s1
Download
View in JSmol
Synonyms
ValueSource
(2E,4R,8R)-4,8,12-Trimethyl-tridecenoyl-CoAHMDB
(2E,4R,8R)-4,8,12-Trimethyl-tridecenoyl-coenzyme AHMDB
(4R,8R)-4,8,12-Trimethyl-trans-2-tridecenoyl-CoAHMDB
(4R,8R)-4,8,12-Trimethyl-trans-2-tridecenoyl-coenzyme AHMDB
(4R,8R,12)-Trimethyl-(2E)-tridecenoyl-CoAHMDB
(4R,8R,12)-Trimethyl-(2E)-tridecenoyl-coenzyme AHMDB
Chemical FormulaC37H60N7O17P3S
Average Mass999.8950 Da
Monoisotopic Mass999.29792 Da
IUPAC Name3-hydroxy-2,2-dimethyl-3-({2-[(2-{[(2E,4S,8S)-4,8,12-trimethyltridec-2-enoyl]sulfanyl}ethyl)carbamoyl]ethyl}carbamoyl)propyl ({[(2R,3R,4S,5R)-5-(6-amino-9H-purin-9-yl)-4-hydroxy-3-(phosphonatooxy)oxolan-2-yl]methyl phosphonato}oxy)phosphonate
Traditional Name3-hydroxy-2,2-dimethyl-3-({2-[(2-{[(2E,4S,8S)-4,8,12-trimethyltridec-2-enoyl]sulfanyl}ethyl)carbamoyl]ethyl}carbamoyl)propyl {[(2R,3R,4S,5R)-5-(6-aminopurin-9-yl)-4-hydroxy-3-(phosphonatooxy)oxolan-2-yl]methyl phosphonato}oxyphosphonate
CAS Registry NumberNot Available
SMILES
CC(C)CCC[C@H](C)CCC[C@H](C)\C=C\C(=O)SCCNC(=O)CCNC(=O)C(O)C(C)(C)COP([O-])(=O)OP([O-])(=O)OC[C@H]1O[C@H]([C@@H](O)[C@H]1OP([O-])([O-])=O)N1C=NC2=C1N=CN=C2N
InChI Identifier
InChI=1S/C37H64N7O17P3S/c1-23(2)9-7-10-24(3)11-8-12-25(4)13-14-28(46)65-18-17-39-27(45)15-16-40-35(49)32(48)37(5,6)20-58-64(55,56)61-63(53,54)57-19-26-31(60-62(50,51)52)30(47)36(59-26)44-22-43-29-33(38)41-21-42-34(29)44/h13-14,21-26,30-32,36,47-48H,7-12,15-20H2,1-6H3,(H,39,45)(H,40,49)(H,53,54)(H,55,56)(H2,38,41,42)(H2,50,51,52)/p-4/b14-13+/t24-,25-,26+,30-,31-,32?,36+/m0/s1
InChI KeyXDRCVDXWYZRMDN-BFEXNXLWSA-J
Experimental Spectra
Not Available
Predicted Spectra
Not Available
Chemical Shift Submissions
Not Available
Species
Species of OriginNot Available
Chemical Taxonomy
Description Belongs to the class of organic compounds known as long-chain 2-enoyl coas. These are organic compounds containing a coenzyme A substructure linked to a long-chain 2-enoyl chain of 13 to 21 carbon atoms.
KingdomOrganic compounds  
Super ClassLipids and lipid-like molecules  
ClassFatty Acyls  
Sub ClassFatty acyl thioesters  
Direct ParentLong-chain 2-enoyl CoAs  
Alternative Parents
Substituents
  • Coenzyme a or derivatives
    • 

  • Purine ribonucleoside diphosphate
    • 

  • Purine ribonucleoside bisphosphate
    • 

  • Purine ribonucleoside 3',5'-bisphosphate
    • 

  • Pentose phosphate
    • 

  • Pentose-5-phosphate
    • 

  • Ribonucleoside 3'-phosphate
    • 

  • Sesquiterpenoid
    • 

  • Farsesane sesquiterpenoid
    • 

  • Glycosyl compound
    • 

  • N-glycosyl compound
    • 

  • Beta amino acid or derivatives
    • 

  • 6-aminopurine
    • 

  • Monosaccharide phosphate
    • 

  • Organic pyrophosphate
    • 

  • Imidazopyrimidine
    • 

  • Purine
    • 

  • Aminopyrimidine
    • 

  • Fatty amide
    • 

  • Monosaccharide
    • 

  • N-acyl-amine
    • 

  • N-substituted imidazole
    • 

  • Organic phosphoric acid derivative
    • 

  • Imidolactam
    • 

  • Phosphoric acid ester
    • 

  • Alkyl phosphate
    • 

  • Pyrimidine
    • 

  • Tetrahydrofuran
    • 

  • Azole
    • 

  • Heteroaromatic compound
    • 

  • Imidazole
    • 

  • Carbothioic s-ester
    • 

  • Secondary carboxylic acid amide
    • 

  • Secondary alcohol
    • 

  • Thiocarboxylic acid ester
    • 

  • Carboxamide group
    • 

  • Amino acid or derivatives
    • 

  • Thiocarboxylic acid or derivatives
    • 

  • Sulfenyl compound
    • 

  • Carboxylic acid derivative
    • 

  • Organoheterocyclic compound
    • 

  • Oxacycle
    • 

  • Azacycle
    • 

  • Hydrocarbon derivative
    • 

  • Organic nitrogen compound
    • 

  • Organic oxide
    • 

  • Organonitrogen compound
    • 

  • Organopnictogen compound
    • 

  • Primary amine
    • 

  • Organosulfur compound
    • 

  • Organic oxygen compound
    • 

  • Carbonyl group
    • 

  • Organooxygen compound
    • 

  • Alcohol
    • 

  • Amine
    • 

  • Organic anion
    • 

  • Aromatic heteropolycyclic compound
Molecular FrameworkAromatic heteropolycyclic compounds
External DescriptorsNot Available
Physical Properties
StateNot Available
Experimental Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Predicted Properties
PropertyValueSource
logP2.86ALOGPS
logP-0.74ChemAxon
logS-2.8ALOGPS
pKa (Strongest Acidic)0.83ChemAxon
pKa (Strongest Basic)4.95ChemAxon
Physiological Charge-4ChemAxon
Hydrogen Acceptor Count17ChemAxon
Hydrogen Donor Count5ChemAxon
Polar Surface Area374.95 ŲChemAxon
Rotatable Bond Count30ChemAxon
Refractivity233.1 m³·mol⁻¹ChemAxon
Polarizability97.94 ųChemAxon
Number of Rings3ChemAxon
BioavailabilityNoChemAxon
Rule of FiveNoChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleYesChemAxon
HMDB IDNot Available
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FoodDB IDFDB029089  
KNApSAcK IDNot Available
Chemspider IDNot Available
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound53481434  
PDB IDNot Available
ChEBI IDNot Available
Good Scents IDNot Available
References
General ReferencesNot Available