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Showing NP-Card for Sarcodon scabrosus Depsipeptide (NP0049850)

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Record Information
Version2.0
Created at2022-03-17 21:19:08 UTC
Updated at2022-03-17 21:19:08 UTC
NP-MRD IDNP0049850
Secondary Accession NumbersNone
Natural Product Identification
Common NameSarcodon scabrosus Depsipeptide
DescriptionSarcodon scabrosus Depsipeptide belongs to the class of organic compounds known as cyclic depsipeptides. These are natural or synthetic compounds having sequences of amino and hydroxy carboxylic acid residues (usually α-amino and α-hydroxy acids) connected in a ring. The residues are commonly but not necessarily regularly alternating. Sarcodon scabrosus Depsipeptide is an extremely weak basic (essentially neutral) compound (based on its pKa). Outside of the human body, Sarcodon scabrosus Depsipeptide has been detected, but not quantified in, mushrooms. This could make sarcodon scabrosus depsipeptide a potential biomarker for the consumption of these foods.
Structure
Thumb
MOLSDFPDBSMILESInChI

MOL for NP0049850 (Sarcodon scabrosus Depsipeptide)


  Mrv0541 02241215462D          

 34 34  0  0  0  0            999 V2000
   -3.2168    0.4593    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7569   -0.1526    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1398   -0.8422    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2296   -2.9102    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3829   -2.2976    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0717   -2.6035    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1488   -3.4464    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7659    3.4464    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3022    2.8339    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0680    3.0635    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.9146    2.2976    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2251    1.7613    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4593    2.2206    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5356    2.9865    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.4509   -1.6080    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4509   -0.7659    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2168   -0.4593    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9146   -1.3785    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4547   -0.6889    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9146    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9146    0.7659    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.0717   -0.6126    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.7613   -0.3829    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9146    0.4593    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6805    0.7659    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6889   -0.9184    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1533   -1.5318    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6889   -1.3014    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1488   -1.9910    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3739    1.9146    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6080    1.4547    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9955    1.9910    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2296    1.8376    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.3014    0.9955    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  2 20  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  5 27  1  0  0  0  0
  6  7  1  0  0  0  0
  8  9  1  0  0  0  0
  9 10  1  0  0  0  0
  9 32  1  0  0  0  0
 11 12  1  0  0  0  0
 12 13  1  0  0  0  0
 12 34  1  0  0  0  0
 13 14  2  0  0  0  0
 13 33  1  0  0  0  0
 15 16  1  0  0  0  0
 16 17  1  0  0  0  0
 16 23  1  0  0  0  0
 18 19  2  0  0  0  0
 19 20  1  0  0  0  0
 19 26  1  0  0  0  0
 20 21  1  0  0  0  0
 21 31  1  0  0  0  0
 22 23  1  0  0  0  0
 22 28  1  0  0  0  0
 23 24  1  0  0  0  0
 24 25  2  0  0  0  0
 24 34  1  0  0  0  0
 26 27  1  0  0  0  0
 27 28  1  0  0  0  0
 28 29  2  0  0  0  0
 30 31  2  0  0  0  0
 31 32  1  0  0  0  0
 32 33  1  0  0  0  0
M  END
Download

3D MOL for NP0049850 (Sarcodon scabrosus Depsipeptide)

Download
3D SDF for NP0049850 (Sarcodon scabrosus Depsipeptide)

  Mrv0541 02241215462D          

 34 34  0  0  0  0            999 V2000
   -3.2168    0.4593    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7569   -0.1526    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1398   -0.8422    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2296   -2.9102    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3829   -2.2976    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0717   -2.6035    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1488   -3.4464    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7659    3.4464    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3022    2.8339    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0680    3.0635    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.9146    2.2976    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2251    1.7613    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4593    2.2206    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5356    2.9865    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.4509   -1.6080    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4509   -0.7659    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2168   -0.4593    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9146   -1.3785    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4547   -0.6889    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9146    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9146    0.7659    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.0717   -0.6126    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.7613   -0.3829    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9146    0.4593    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6805    0.7659    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6889   -0.9184    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1533   -1.5318    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6889   -1.3014    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1488   -1.9910    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3739    1.9146    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6080    1.4547    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9955    1.9910    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2296    1.8376    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.3014    0.9955    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  2 20  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  5 27  1  0  0  0  0
  6  7  1  0  0  0  0
  8  9  1  0  0  0  0
  9 10  1  0  0  0  0
  9 32  1  0  0  0  0
 11 12  1  0  0  0  0
 12 13  1  0  0  0  0
 12 34  1  0  0  0  0
 13 14  2  0  0  0  0
 13 33  1  0  0  0  0
 15 16  1  0  0  0  0
 16 17  1  0  0  0  0
 16 23  1  0  0  0  0
 18 19  2  0  0  0  0
 19 20  1  0  0  0  0
 19 26  1  0  0  0  0
 20 21  1  0  0  0  0
 21 31  1  0  0  0  0
 22 23  1  0  0  0  0
 22 28  1  0  0  0  0
 23 24  1  0  0  0  0
 24 25  2  0  0  0  0
 24 34  1  0  0  0  0
 26 27  1  0  0  0  0
 27 28  1  0  0  0  0
 28 29  2  0  0  0  0
 30 31  2  0  0  0  0
 31 32  1  0  0  0  0
 32 33  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0049850

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CCC(C)C1NC(=O)C(OC(=O)C(NC(=O)C(C)NC(=O)C(OC1=O)C(C)C)C(C)O)C(C)C

> <INCHI_IDENTIFIER>
InChI=1S/C23H39N3O8/c1-9-12(6)15-22(31)33-17(10(2)3)20(29)24-13(7)19(28)26-16(14(8)27)23(32)34-18(11(4)5)21(30)25-15/h10-18,27H,9H2,1-8H3,(H,24,29)(H,25,30)(H,26,28)

> <INCHI_KEY>
ZZZCVVSDKFDQJU-UHFFFAOYSA-N

> <FORMULA>
C23H39N3O8

> <MOLECULAR_WEIGHT>
485.5711

> <EXACT_MASS>
485.273715239

> <JCHEM_ACCEPTOR_COUNT>
6

> <JCHEM_AVERAGE_POLARIZABILITY>
50.302756646959

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
3-(butan-2-yl)-9-(1-hydroxyethyl)-12-methyl-6,15-bis(propan-2-yl)-1,7-dioxa-4,10,13-triazacyclopentadecane-2,5,8,11,14-pentone

> <ALOGPS_LOGP>
1.32

> <JCHEM_LOGP>
1.2524456083333333

> <ALOGPS_LOGS>
-2.86

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
10.957494970280532

> <JCHEM_PKA_STRONGEST_ACIDIC>
10.405073748534434

> <JCHEM_PKA_STRONGEST_BASIC>
-2.953538071540323

> <JCHEM_POLAR_SURFACE_AREA>
160.13

> <JCHEM_REFRACTIVITY>
120.13769999999997

> <JCHEM_ROTATABLE_BOND_COUNT>
5

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
6.77e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
9-(1-hydroxyethyl)-6,15-diisopropyl-12-methyl-3-(sec-butyl)-1,7-dioxa-4,10,13-triazacyclopentadecane-2,5,8,11,14-pentone

> <JCHEM_VEBER_RULE>
0

$$$$

Download
3D-SDF for NP0049850 (Sarcodon scabrosus Depsipeptide)
Download
PDB for NP0049850 (Sarcodon scabrosus Depsipeptide)
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  C   UNK     0      -6.005   0.857   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -5.146  -0.285   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -5.861  -1.572   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       0.429  -5.432   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      -0.715  -4.289   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      -2.001  -4.860   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      -2.144  -6.433   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      -1.430   6.433   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      -2.431   5.290   0.000  0.00  0.00           C+0
HETATM   10  O   UNK     0      -3.860   5.719   0.000  0.00  0.00           O+0
HETATM   11  C   UNK     0       3.574   4.289   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       2.287   3.288   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       0.857   4.145   0.000  0.00  0.00           C+0
HETATM   14  O   UNK     0       1.000   5.575   0.000  0.00  0.00           O+0
HETATM   15  C   UNK     0       4.575  -3.002   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       4.575  -1.430   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       6.005  -0.857   0.000  0.00  0.00           C+0
HETATM   18  O   UNK     0      -3.574  -2.573   0.000  0.00  0.00           O+0
HETATM   19  C   UNK     0      -2.715  -1.286   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0      -3.574   0.000   0.000  0.00  0.00           C+0
HETATM   21  O   UNK     0      -3.574   1.430   0.000  0.00  0.00           O+0
HETATM   22  O   UNK     0       2.001  -1.144   0.000  0.00  0.00           O+0
HETATM   23  C   UNK     0       3.288  -0.715   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0       3.574   0.857   0.000  0.00  0.00           C+0
HETATM   25  O   UNK     0       5.004   1.430   0.000  0.00  0.00           O+0
HETATM   26  N   UNK     0      -1.286  -1.714   0.000  0.00  0.00           N+0
HETATM   27  C   UNK     0      -0.286  -2.859   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0       1.286  -2.429   0.000  0.00  0.00           C+0
HETATM   29  O   UNK     0       2.144  -3.717   0.000  0.00  0.00           O+0
HETATM   30  O   UNK     0      -4.431   3.574   0.000  0.00  0.00           O+0
HETATM   31  C   UNK     0      -3.002   2.715   0.000  0.00  0.00           C+0
HETATM   32  C   UNK     0      -1.858   3.717   0.000  0.00  0.00           C+0
HETATM   33  N   UNK     0      -0.429   3.430   0.000  0.00  0.00           N+0
HETATM   34  N   UNK     0       2.429   1.858   0.000  0.00  0.00           N+0
CONECT    1    2                                                            
CONECT    2    1    3   20                                                  
CONECT    3    2                                                            
CONECT    4    5                                                            
CONECT    5    4    6   27                                                  
CONECT    6    5    7                                                       
CONECT    7    6                                                            
CONECT    8    9                                                            
CONECT    9    8   10   32                                                  
CONECT   10    9                                                            
CONECT   11   12                                                            
CONECT   12   11   13   34                                                  
CONECT   13   12   14   33                                                  
CONECT   14   13                                                            
CONECT   15   16                                                            
CONECT   16   15   17   23                                                  
CONECT   17   16                                                            
CONECT   18   19                                                            
CONECT   19   18   20   26                                                  
CONECT   20    2   19   21                                                  
CONECT   21   20   31                                                       
CONECT   22   23   28                                                       
CONECT   23   16   22   24                                                  
CONECT   24   23   25   34                                                  
CONECT   25   24                                                            
CONECT   26   19   27                                                       
CONECT   27    5   26   28                                                  
CONECT   28   22   27   29                                                  
CONECT   29   28                                                            
CONECT   30   31                                                            
CONECT   31   21   30   32                                                  
CONECT   32    9   31   33                                                  
CONECT   33   13   32                                                       
CONECT   34   12   24                                                       
MASTER        0    0    0    0    0    0    0    0   34    0   68    0
END

Download
3D PDB for NP0049850 (Sarcodon scabrosus Depsipeptide)
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SMILES for NP0049850 (Sarcodon scabrosus Depsipeptide)
CCC(C)C1NC(=O)C(OC(=O)C(NC(=O)C(C)NC(=O)C(OC1=O)C(C)C)C(C)O)C(C)C
Download
INCHI for NP0049850 (Sarcodon scabrosus Depsipeptide)
InChI=1S/C23H39N3O8/c1-9-12(6)15-22(31)33-17(10(2)3)20(29)24-13(7)19(28)26-16(14(8)27)23(32)34-18(11(4)5)21(30)25-15/h10-18,27H,9H2,1-8H3,(H,24,29)(H,25,30)(H,26,28)
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View in JSmol
SynonymsNot Available
Chemical FormulaC23H39N3O8
Average Mass485.5711 Da
Monoisotopic Mass485.27372 Da
IUPAC Name3-(butan-2-yl)-9-(1-hydroxyethyl)-12-methyl-6,15-bis(propan-2-yl)-1,7-dioxa-4,10,13-triazacyclopentadecane-2,5,8,11,14-pentone
Traditional Name9-(1-hydroxyethyl)-6,15-diisopropyl-12-methyl-3-(sec-butyl)-1,7-dioxa-4,10,13-triazacyclopentadecane-2,5,8,11,14-pentone
CAS Registry NumberNot Available
SMILES
CCC(C)C1NC(=O)C(OC(=O)C(NC(=O)C(C)NC(=O)C(OC1=O)C(C)C)C(C)O)C(C)C
InChI Identifier
InChI=1S/C23H39N3O8/c1-9-12(6)15-22(31)33-17(10(2)3)20(29)24-13(7)19(28)26-16(14(8)27)23(32)34-18(11(4)5)21(30)25-15/h10-18,27H,9H2,1-8H3,(H,24,29)(H,25,30)(H,26,28)
InChI KeyZZZCVVSDKFDQJU-UHFFFAOYSA-N
Experimental Spectra
Not Available
Predicted Spectra
Not Available
Chemical Shift Submissions
Not Available
Species
Species of Origin
Species NameSourceReference
Agaricus bisporusFooDB
    • Shmuel Yannai Dictionary of Food Compounds with CD-ROM: Additives, Flavors, and Ingredients. Chap...
Pleurotus ostreatusFooDB
    • Shmuel Yannai Dictionary of Food Compounds with CD-ROM: Additives, Flavors, and Ingredients. Chap...
Chemical Taxonomy
Description Belongs to the class of organic compounds known as cyclic depsipeptides. These are natural or synthetic compounds having sequences of amino and hydroxy carboxylic acid residues (usually α-amino and α-hydroxy acids) connected in a ring. The residues are commonly but not necessarily regularly alternating.
KingdomOrganic compounds  
Super ClassOrganic acids and derivatives  
ClassPeptidomimetics  
Sub ClassDepsipeptides  
Direct ParentCyclic depsipeptides  
Alternative Parents
Substituents
  • Cyclic depsipeptide
    • 

  • Macrolide lactam
    • 

  • Alpha-amino acid ester
    • 

  • Macrolactam
    • 

  • Macrolide
    • 

  • Alpha-amino acid or derivatives
    • 

  • Dicarboxylic acid or derivatives
    • 

  • Carboxamide group
    • 

  • Carboxylic acid ester
    • 

  • Lactam
    • 

  • Lactone
    • 

  • Secondary carboxylic acid amide
    • 

  • Secondary alcohol
    • 

  • Carboxylic acid derivative
    • 

  • Oxacycle
    • 

  • Azacycle
    • 

  • Organoheterocyclic compound
    • 

  • Hydrocarbon derivative
    • 

  • Organic oxide
    • 

  • Alcohol
    • 

  • Organopnictogen compound
    • 

  • Carbonyl group
    • 

  • Organic nitrogen compound
    • 

  • Organic oxygen compound
    • 

  • Organooxygen compound
    • 

  • Organonitrogen compound
    • 

  • Aliphatic heteromonocyclic compound
Molecular FrameworkAliphatic heteromonocyclic 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
logP1.32ALOGPS
logP1.25ChemAxon
logS-2.9ALOGPS
pKa (Strongest Acidic)10.41ChemAxon
pKa (Strongest Basic)-3ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count6ChemAxon
Hydrogen Donor Count4ChemAxon
Polar Surface Area160.13 ŲChemAxon
Rotatable Bond Count5ChemAxon
Refractivity120.14 m³·mol⁻¹ChemAxon
Polarizability50.3 ųChemAxon
Number of Rings1ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
HMDB IDHMDB0041421  
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FoodDB IDFDB021367  
KNApSAcK IDNot Available
Chemspider IDNot Available
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound131753140  
PDB IDNot Available
ChEBI IDNot Available
Good Scents IDNot Available
References
General ReferencesNot Available