NP-MRD: Showing NP-Card for Pseudodesmin B (NP0333718)

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Record Information

Version

2.0

Created at

2024-08-11 15:45:12 UTC

Updated at

2024-09-16 10:47:00 UTC

NP-MRD ID

NP0333718

Natural Product DOI

https://doi.org/10.57994/3197

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Pseudodesmin B

Description

Based on a literature review very few articles have been published on Pseudodesmin B.

Structure

MOL SDF PDB SMILES InChI


  Mrv2104 04252318182D          

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M  END


  Mrv2104 04252318182D          

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 20 23  1  0  0  0  0
 23 24  1  0  0  0  0
 25 24  1  0  0  0  0
 25 26  1  1  0  0  0
 26 27  1  0  0  0  0
 27 28  1  0  0  0  0
 27 29  1  0  0  0  0
 25 30  1  0  0  0  0
 30 31  1  0  0  0  0
 32 31  1  6  0  0  0
 32 33  1  1  0  0  0
 33 34  1  0  0  0  0
 32 35  1  0  0  0  0
 35 36  1  0  0  0  0
 37 36  1  0  0  0  0
 37 38  1  1  0  0  0
 38 39  1  0  0  0  0
 38 40  1  0  0  0  0
 37 41  1  0  0  0  0
 41 42  1  0  0  0  0
 43 42  1  0  0  0  0
  4 43  1  0  0  0  0
 43 44  1  6  0  0  0
 41 45  2  0  0  0  0
 35 46  2  0  0  0  0
 30 47  2  0  0  0  0
 23 48  2  0  0  0  0
 18 49  2  0  0  0  0
 11 50  2  0  0  0  0
  5 51  2  0  0  0  0
 52  2  1  0  0  0  0
 52 53  1  1  0  0  0
 53 54  1  0  0  0  0
 55 54  1  0  0  0  0
 55 56  1  1  0  0  0
 56 57  1  0  0  0  0
 57 58  1  0  0  0  0
 59 58  1  0  0  0  0
 59 60  1  1  0  0  0
 59 61  1  0  0  0  0
 61 62  1  0  0  0  0
 62 63  1  0  0  0  0
 63 64  1  0  0  0  0
 64 65  1  0  0  0  0
 65 66  1  0  0  0  0
 66 67  1  0  0  0  0
 57 68  2  0  0  0  0
 55 69  1  0  0  0  0
 69 70  1  0  0  0  0
 70 71  1  0  0  0  0
 70 72  1  0  0  0  0
 54 73  2  0  0  0  0
 52 74  1  0  0  0  0
 74 75  1  0  0  0  0
 75 76  1  0  0  0  0
 76 77  1  0  0  0  0
 76 78  2  0  0  0  0
M  END
> <DATABASE_ID>
NP0333718

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CCCCCCC[C@@H](O)CC(=O)N[C@@H](CC(C)C)C(=O)N[C@H](CCC(N)=O)C(=O)N[C@@H]1[C@@H](C)OC(=O)[C@@H](NC(=O)[C@@H](CO)NC(=O)[C@H](CC(C)C)NC(=O)[C@@H](CO)NC(=O)[C@@H](CC(C)C)NC(=O)[C@H](NC1=O)C(C)C)C(C)C

> <INCHI_IDENTIFIER>
InChI=1S/C53H94N10O15/c1-13-14-15-16-17-18-33(66)24-41(68)55-35(21-27(2)3)46(70)56-34(19-20-40(54)67)45(69)63-44-32(12)78-53(77)43(31(10)11)62-50(74)39(26-65)60-47(71)36(22-28(4)5)57-49(73)38(25-64)59-48(72)37(23-29(6)7)58-51(75)42(30(8)9)61-52(44)76/h27-39,42-44,64-66H,13-26H2,1-12H3,(H2,54,67)(H,55,68)(H,56,70)(H,57,73)(H,58,75)(H,59,72)(H,60,71)(H,61,76)(H,62,74)(H,63,69)/t32-,33-,34-,35+,36+,37?,38-,39?,42-,43+,44?/m1/s1

> <INCHI_KEY>
QMZPYQGXHUSNRN-NXASQNSBSA-N

> <FORMULA>
C53H94N10O15

> <MOLECULAR_WEIGHT>
1111.39

> <EXACT_MASS>
1110.690012367

> <JCHEM_ACCEPTOR_COUNT>
14

> <JCHEM_ATOM_COUNT>
172

> <JCHEM_AVERAGE_POLARIZABILITY>
119.4851513963601

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
13

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2R)-N-[(3S,6R,9S,12R,15R,18R,21R,22R)-6,12-bis(hydroxymethyl)-22-methyl-9,15-bis(2-methylpropyl)-2,5,8,11,14,17,20-heptaoxo-3,18-bis(propan-2-yl)-1-oxa-4,7,10,13,16,19-hexaazacyclodocosan-21-yl]-2-[(2S)-2-[(3R)-3-hydroxydecanamido]-4-methylpentanamido]pentanediamide

> <JCHEM_LOGP>
-0.15276741299999747

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
11.561588104398368

> <JCHEM_PKA_STRONGEST_ACIDIC>
11.175889843182999

> <JCHEM_POLAR_SURFACE_AREA>
391.9799999999999

> <JCHEM_REFRACTIVITY>
283.8520000000002

> <JCHEM_ROTATABLE_BOND_COUNT>
26

> <JCHEM_RULE_OF_FIVE>
0

> <JCHEM_TRADITIONAL_IUPAC>
(2R)-N-[(3S,6R,9S,12R,15R,18R,21R,22R)-6,12-bis(hydroxymethyl)-3,18-diisopropyl-22-methyl-9,15-bis(2-methylpropyl)-2,5,8,11,14,17,20-heptaoxo-1-oxa-4,7,10,13,16,19-hexaazacyclodocosan-21-yl]-2-[(2S)-2-[(3R)-3-hydroxydecanamido]-4-methylpentanamido]pentanediamide

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 25-APR-23   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   25-APR-23         0                                  
HETATM    1  O   UNK     0      -2.493   5.888   0.000  0.00  0.00           O+0
HETATM    2  C   UNK     0      -2.066   4.409   0.000  0.00  0.00           C+0
HETATM    3  N   UNK     0      -0.571   4.039   0.000  0.00  0.00           N+0
HETATM    4  C   UNK     0       0.497   5.148   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      -0.998   5.518   0.000  0.00  0.00           C+0
HETATM    6  N   UNK     0      -1.426   6.998   0.000  0.00  0.00           N+0
HETATM    7  C   UNK     0      -0.358   8.108   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      -0.785   9.587   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       0.283  10.697   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      -2.280   9.957   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       1.137   7.738   0.000  0.00  0.00           C+0
HETATM   12  N   UNK     0       2.205   8.847   0.000  0.00  0.00           N+0
HETATM   13  C   UNK     0       3.700   8.477   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       3.273   9.957   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       1.778  10.327   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       0.710   9.217   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       1.351  11.806   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       4.768   9.587   0.000  0.00  0.00           C+0
HETATM   19  N   UNK     0       6.263   9.217   0.000  0.00  0.00           N+0
HETATM   20  C   UNK     0       7.330  10.327   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0       6.903  11.806   0.000  0.00  0.00           C+0
HETATM   22  O   UNK     0       7.971  12.916   0.000  0.00  0.00           O+0
HETATM   23  C   UNK     0       8.825   9.957   0.000  0.00  0.00           C+0
HETATM   24  N   UNK     0       9.252   8.477   0.000  0.00  0.00           N+0
HETATM   25  C   UNK     0      10.747   8.108   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0      11.815   9.217   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0      13.310   8.847   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0      13.737   7.368   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0      14.378   9.957   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0      11.175   6.628   0.000  0.00  0.00           C+0
HETATM   31  N   UNK     0      10.107   5.518   0.000  0.00  0.00           N+0
HETATM   32  C   UNK     0       8.612   5.888   0.000  0.00  0.00           C+0
HETATM   33  C   UNK     0       9.039   4.409   0.000  0.00  0.00           C+0
HETATM   34  O   UNK     0      10.534   4.039   0.000  0.00  0.00           O+0
HETATM   35  C   UNK     0       7.544   4.778   0.000  0.00  0.00           C+0
HETATM   36  N   UNK     0       6.049   5.148   0.000  0.00  0.00           N+0
HETATM   37  C   UNK     0       4.981   4.039   0.000  0.00  0.00           C+0
HETATM   38  C   UNK     0       5.408   2.559   0.000  0.00  0.00           C+0
HETATM   39  C   UNK     0       4.341   1.449   0.000  0.00  0.00           C+0
HETATM   40  C   UNK     0       6.903   2.189   0.000  0.00  0.00           C+0
HETATM   41  C   UNK     0       3.486   4.409   0.000  0.00  0.00           C+0
HETATM   42  O   UNK     0       2.419   3.299   0.000  0.00  0.00           O+0
HETATM   43  C   UNK     0       0.924   3.669   0.000  0.00  0.00           C+0
HETATM   44  C   UNK     0      -0.144   2.559   0.000  0.00  0.00           C+0
HETATM   45  O   UNK     0       3.059   5.888   0.000  0.00  0.00           O+0
HETATM   46  O   UNK     0       7.971   3.299   0.000  0.00  0.00           O+0
HETATM   47  O   UNK     0      12.669   6.258   0.000  0.00  0.00           O+0
HETATM   48  O   UNK     0       9.893  11.067   0.000  0.00  0.00           O+0
HETATM   49  O   UNK     0       4.341  11.067   0.000  0.00  0.00           O+0
HETATM   50  O   UNK     0       1.564   6.258   0.000  0.00  0.00           O+0
HETATM   51  O   UNK     0      -2.515   5.248   0.000  0.00  0.00           O+0
HETATM   52  C   UNK     0      -3.134   3.299   0.000  0.00  0.00           C+0
HETATM   53  N   UNK     0      -4.629   3.669   0.000  0.00  0.00           N+0
HETATM   54  C   UNK     0      -5.697   2.559   0.000  0.00  0.00           C+0
HETATM   55  C   UNK     0      -7.192   2.929   0.000  0.00  0.00           C+0
HETATM   56  N   UNK     0      -8.259   1.819   0.000  0.00  0.00           N+0
HETATM   57  C   UNK     0      -9.754   2.189   0.000  0.00  0.00           C+0
HETATM   58  C   UNK     0     -10.822   1.079   0.000  0.00  0.00           C+0
HETATM   59  C   UNK     0     -12.317   1.449   0.000  0.00  0.00           C+0
HETATM   60  O   UNK     0     -12.744   2.929   0.000  0.00  0.00           O+0
HETATM   61  C   UNK     0     -13.385   0.340   0.000  0.00  0.00           C+0
HETATM   62  C   UNK     0     -14.880   0.710   0.000  0.00  0.00           C+0
HETATM   63  C   UNK     0     -15.948  -0.400   0.000  0.00  0.00           C+0
HETATM   64  C   UNK     0     -17.442  -0.030   0.000  0.00  0.00           C+0
HETATM   65  C   UNK     0     -18.510  -1.140   0.000  0.00  0.00           C+0
HETATM   66  C   UNK     0     -20.005  -0.770   0.000  0.00  0.00           C+0
HETATM   67  C   UNK     0     -21.073  -1.880   0.000  0.00  0.00           C+0
HETATM   68  O   UNK     0     -10.181   3.669   0.000  0.00  0.00           O+0
HETATM   69  C   UNK     0      -7.619   4.409   0.000  0.00  0.00           C+0
HETATM   70  C   UNK     0      -6.551   5.518   0.000  0.00  0.00           C+0
HETATM   71  C   UNK     0      -6.978   6.998   0.000  0.00  0.00           C+0
HETATM   72  C   UNK     0      -5.056   5.148   0.000  0.00  0.00           C+0
HETATM   73  O   UNK     0      -5.270   1.079   0.000  0.00  0.00           O+0
HETATM   74  C   UNK     0      -2.707   1.819   0.000  0.00  0.00           C+0
HETATM   75  C   UNK     0      -3.775   0.710   0.000  0.00  0.00           C+0
HETATM   76  C   UNK     0      -3.348  -0.770   0.000  0.00  0.00           C+0
HETATM   77  N   UNK     0      -1.853  -1.140   0.000  0.00  0.00           N+0
HETATM   78  O   UNK     0      -4.415  -1.880   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3   52                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5   43                                                  
CONECT    5    4    6   51                                                  
CONECT    6    5    7                                                       
CONECT    7    6    8   11                                                  
CONECT    8    7    9   10                                                  
CONECT    9    8                                                            
CONECT   10    8                                                            
CONECT   11    7   12   50                                                  
CONECT   12   11   13                                                       
CONECT   13   12   14   18                                                  
CONECT   14   13   15                                                       
CONECT   15   14   16   17                                                  
CONECT   16   15                                                            
CONECT   17   15                                                            
CONECT   18   13   19   49                                                  
CONECT   19   18   20                                                       
CONECT   20   19   21   23                                                  
CONECT   21   20   22                                                       
CONECT   22   21                                                            
CONECT   23   20   24   48                                                  
CONECT   24   23   25                                                       
CONECT   25   24   26   30                                                  
CONECT   26   25   27                                                       
CONECT   27   26   28   29                                                  
CONECT   28   27                                                            
CONECT   29   27                                                            
CONECT   30   25   31   47                                                  
CONECT   31   30   32                                                       
CONECT   32   31   33   35                                                  
CONECT   33   32   34                                                       
CONECT   34   33                                                            
CONECT   35   32   36   46                                                  
CONECT   36   35   37                                                       
CONECT   37   36   38   41                                                  
CONECT   38   37   39   40                                                  
CONECT   39   38                                                            
CONECT   40   38                                                            
CONECT   41   37   42   45                                                  
CONECT   42   41   43                                                       
CONECT   43   42    4   44                                                  
CONECT   44   43                                                            
CONECT   45   41                                                            
CONECT   46   35                                                            
CONECT   47   30                                                            
CONECT   48   23                                                            
CONECT   49   18                                                            
CONECT   50   11                                                            
CONECT   51    5                                                            
CONECT   52    2   53   74                                                  
CONECT   53   52   54                                                       
CONECT   54   53   55   73                                                  
CONECT   55   54   56   69                                                  
CONECT   56   55   57                                                       
CONECT   57   56   58   68                                                  
CONECT   58   57   59                                                       
CONECT   59   58   60   61                                                  
CONECT   60   59                                                            
CONECT   61   59   62                                                       
CONECT   62   61   63                                                       
CONECT   63   62   64                                                       
CONECT   64   63   65                                                       
CONECT   65   64   66                                                       
CONECT   66   65   67                                                       
CONECT   67   66                                                            
CONECT   68   57                                                            
CONECT   69   55   70                                                       
CONECT   70   69   71   72                                                  
CONECT   71   70                                                            
CONECT   72   70                                                            
CONECT   73   54                                                            
CONECT   74   52   75                                                       
CONECT   75   74   76                                                       
CONECT   76   75   77   78                                                  
CONECT   77   76                                                            
CONECT   78   76                                                            
MASTER        0    0    0    0    0    0    0    0   78    0  156    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₅₃H₉₄N₁₀O₁₅

Average Mass

1111.3900 Da

Monoisotopic Mass

1110.69001 Da

IUPAC Name

(2R)-N-[(3S,6R,9S,12R,15R,18R,21R,22R)-6,12-bis(hydroxymethyl)-22-methyl-9,15-bis(2-methylpropyl)-2,5,8,11,14,17,20-heptaoxo-3,18-bis(propan-2-yl)-1-oxa-4,7,10,13,16,19-hexaazacyclodocosan-21-yl]-2-[(2S)-2-[(3R)-3-hydroxydecanamido]-4-methylpentanamido]pentanediamide

Traditional Name

(2R)-N-[(3S,6R,9S,12R,15R,18R,21R,22R)-6,12-bis(hydroxymethyl)-3,18-diisopropyl-22-methyl-9,15-bis(2-methylpropyl)-2,5,8,11,14,17,20-heptaoxo-1-oxa-4,7,10,13,16,19-hexaazacyclodocosan-21-yl]-2-[(2S)-2-[(3R)-3-hydroxydecanamido]-4-methylpentanamido]pentanediamide

CAS Registry Number

Not Available

SMILES

CCCCCCC[C@@H](O)CC(=O)N[C@@H](CC(C)C)C(=O)N[C@H](CCC(N)=O)C(=O)N[C@@H]1[C@@H](C)OC(=O)[C@@H](NC(=O)[C@@H](CO)NC(=O)[C@H](CC(C)C)NC(=O)[C@@H](CO)NC(=O)[C@@H](CC(C)C)NC(=O)[C@H](NC1=O)C(C)C)C(C)C

InChI Identifier

InChI=1S/C53H94N10O15/c1-13-14-15-16-17-18-33(66)24-41(68)55-35(21-27(2)3)46(70)56-34(19-20-40(54)67)45(69)63-44-32(12)78-53(77)43(31(10)11)62-50(74)39(26-65)60-47(71)36(22-28(4)5)57-49(73)38(25-64)59-48(72)37(23-29(6)7)58-51(75)42(30(8)9)61-52(44)76/h27-39,42-44,64-66H,13-26H2,1-12H3,(H2,54,67)(H,55,68)(H,56,70)(H,57,73)(H,58,75)(H,59,72)(H,60,71)(H,61,76)(H,62,74)(H,63,69)/t32-,33-,34-,35+,36+,37?,38-,39?,42-,43+,44?/m1/s1

InChI Key

QMZPYQGXHUSNRN-NXASQNSBSA-N

Experimental Spectra

Spectrum Type	Description	Depositor Email	Depositor Organization	Depositor	Deposition Date	View
HSQC NMR	[¹H, ¹³C] NMR Spectrum (2D, 400 MHz, CD3OD, experimental)	harald.gross@uni-tuebingen.de	University of Tuebingen, Germany	Harald Gross	2024-08-11	View Spectrum
HSQC NMR	[¹H, ¹³C] NMR Spectrum (2D, 400 MHz, CD3OD, experimental)	harald.gross@uni-tuebingen.de	University of Tuebingen, Germany	Harald Gross	2024-08-11	View Spectrum
HSQC NMR	[¹H, ¹³C] NMR Spectrum (2D, 400 MHz, CD3CN, experimental)	harald.gross@uni-tuebingen.de	University of Tuebingen, Germany	Harald Gross	2024-08-11	View Spectrum
COSY NMR	[¹H, ¹H] NMR Spectrum (2D, 400 MHz, CD3OD, experimental)	harald.gross@uni-tuebingen.de	University of Tuebingen, Germany	Harald Gross	2024-08-11	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, CD3OD, experimental)	harald.gross@uni-tuebingen.de	University of Tuebingen, Germany	Harald Gross	2024-08-11	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, CD3CN, experimental)	harald.gross@uni-tuebingen.de	University of Tuebingen, Germany	Harald Gross	2024-08-11	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 101 MHz, CD3OD, experimental)	harald.gross@uni-tuebingen.de	University of Tuebingen, Germany	Harald Gross	2024-08-11	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 101 MHz, CD3CN, experimental)	harald.gross@uni-tuebingen.de	University of Tuebingen, Germany	Harald Gross	2024-08-11	View Spectrum

Predicted Spectra

Spectrum Type	Description	Depositor ID	Depositor Organization	Depositor	Deposition Date	View

Chemical Shift Submissions

Not Available

Species

Species of Origin

Species Name	Source	Reference
tolaasii		Not Available

Chemical Taxonomy

Classification

Not classified

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	-0.15	ChemAxon
pKa (Strongest Acidic)	11.18	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	14	ChemAxon
Hydrogen Donor Count	13	ChemAxon
Polar Surface Area	391.98 Å²	ChemAxon
Rotatable Bond Count	26	ChemAxon
Refractivity	283.85 m³·mol⁻¹	ChemAxon
Polarizability	119.49 Å³	ChemAxon
Number of Rings	1	ChemAxon
Bioavailability	No	ChemAxon
Rule of Five	No	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

Not Available

Chemspider ID

Not Available

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

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METLIN ID

Not Available

PubChem Compound

Not Available

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

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Showing NP-Card for Pseudodesmin B (NP0333718)

MOL for NP0333718 (Pseudodesmin B)

3D MOL for NP0333718 (Pseudodesmin B)

3D SDF for NP0333718 (Pseudodesmin B)

3D-SDF for NP0333718 (Pseudodesmin B)

PDB for NP0333718 (Pseudodesmin B)

3D PDB for NP0333718 (Pseudodesmin B)

SMILES for NP0333718 (Pseudodesmin B)

INCHI for NP0333718 (Pseudodesmin B)

Structure for NP0333718 (Pseudodesmin B)

3D Structure for NP0333718 (Pseudodesmin B)