NP-MRD: Showing NP-Card for Holothurin B5 (NP0351681)

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Record Information

Version

2.0

Created at

2025-10-13 16:45:19 UTC

Updated at

2025-10-14 01:00:52 UTC

NP-MRD ID

NP0351681

Natural Product DOI

https://doi.org/10.57994/4749

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Holothurin B5

Description

Holothurin B5 was first documented in 2025 (PMID: 41025291).

Structure

MOL SDF PDB SMILES InChI


  Mrv2104 04192309572D          

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M  END


  Mrv2104 04192309572D          

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M  END
> <DATABASE_ID>
NP0351681

> <DATABASE_NAME>
NP-MRD

> <SMILES>
[H][C@]12CC[C@@]3(C)C4CCC5C(C)(C)[C@H](CC[C@]5(C)C4=C[C@H](O)C13C(=O)O[C@@]2(C)C(=O)CCC(C)(C)OC(C)=O)O[C@@H]1OC[C@@H](OS(=O)(=O)O[Na])[C@H](O)[C@H]1O[C@@H]1O[C@H](C)[C@@H](O)[C@H](O)[C@H]1O

> <INCHI_IDENTIFIER>
InChI=1S/C43H66O18S.Na/c1-20-30(47)32(49)33(50)35(56-20)58-34-31(48)24(61-62(52,53)54)19-55-36(34)57-29-14-16-40(7)23-18-28(46)43-26(12-17-41(43,8)22(23)10-11-25(40)39(29,5)6)42(9,60-37(43)51)27(45)13-15-38(3,4)59-21(2)44;/h18,20,22,24-26,28-36,46-50H,10-17,19H2,1-9H3,(H,52,53,54);/q;+1/p-1/t20-,22?,24-,25?,26-,28+,29+,30-,31+,32+,33-,34-,35+,36+,40-,41+,42-,43?;/m1./s1

> <INCHI_KEY>
UQQWRNCDOCUGGY-UKQOPJRPSA-M

> <FORMULA>
C43H65NaO18S

> <MOLECULAR_WEIGHT>
925.02

> <EXACT_MASS>
924.37893071

$$$$

HEADER    PROTEIN                                 19-APR-23   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   19-APR-23         0                                  
HETATM    1  O   UNK     0       0.596  -2.975   0.000  0.00  0.00           O+0
HETATM    2  C   UNK     0       0.302  -1.463   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -1.154  -0.962   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -2.316  -1.972   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      -3.772  -1.470   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0      -5.228  -0.969   0.000  0.00  0.00           O+0
HETATM    7  C   UNK     0      -6.390  -1.979   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      -7.846  -1.478   0.000  0.00  0.00           C+0
HETATM    9  O   UNK     0      -6.097  -3.491   0.000  0.00  0.00           O+0
HETATM   10  C   UNK     0      -4.273  -2.926   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      -3.270  -0.014   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       1.465  -0.453   0.000  0.00  0.00           C+0
HETATM   13  O   UNK     0       2.348  -1.714   0.000  0.00  0.00           O+0
HETATM   14  C   UNK     0       0.339   0.597   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       2.392   0.777   0.000  0.00  0.00           C+0
HETATM   16  H   UNK     0       0.936   1.278   0.000  0.00  0.00           H+0
HETATM   17  C   UNK     0       2.419   2.317   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       3.892   2.767   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       4.775   1.505   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       5.568   2.825   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0       6.303   1.317   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0       7.230   2.547   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0       8.759   2.359   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0       9.360   0.942   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0      10.889   0.754   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0      10.808   2.292   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0      12.389   1.100   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0      11.490  -0.664   0.000  0.00  0.00           C+0
HETATM   29  O   UNK     0      13.019  -0.852   0.000  0.00  0.00           O+0
HETATM   30  C   UNK     0      13.620  -2.269   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0      15.149  -2.457   0.000  0.00  0.00           C+0
HETATM   32  O   UNK     0      16.076  -1.227   0.000  0.00  0.00           O+0
HETATM   33  C   UNK     0      17.604  -1.415   0.000  0.00  0.00           C+0
HETATM   34  C   UNK     0      18.531  -0.185   0.000  0.00  0.00           C+0
HETATM   35  O   UNK     0      17.930   1.232   0.000  0.00  0.00           O+0
HETATM   36  C   UNK     0      20.060  -0.373   0.000  0.00  0.00           C+0
HETATM   37  O   UNK     0      20.987   0.857   0.000  0.00  0.00           O+0
HETATM   38  C   UNK     0      20.661  -1.791   0.000  0.00  0.00           C+0
HETATM   39  O   UNK     0      22.190  -1.978   0.000  0.00  0.00           O+0
HETATM   40  C   UNK     0      19.734  -3.020   0.000  0.00  0.00           C+0
HETATM   41  C   UNK     0      20.336  -4.438   0.000  0.00  0.00           C+0
HETATM   42  O   UNK     0      18.206  -2.833   0.000  0.00  0.00           O+0
HETATM   43  C   UNK     0      15.751  -3.875   0.000  0.00  0.00           C+0
HETATM   44  O   UNK     0      17.279  -4.062   0.000  0.00  0.00           O+0
HETATM   45  C   UNK     0      14.824  -5.104   0.000  0.00  0.00           C+0
HETATM   46  O   UNK     0      15.425  -6.522   0.000  0.00  0.00           O+0
HETATM   47  S   UNK     0      14.498  -7.752   0.000  0.00  0.00           S+0
HETATM   48  O   UNK     0      15.728  -8.679   0.000  0.00  0.00           O+0
HETATM   49  O   UNK     0      13.571  -8.982   0.000  0.00  0.00           O+0
HETATM   50 Na   UNK     0      12.043  -8.794   0.000  0.00  0.00          Na+0
HETATM   51  O   UNK     0      13.268  -6.825   0.000  0.00  0.00           O+0
HETATM   52  C   UNK     0      13.295  -4.917   0.000  0.00  0.00           C+0
HETATM   53  O   UNK     0      12.693  -3.499   0.000  0.00  0.00           O+0
HETATM   54  C   UNK     0      10.563  -1.894   0.000  0.00  0.00           C+0
HETATM   55  C   UNK     0       9.035  -1.706   0.000  0.00  0.00           C+0
HETATM   56  C   UNK     0       8.433  -0.288   0.000  0.00  0.00           C+0
HETATM   57  C   UNK     0       7.506  -1.518   0.000  0.00  0.00           C+0
HETATM   58  C   UNK     0       6.905  -0.100   0.000  0.00  0.00           C+0
HETATM   59  C   UNK     0       5.978  -1.330   0.000  0.00  0.00           C+0
HETATM   60  C   UNK     0       4.449  -1.142   0.000  0.00  0.00           C+0
HETATM   61  O   UNK     0       3.522  -2.372   0.000  0.00  0.00           O+0
HETATM   62  C   UNK     0       3.848   0.275   0.000  0.00  0.00           C+0
HETATM   63  C   UNK     0       3.821  -1.264   0.000  0.00  0.00           C+0
HETATM   64  O   UNK     0       5.051  -2.191   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3   12                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4    6   10   11                                             
CONECT    6    5    7                                                       
CONECT    7    6    8    9                                                  
CONECT    8    7                                                            
CONECT    9    7                                                            
CONECT   10    5                                                            
CONECT   11    5                                                            
CONECT   12    2   13   14   15                                             
CONECT   13   12   63                                                       
CONECT   14   12                                                            
CONECT   15   12   16   17   62                                             
CONECT   16   15                                                            
CONECT   17   15   18                                                       
CONECT   18   17   19                                                       
CONECT   19   18   20   21   62                                             
CONECT   20   19                                                            
CONECT   21   19   22   58                                                  
CONECT   22   21   23                                                       
CONECT   23   22   24                                                       
CONECT   24   23   25   56                                                  
CONECT   25   24   26   27   28                                             
CONECT   26   25                                                            
CONECT   27   25                                                            
CONECT   28   25   29   54                                                  
CONECT   29   28   30                                                       
CONECT   30   29   31   53                                                  
CONECT   31   30   32   43                                                  
CONECT   32   31   33                                                       
CONECT   33   32   34   42                                                  
CONECT   34   33   35   36                                                  
CONECT   35   34                                                            
CONECT   36   34   37   38                                                  
CONECT   37   36                                                            
CONECT   38   36   39   40                                                  
CONECT   39   38                                                            
CONECT   40   38   41   42                                                  
CONECT   41   40                                                            
CONECT   42   40   33                                                       
CONECT   43   31   44   45                                                  
CONECT   44   43                                                            
CONECT   45   43   46   52                                                  
CONECT   46   45   47                                                       
CONECT   47   46   48   49   51                                             
CONECT   48   47                                                            
CONECT   49   47   50                                                       
CONECT   50   49                                                            
CONECT   51   47                                                            
CONECT   52   45   53                                                       
CONECT   53   52   30                                                       
CONECT   54   28   55                                                       
CONECT   55   54   56                                                       
CONECT   56   55   24   57   58                                             
CONECT   57   56                                                            
CONECT   58   56   21   59                                                  
CONECT   59   58   60                                                       
CONECT   60   59   61   62                                                  
CONECT   61   60                                                            
CONECT   62   60   19   15   63                                             
CONECT   63   62   13   64                                                  
CONECT   64   63                                                            
MASTER        0    0    0    0    0    0    0    0   64    0  140    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₄₃H₆₅NaO₁₈S

Average Mass

925.0200 Da

Monoisotopic Mass

924.37893 Da

IUPAC Name

Not Available

Traditional Name

Not Available

CAS Registry Number

Not Available

SMILES

[H][C@]12CC[C@@]3(C)C4CCC5C(C)(C)[C@H](CC[C@]5(C)C4=C[C@H](O)C13C(=O)O[C@@]2(C)C(=O)CCC(C)(C)OC(C)=O)O[C@@H]1OC[C@@H](OS(=O)(=O)O[Na])[C@H](O)[C@H]1O[C@@H]1O[C@H](C)[C@@H](O)[C@H](O)[C@H]1O

InChI Identifier

InChI=1S/C43H66O18S.Na/c1-20-30(47)32(49)33(50)35(56-20)58-34-31(48)24(61-62(52,53)54)19-55-36(34)57-29-14-16-40(7)23-18-28(46)43-26(12-17-41(43,8)22(23)10-11-25(40)39(29,5)6)42(9,60-37(43)51)27(45)13-15-38(3,4)59-21(2)44;/h18,20,22,24-26,28-36,46-50H,10-17,19H2,1-9H3,(H,52,53,54);/q;+1/p-1/t20-,22?,24-,25?,26-,28+,29+,30-,31+,32+,33-,34-,35+,36+,40-,41+,42-,43?;/m1./s1

InChI Key

UQQWRNCDOCUGGY-UKQOPJRPSA-M

Experimental Spectra

Spectrum Type	Description	Depositor Email	Depositor Organization	Depositor	Deposition Date	View
HMBC NMR	[¹H, ¹³C] NMR Spectrum (2D, 600 MHz, C5D5N, experimental)	chinmayeebawkar@kiost.ac.kr	Korea Institute of Ocean Science and Technology	Bawkar Chinmayee Harish	2025-10-13	View Spectrum
HSQC NMR	[¹H, ¹³C] NMR Spectrum (2D, 600 MHz, C5D5N, experimental)	chinmayeebawkar@kiost.ac.kr	Korea Institute of Ocean Science and Technology	Bawkar Chinmayee Harish	2025-10-13	View Spectrum
COSY NMR	[¹H, ¹H] NMR Spectrum (2D, 600 MHz, C5D5N, experimental)	chinmayeebawkar@kiost.ac.kr	Korea Institute of Ocean Science and Technology	Bawkar Chinmayee Harish	2025-10-13	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, C5D5N, experimental)	chinmayeebawkar@kiost.ac.kr	Korea Institute of Ocean Science and Technology	Bawkar Chinmayee Harish	2025-10-13	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 151 MHz, C5D5N, experimental)	chinmayeebawkar@kiost.ac.kr	Korea Institute of Ocean Science and Technology	Bawkar Chinmayee Harish	2025-10-13	View Spectrum

Predicted Spectra

Not Available

Chemical Shift Submissions

Not Available

Species

Species of Origin

Species Name	Source	Reference
Holothuria atra		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

External Links

Not Available

References

General References

Showing NP-Card for Holothurin B5 (NP0351681)

MOL for NP0351681 (Holothurin B5)

3D MOL for NP0351681 (Holothurin B5)

3D SDF for NP0351681 (Holothurin B5)

3D-SDF for NP0351681 (Holothurin B5)

PDB for NP0351681 (Holothurin B5)

3D PDB for NP0351681 (Holothurin B5)

SMILES for NP0351681 (Holothurin B5)

INCHI for NP0351681 (Holothurin B5)

Structure for NP0351681 (Holothurin B5)

3D Structure for NP0351681 (Holothurin B5)