NP-MRD: Showing NP-Card for Sptrimycin D (NP0351045)

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Record Information

Version

2.0

Created at

2025-05-24 02:10:07 UTC

Updated at

2025-07-31 02:36:15 UTC

NP-MRD ID

NP0351045

Natural Product DOI

https://doi.org/10.57994/4034

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Sptrimycin D

Description

Based on a literature review very few articles have been published on Sptrimycin D.

Structure

MOL SDF PDB SMILES InChI


  Mrv2104 03062304352D          

 26 25  0  0  1  0            999 V2000
   -6.0987    0.6039    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -6.0987    1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.8131    1.8414    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -7.5276    1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.3842    1.8414    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6697    1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9552    1.8414    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2408    1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5263    1.8414    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8118    1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0974    1.8414    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.0974    2.6664    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3829    1.4289    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.3829    0.6039    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.3316    1.8414    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3316    2.6664    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0461    1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7605    1.8414    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.4750    1.4289    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.1895    1.8414    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9039    1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.6184    1.8414    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.3329    1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.0474    1.8414    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1895    2.6664    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.7605    2.6664    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  2  5  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  1  0  0  0  0
  7  8  2  0  0  0  0
  8  9  1  0  0  0  0
  9 10  2  0  0  0  0
 11 10  1  0  0  0  0
 11 12  1  1  0  0  0
 11 13  1  0  0  0  0
 13 14  1  6  0  0  0
 13 15  1  0  0  0  0
 15 16  1  0  0  0  0
 15 17  2  0  0  0  0
 18 17  1  0  0  0  0
 18 19  1  0  0  0  0
 19 20  1  0  0  0  0
 20 21  1  0  0  0  0
 21 22  1  0  0  0  0
 22 23  1  0  0  0  0
 23 24  1  0  0  0  0
 20 25  2  0  0  0  0
 18 26  1  1  0  0  0
M  END


  Mrv2104 03062304352D          

 26 25  0  0  1  0            999 V2000
   -6.0987    0.6039    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -6.0987    1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.8131    1.8414    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -7.5276    1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.3842    1.8414    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6697    1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9552    1.8414    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2408    1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5263    1.8414    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8118    1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0974    1.8414    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.0974    2.6664    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3829    1.4289    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.3829    0.6039    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.3316    1.8414    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3316    2.6664    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0461    1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7605    1.8414    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.4750    1.4289    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.1895    1.8414    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9039    1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.6184    1.8414    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.3329    1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.0474    1.8414    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1895    2.6664    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.7605    2.6664    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  2  5  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  1  0  0  0  0
  7  8  2  0  0  0  0
  8  9  1  0  0  0  0
  9 10  2  0  0  0  0
 11 10  1  0  0  0  0
 11 12  1  1  0  0  0
 11 13  1  0  0  0  0
 13 14  1  6  0  0  0
 13 15  1  0  0  0  0
 15 16  1  0  0  0  0
 15 17  2  0  0  0  0
 18 17  1  0  0  0  0
 18 19  1  0  0  0  0
 19 20  1  0  0  0  0
 20 21  1  0  0  0  0
 21 22  1  0  0  0  0
 22 23  1  0  0  0  0
 23 24  1  0  0  0  0
 20 25  2  0  0  0  0
 18 26  1  1  0  0  0
M  END
> <DATABASE_ID>
NP0351045

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CCCCC(=O)O[C@H](C)\C=C(/C)[C@H](O)[C@H](C)\C=C\C=C\CCC(=O)OC

> <INCHI_IDENTIFIER>
InChI=1S/C21H34O5/c1-6-7-13-20(23)26-18(4)15-17(3)21(24)16(2)12-10-8-9-11-14-19(22)25-5/h8-10,12,15-16,18,21,24H,6-7,11,13-14H2,1-5H3/b9-8+,12-10+,17-15+/t16-,18-,21-/m1/s1

> <INCHI_KEY>
ZEOCOSVQDCEOSI-ONJDEHMDSA-N

> <FORMULA>
C21H34O5

> <MOLECULAR_WEIGHT>
366.498

> <EXACT_MASS>
366.240624195

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_ATOM_COUNT>
60

> <JCHEM_AVERAGE_POLARIZABILITY>
42.81129877471092

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
methyl (4E,6E,8R,9R,10E,12R)-9-hydroxy-8,10-dimethyl-12-(pentanoyloxy)trideca-4,6,10-trienoate

> <JCHEM_LOGP>
4.08256269

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_ACIDIC>
14.304807941191244

> <JCHEM_PKA_STRONGEST_BASIC>
-3.102877006522949

> <JCHEM_POLAR_SURFACE_AREA>
72.83000000000001

> <JCHEM_REFRACTIVITY>
106.2415

> <JCHEM_ROTATABLE_BOND_COUNT>
14

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
methyl (4E,6E,8R,9R,10E,12R)-9-hydroxy-8,10-dimethyl-12-(pentanoyloxy)trideca-4,6,10-trienoate

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 06-MAR-23   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   06-MAR-23         0                                  
HETATM    1  O   UNK     0     -11.384   1.127   0.000  0.00  0.00           O+0
HETATM    2  C   UNK     0     -11.384   2.667   0.000  0.00  0.00           C+0
HETATM    3  O   UNK     0     -12.718   3.437   0.000  0.00  0.00           O+0
HETATM    4  C   UNK     0     -14.052   2.667   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0     -10.050   3.437   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      -8.717   2.667   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      -7.383   3.437   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      -6.049   2.667   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      -4.716   3.437   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      -3.382   2.667   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      -2.048   3.437   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      -2.048   4.977   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      -0.715   2.667   0.000  0.00  0.00           C+0
HETATM   14  O   UNK     0      -0.715   1.127   0.000  0.00  0.00           O+0
HETATM   15  C   UNK     0       0.619   3.437   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       0.619   4.977   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       1.953   2.667   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       3.286   3.437   0.000  0.00  0.00           C+0
HETATM   19  O   UNK     0       4.620   2.667   0.000  0.00  0.00           O+0
HETATM   20  C   UNK     0       5.954   3.437   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0       7.287   2.667   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0       8.621   3.437   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0       9.955   2.667   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0      11.288   3.437   0.000  0.00  0.00           C+0
HETATM   25  O   UNK     0       5.954   4.977   0.000  0.00  0.00           O+0
HETATM   26  C   UNK     0       3.286   4.977   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3    5                                                  
CONECT    3    2    4                                                       
CONECT    4    3                                                            
CONECT    5    2    6                                                       
CONECT    6    5    7                                                       
CONECT    7    6    8                                                       
CONECT    8    7    9                                                       
CONECT    9    8   10                                                       
CONECT   10    9   11                                                       
CONECT   11   10   12   13                                                  
CONECT   12   11                                                            
CONECT   13   11   14   15                                                  
CONECT   14   13                                                            
CONECT   15   13   16   17                                                  
CONECT   16   15                                                            
CONECT   17   15   18                                                       
CONECT   18   17   19   26                                                  
CONECT   19   18   20                                                       
CONECT   20   19   21   25                                                  
CONECT   21   20   22                                                       
CONECT   22   21   23                                                       
CONECT   23   22   24                                                       
CONECT   24   23                                                            
CONECT   25   20                                                            
CONECT   26   18                                                            
MASTER        0    0    0    0    0    0    0    0   26    0   50    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₂₁H₃₄O₅

Average Mass

366.4980 Da

Monoisotopic Mass

366.24062 Da

IUPAC Name

methyl (4E,6E,8R,9R,10E,12R)-9-hydroxy-8,10-dimethyl-12-(pentanoyloxy)trideca-4,6,10-trienoate

Traditional Name

methyl (4E,6E,8R,9R,10E,12R)-9-hydroxy-8,10-dimethyl-12-(pentanoyloxy)trideca-4,6,10-trienoate

CAS Registry Number

Not Available

SMILES

CCCCC(=O)O[C@H](C)\C=C(/C)[C@H](O)[C@H](C)\C=C\C=C\CCC(=O)OC

InChI Identifier

InChI=1S/C21H34O5/c1-6-7-13-20(23)26-18(4)15-17(3)21(24)16(2)12-10-8-9-11-14-19(22)25-5/h8-10,12,15-16,18,21,24H,6-7,11,13-14H2,1-5H3/b9-8+,12-10+,17-15+/t16-,18-,21-/m1/s1

InChI Key

ZEOCOSVQDCEOSI-ONJDEHMDSA-N

Experimental Spectra

Spectrum Type	Description	Depositor Email	Depositor Organization	Depositor	Deposition Date	View
ROESY NMR	[¹H, ¹H] NMR Spectrum (2D, 800 MHz, CD3OD, experimental)	939388911@qq.com	Chengdu University of Traditional Chinese Medicine	zhiyin	2025-05-24	View Spectrum
HMBC NMR	[¹H, ¹³C] NMR Spectrum (2D, 800 MHz, CD3OD, experimental)	939388911@qq.com	Chengdu University of Traditional Chinese Medicine	zhiyin	2025-05-24	View Spectrum
HSQC NMR	[¹H, ¹³C] NMR Spectrum (2D, 800 MHz, CD3OD, experimental)	939388911@qq.com	Chengdu University of Traditional Chinese Medicine	zhiyin	2025-05-24	View Spectrum
1D_DEPT NMR	¹³C NMR Spectrum (1D, 201 MHz, CD3OD, experimental)	939388911@qq.com	Chengdu University of Traditional Chinese Medicine	zhiyin	2025-05-24	View Spectrum
COSY NMR	[¹H, ¹H] NMR Spectrum (2D, 800 MHz, CD3OD, experimental)	939388911@qq.com	Chengdu University of Traditional Chinese Medicine	zhiyin	2025-05-24	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, CD3OD, experimental)	939388911@qq.com	Chengdu University of Traditional Chinese Medicine	zhiyin	2025-05-24	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 201 MHz, CD3OD, experimental)	939388911@qq.com	Chengdu University of Traditional Chinese Medicine	zhiyin	2025-05-24	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
Sphaerimonospora Sphaerimonospora triticiradicis NEAU-HRGS1-10		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	4.08	ChemAxon
pKa (Strongest Acidic)	14.3	ChemAxon
pKa (Strongest Basic)	-3.1	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	3	ChemAxon
Hydrogen Donor Count	1	ChemAxon
Polar Surface Area	72.83 Å²	ChemAxon
Rotatable Bond Count	14	ChemAxon
Refractivity	106.24 m³·mol⁻¹	ChemAxon
Polarizability	42.81 Å³	ChemAxon
Number of Rings	0	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	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

Not Available

METLIN ID

Not Available

PubChem Compound

Not Available

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Showing NP-Card for Sptrimycin D (NP0351045)

MOL for NP0351045 (Sptrimycin D)

3D MOL for NP0351045 (Sptrimycin D)

3D SDF for NP0351045 (Sptrimycin D)

3D-SDF for NP0351045 (Sptrimycin D)

PDB for NP0351045 (Sptrimycin D)

3D PDB for NP0351045 (Sptrimycin D)

SMILES for NP0351045 (Sptrimycin D)

INCHI for NP0351045 (Sptrimycin D)

Structure for NP0351045 (Sptrimycin D)

3D Structure for NP0351045 (Sptrimycin D)