NP-MRD: Showing NP-Card for Sarkomycin D (NP0062231)

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Record Information

Version

2.0

Created at

2022-04-28 06:53:58 UTC

Updated at

2022-04-28 06:53:58 UTC

NP-MRD ID

NP0062231

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Sarkomycin D

Description

Sarkomycin D belongs to the class of organic compounds known as iridoids and derivatives. These are monoterpenes containing a skeleton structurally characterized by the presence of a cylopentane fused to a pyran ( forming a 4,7-dimethylcyclopenta[c]pyran), or a derivative where the pentane moiety is open. Sarkomycin D is found in Streptomyces erythrochromogenes. Based on a literature review very few articles have been published on Sarkomycin D.

Structure

MOL 3D MOL SDF PDB SMILES InChI

     RDKit          3D

 39 41  0  0  0  0  0  0  0  0999 V2000
    2.9595    0.3328   -2.5687 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.0223    0.6208   -1.3525 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4737    1.8787   -1.0124 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.6250   -0.3599   -0.3488 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.1648   -1.6719   -1.0011 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6697   -1.3443   -1.1722 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3325   -0.9251    0.2165 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.4902   -2.0215    1.0672 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4902    0.0394    0.5151 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.7606    0.1043    1.8575 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.8294    1.3528    0.0775 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5062    1.2116    0.7752 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9216   -0.1839    0.4230 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.6093   -0.8271    1.6106 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0969   -1.3966    2.5580 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0787   -0.6574    1.4504 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2206    0.1601    0.1712 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9714   -0.2817   -0.6076 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.8623    0.6213   -1.7593 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7757    0.1238   -2.9092 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8474    2.0012   -1.6763 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.1996    2.0949   -0.3702 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.5002   -0.6144    0.3168 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.6550   -1.8558   -1.9549 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2681   -2.4629   -0.2485 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6841   -0.4535   -1.8583 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1068   -2.1892   -1.5645 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.0863   -1.7873    1.8214 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.1090    1.0271    2.0630 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3930    2.2186    0.4801 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7504    1.3964   -1.0086 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2203    1.9950    0.5638 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3098    1.2192    1.8759 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5954   -1.6413    1.3491 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5095   -0.1238    2.3244 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1320   -0.0599   -0.3806 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1503    1.2217    0.4662 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1647   -1.3301   -0.8923 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5987    2.5681   -1.3243 H   0  0  0  0  0  0  0  0  0  0  0  0
  3  2  1  0
  2  1  2  0
  2  4  1  0
  4  5  1  0
  5  6  1  0
  6  7  1  0
  7  8  1  1
  7  9  1  0
  9 10  1  1
  9 11  1  0
 11 12  1  0
 13 12  1  1
 13 18  1  0
 18 17  1  0
 17 16  1  0
 16 14  1  0
 14 15  2  0
 18 19  1  0
 19 21  1  0
 19 20  2  0
  9  4  1  0
 13 14  1  0
 13  7  1  0
  3 22  1  0
  4 23  1  1
  5 24  1  0
  5 25  1  0
  6 26  1  0
  6 27  1  0
  8 28  1  0
 10 29  1  0
 11 30  1  0
 11 31  1  0
 12 32  1  0
 12 33  1  0
 18 38  1  6
 17 36  1  0
 17 37  1  0
 16 34  1  0
 16 35  1  0
 21 39  1  0
M  END


  Mrv1652304282208532D          

 21 23  0  0  1  0            999 V2000
    2.0168    0.7282    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0973    1.5492    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.3412    1.8795    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.7935    1.2625    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.1259    0.7682    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0375    1.5927    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.1179    2.4138    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9237    2.5910    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0429    0.7716    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.8487    0.5944    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2662    1.3059    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7185    1.9229    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2347    2.6176    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.6756   -0.0066    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5732   -0.8921    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.6891    0.1201    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.3650    0.4670    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.8206    2.6178    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.9132    1.9599    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2990    2.7397    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.7094    1.6299    0.0000 O   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
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  1  5  1  0  0  0  0
  4  6  1  0  0  0  0
  6  7  1  6  0  0  0
  7  8  1  0  0  0  0
  3  8  1  0  0  0  0
  6  9  1  0  0  0  0
  9 10  1  0  0  0  0
 10 11  1  0  0  0  0
 11 12  1  0  0  0  0
  6 12  1  0  0  0  0
 12 13  2  0  0  0  0
  9 14  1  6  0  0  0
 14 15  2  0  0  0  0
 14 16  1  0  0  0  0
  4 17  1  1  0  0  0
  3 18  1  1  0  0  0
  2 19  1  6  0  0  0
 19 20  2  0  0  0  0
 19 21  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0062231

> <DATABASE_NAME>
NP-MRD

> <SMILES>
OC(=O)[C@@H]1CC[C@@]2(O)[C@]1(O)CC[C@@]21[C@@H](CCC1=O)C(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C14H18O7/c15-9-2-1-7(10(16)17)12(9)5-6-13(20)8(11(18)19)3-4-14(12,13)21/h7-8,20-21H,1-6H2,(H,16,17)(H,18,19)/t7-,8-,12-,13-,14-/m0/s1

> <INCHI_KEY>
HAFIUWLRFZKAJJ-NTPXCIOMSA-N

> <FORMULA>
C14H18O7

> <MOLECULAR_WEIGHT>
298.291

> <EXACT_MASS>
298.10525292

> <JCHEM_ACCEPTOR_COUNT>
7

> <JCHEM_ATOM_COUNT>
39

> <JCHEM_AVERAGE_POLARIZABILITY>
27.771168707454514

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(1R,3'aS,4'R,5R,6'aS)-3'a,6'a-dihydroxy-2-oxo-hexahydro-2'H-spiro[cyclopentane-1,1'-pentalene]-4',5-dicarboxylic acid

> <ALOGPS_LOGP>
-0.81

> <JCHEM_LOGP>
-0.438377021

> <ALOGPS_LOGS>
-0.51

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-2

> <JCHEM_PKA>
4.308220360547154

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.627093713502143

> <JCHEM_PKA_STRONGEST_BASIC>
-3.5834332976216396

> <JCHEM_POLAR_SURFACE_AREA>
132.13

> <JCHEM_REFRACTIVITY>
67.2457

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
9.29e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(1R,3'aS,4'R,5R,6'aS)-3'a,6'a-dihydroxy-2-oxo-tetrahydro-2'H-spiro[cyclopentane-1,1'-pentalene]-4',5-dicarboxylic acid

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 28-APR-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   28-APR-22         0                                  
HETATM    1  C   UNK     0       3.765   1.359   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       3.915   2.892   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       2.504   3.508   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       1.481   2.357   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       2.102   1.434   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       0.070   2.973   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       0.220   4.506   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       1.724   4.837   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      -0.080   1.440   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      -1.584   1.110   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      -2.364   2.438   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      -1.341   3.589   0.000  0.00  0.00           C+0
HETATM   13  O   UNK     0      -2.305   4.886   0.000  0.00  0.00           O+0
HETATM   14  C   UNK     0       1.261  -0.012   0.000  0.00  0.00           C+0
HETATM   15  O   UNK     0       1.070  -1.665   0.000  0.00  0.00           O+0
HETATM   16  O   UNK     0       3.153   0.224   0.000  0.00  0.00           O+0
HETATM   17  O   UNK     0       0.681   0.872   0.000  0.00  0.00           O+0
HETATM   18  O   UNK     0       3.398   4.886   0.000  0.00  0.00           O+0
HETATM   19  C   UNK     0       5.438   3.658   0.000  0.00  0.00           C+0
HETATM   20  O   UNK     0       6.158   5.114   0.000  0.00  0.00           O+0
HETATM   21  O   UNK     0       6.924   3.042   0.000  0.00  0.00           O+0
CONECT    1    2    5                                                       
CONECT    2    1    3   19                                                  
CONECT    3    2    4    8   18                                             
CONECT    4    3    5    6   17                                             
CONECT    5    4    1                                                       
CONECT    6    4    7    9   12                                             
CONECT    7    6    8                                                       
CONECT    8    7    3                                                       
CONECT    9    6   10   14                                                  
CONECT   10    9   11                                                       
CONECT   11   10   12                                                       
CONECT   12   11    6   13                                                  
CONECT   13   12                                                            
CONECT   14    9   15   16                                                  
CONECT   15   14                                                            
CONECT   16   14                                                            
CONECT   17    4                                                            
CONECT   18    3                                                            
CONECT   19    2   20   21                                                  
CONECT   20   19                                                            
CONECT   21   19                                                            
MASTER        0    0    0    0    0    0    0    0   21    0   46    0
END

View in JSmol

Synonyms

Value	Source
Sarcomycin D	MeSH

Chemical Formula

C₁₄H₁₈O₇

Average Mass

298.2910 Da

Monoisotopic Mass

298.10525 Da

IUPAC Name

(1R,3'aS,4'R,5R,6'aS)-3'a,6'a-dihydroxy-2-oxo-hexahydro-2'H-spiro[cyclopentane-1,1'-pentalene]-4',5-dicarboxylic acid

Traditional Name

(1R,3'aS,4'R,5R,6'aS)-3'a,6'a-dihydroxy-2-oxo-tetrahydro-2'H-spiro[cyclopentane-1,1'-pentalene]-4',5-dicarboxylic acid

CAS Registry Number

Not Available

SMILES

OC(=O)[C@@H]1CC[C@@]2(O)[C@]1(O)CC[C@@]21[C@@H](CCC1=O)C(O)=O

InChI Identifier

InChI=1S/C14H18O7/c15-9-2-1-7(10(16)17)12(9)5-6-13(20)8(11(18)19)3-4-14(12,13)21/h7-8,20-21H,1-6H2,(H,16,17)(H,18,19)/t7-,8-,12-,13-,14-/m0/s1

InChI Key

HAFIUWLRFZKAJJ-NTPXCIOMSA-N

Experimental Spectra

Not Available

Predicted Spectra

Spectrum Type	Description	Depositor ID	Depositor Organization	Depositor	Deposition Date	View
1D NMR	¹³C NMR Spectrum (1D, 25 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 252 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 50 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 75 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 101 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 126 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 151 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 176 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 201 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 226 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum

Chemical Shift Submissions

Not Available

Species

Species of Origin

Species Name	Source	Reference
Streptomyces erythrochromogenes	Bacteria	KNApSAcK

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as iridoids and derivatives. These are monoterpenes containing a skeleton structurally characterized by the presence of a cylopentane fused to a pyran ( forming a 4,7-dimethylcyclopenta[c]pyran), or a derivative where the pentane moiety is open.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Prenol lipids

Sub Class

Monoterpenoids

Direct Parent

Iridoids and derivatives

Alternative Parents

Substituents

Bicyclic monoterpenoid
11-noriridane monoterpenoid
Dicarboxylic acid or derivatives
Cyclic alcohol
Tertiary alcohol
Ketone
1,2-diol
Carboxylic acid
Carboxylic acid derivative
Hydrocarbon derivative
Organic oxide
Carbonyl group
Organic oxygen compound
Organooxygen compound
Alcohol
Aliphatic homopolycyclic compound

Molecular Framework

Aliphatic homopolycyclic compounds

External Descriptors

Not Available

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	-0.81	ALOGPS
logP	-0.44	ChemAxon
logS	-0.51	ALOGPS
pKa (Strongest Acidic)	3.63	ChemAxon
pKa (Strongest Basic)	-3.6	ChemAxon
Physiological Charge	-2	ChemAxon
Hydrogen Acceptor Count	7	ChemAxon
Hydrogen Donor Count	4	ChemAxon
Polar Surface Area	132.13 Å²	ChemAxon
Rotatable Bond Count	2	ChemAxon
Refractivity	67.25 m³·mol⁻¹	ChemAxon
Polarizability	27.77 Å³	ChemAxon
Number of Rings	3	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	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

C00018675

Chemspider ID

8979307

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

10804002

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Not Available

Showing NP-Card for Sarkomycin D (NP0062231)

MOL for NP0062231 (Sarkomycin D)

3D MOL for NP0062231 (Sarkomycin D)

3D SDF for NP0062231 (Sarkomycin D)

3D-SDF for NP0062231 (Sarkomycin D)

PDB for NP0062231 (Sarkomycin D)

3D PDB for NP0062231 (Sarkomycin D)

SMILES for NP0062231 (Sarkomycin D)

INCHI for NP0062231 (Sarkomycin D)

Structure for NP0062231 (Sarkomycin D)

3D Structure for NP0062231 (Sarkomycin D)