NP-MRD: Showing NP-Card for 13beta,29-Dihydroxymilbemycin A3 (NP0061626)

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Record Information

Version

1.0

Created at

2022-04-28 06:22:59 UTC

Updated at

2022-04-28 06:22:59 UTC

NP-MRD ID

NP0061626

Secondary Accession Numbers

None

Natural Product Identification

Common Name

13beta,29-Dihydroxymilbemycin A3

Description

(1'R,2R,4'S,5R,6S,8'S,10'E,12'R,13'R,14'E,20'S,21'R,24'S)-12',21',24'-trihydroxy-11'-(hydroxymethyl)-5,6,13',22'-tetramethyl-3',7',19'-trioxaspiro[oxane-2,6'-tetracyclo[15.6.1.1⁴,⁸.0²⁰,²⁴]Pentacosane]-10',14',16',22'-tetraen-2'-one belongs to the class of organic compounds known as milbemycins. These are a group of macrolides with a structure containing a 16-membered lactone ring fused to a 1,7-dioxaspiroundecane ring system and to either a benzofuran (or hydrogenated derivative thereof). In some cases (e.G. Milbemycin E), the tetrahydrofuranyl ring is missing. Milbemycins can be o-glycosylated at C13 to form Avermectins. Milbemycins are produced by Streptomyces species. 13beta,29-Dihydroxymilbemycin A3 is found in Streptomyces cavourensis and Streptomyces cavourensis SANK 67386. Based on a literature review very few articles have been published on (1'R,2R,4'S,5R,6S,8'S,10'E,12'R,13'R,14'E,20'S,21'R,24'S)-12',21',24'-trihydroxy-11'-(hydroxymethyl)-5,6,13',22'-tetramethyl-3',7',19'-trioxaspiro[oxane-2,6'-tetracyclo[15.6.1.1⁴,⁸.0²⁰,²⁴]Pentacosane]-10',14',16',22'-tetraen-2'-one.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652304282208232D          

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M  END

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M  END


  Mrv1652304282208232D          

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    7.2098   -1.9146    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.8610   -2.4212    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.7478   -3.2384    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    8.9647    0.3410    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    9.0778    1.1582    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    8.4267    1.6648    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.1910    1.9754    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.9553    2.2861    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.6064    1.7795    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   10.4933    0.9623    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    9.7290    0.6516    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   11.1444    0.4557    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.3707    2.0901    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.6710    2.9432    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.9705    3.3789    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2429    2.9901    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    4.2158    2.1656    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    3.5849    1.6340    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.8955    0.8697    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5423    3.4259    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.9976    4.2035    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.9188    2.5665    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.0301   -2.0293    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.3324   -3.0425    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  2  0  0  0  0
  4  5  1  0  0  0  0
  5  6  2  0  0  0  0
  6  7  1  0  0  0  0
  7  8  1  0  0  0  0
  8  9  1  0  0  0  0
  9 10  2  0  0  0  0
  9 11  1  0  0  0  0
 11 12  1  0  0  0  0
 12 13  1  6  0  0  0
 14 13  1  1  0  0  0
 14 15  1  0  0  0  0
 15 16  1  0  0  0  0
 16 17  2  0  0  0  0
  1 17  1  0  0  0  0
 17 18  1  0  0  0  0
 18 19  1  0  0  0  0
 14 20  1  0  0  0  0
 21 20  1  6  0  0  0
 21 22  1  0  0  0  0
 12 22  1  0  0  0  0
 21 23  1  0  0  0  0
 23 24  1  0  0  0  0
 24 25  1  0  0  0  0
 25 26  1  0  0  0  0
 26 27  1  0  0  0  0
 21 27  1  0  0  0  0
 26 28  1  6  0  0  0
 25 29  1  1  0  0  0
  8 30  1  1  0  0  0
 30 31  2  0  0  0  0
 31 32  1  0  0  0  0
 32 33  1  0  0  0  0
  7 33  1  0  0  0  0
 33 34  1  1  0  0  0
 34 35  1  0  0  0  0
  6 35  1  0  0  0  0
 32 36  1  6  0  0  0
 31 37  1  0  0  0  0
  7 38  1  1  0  0  0
  2 39  1  6  0  0  0
  1 40  1  6  0  0  0
M  END
> <DATABASE_ID>
NP0061626

> <DATABASE_NAME>
NP-MRD

> <SMILES>
C[C@@H]1CC[C@]2(C[C@@H]3C[C@H](C\C=C(CO)\[C@H](O)[C@H](C)\C=C\C=C4/CO[C@H]5[C@H](O)C(C)=C[C@@H](C(=O)O3)[C@]45O)O2)O[C@H]1C

> <INCHI_IDENTIFIER>
InChI=1S/C31H44O9/c1-17-10-11-30(39-20(17)4)14-24-13-23(40-30)9-8-21(15-32)26(33)18(2)6-5-7-22-16-37-28-27(34)19(3)12-25(29(35)38-24)31(22,28)36/h5-8,12,17-18,20,23-28,32-34,36H,9-11,13-16H2,1-4H3/b6-5+,21-8+,22-7+/t17-,18-,20+,23+,24+,25+,26-,27-,28+,30+,31-/m1/s1

> <INCHI_KEY>
KYWVCYGVFODUCB-CVYFFTCRSA-N

> <FORMULA>
C31H44O9

> <MOLECULAR_WEIGHT>
560.684

> <EXACT_MASS>
560.298532997

> <JCHEM_ACCEPTOR_COUNT>
8

> <JCHEM_ATOM_COUNT>
84

> <JCHEM_AVERAGE_POLARIZABILITY>
60.887503858211325

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(1'R,2R,4'S,5R,6S,8'S,10'E,12'R,13'R,14'E,16'E,20'S,21'R,24'S)-12',21',24'-trihydroxy-11'-(hydroxymethyl)-5,6,13',22'-tetramethyl-3',7',19'-trioxaspiro[oxane-2,6'-tetracyclo[15.6.1.1^{4,8}.0^{20,24}]pentacosane]-10',14',16',22'-tetraen-2'-one

> <ALOGPS_LOGP>
2.75

> <JCHEM_LOGP>
1.5732328373333322

> <ALOGPS_LOGS>
-3.56

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
5

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
13.561449434485063

> <JCHEM_PKA_STRONGEST_ACIDIC>
12.543571746995639

> <JCHEM_PKA_STRONGEST_BASIC>
-2.7605349128444665

> <JCHEM_POLAR_SURFACE_AREA>
134.91000000000003

> <JCHEM_REFRACTIVITY>
150.2855000000001

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
1.54e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(1'R,2R,4'S,5R,6S,8'S,10'E,12'R,13'R,14'E,16'E,20'S,21'R,24'S)-12',21',24'-trihydroxy-11'-(hydroxymethyl)-5,6,13',22'-tetramethyl-3',7',19'-trioxaspiro[oxane-2,6'-tetracyclo[15.6.1.1^{4,8}.0^{20,24}]pentacosane]-10',14',16',22'-tetraen-2'-one

> <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      12.032  -4.154   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      10.816  -3.208   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      11.027  -1.683   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       9.812  -0.737   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      10.023   0.788   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       8.808   1.734   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       9.019   3.259   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      10.445   3.839   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      11.661   2.894   0.000  0.00  0.00           C+0
HETATM   10  O   UNK     0      11.450   1.368   0.000  0.00  0.00           O+0
HETATM   11  O   UNK     0      13.088   3.473   0.000  0.00  0.00           O+0
HETATM   12  C   UNK     0      14.303   2.528   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      14.092   1.002   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      15.307   0.057   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0      15.096  -1.469   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0      13.670  -2.049   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0      13.458  -3.574   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0      14.674  -4.520   0.000  0.00  0.00           C+0
HETATM   19  O   UNK     0      14.463  -6.045   0.000  0.00  0.00           O+0
HETATM   20  O   UNK     0      16.734   0.637   0.000  0.00  0.00           O+0
HETATM   21  C   UNK     0      16.945   2.162   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0      15.730   3.108   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0      17.156   3.687   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0      18.583   4.267   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0      19.799   3.322   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0      19.587   1.796   0.000  0.00  0.00           C+0
HETATM   27  O   UNK     0      18.161   1.216   0.000  0.00  0.00           O+0
HETATM   28  C   UNK     0      20.803   0.851   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0      21.225   3.902   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0      10.586   5.494   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0       9.278   6.307   0.000  0.00  0.00           C+0
HETATM   32  C   UNK     0       7.920   5.582   0.000  0.00  0.00           C+0
HETATM   33  C   UNK     0       7.869   4.042   0.000  0.00  0.00           C+0
HETATM   34  O   UNK     0       6.692   3.050   0.000  0.00  0.00           O+0
HETATM   35  C   UNK     0       7.272   1.623   0.000  0.00  0.00           C+0
HETATM   36  O   UNK     0       6.612   6.395   0.000  0.00  0.00           O+0
HETATM   37  C   UNK     0       9.329   7.846   0.000  0.00  0.00           C+0
HETATM   38  O   UNK     0       9.182   4.791   0.000  0.00  0.00           O+0
HETATM   39  C   UNK     0       9.390  -3.788   0.000  0.00  0.00           C+0
HETATM   40  O   UNK     0      11.820  -5.679   0.000  0.00  0.00           O+0
CONECT    1    2   17   40                                                  
CONECT    2    1    3   39                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4    6                                                       
CONECT    6    5    7   35                                                  
CONECT    7    6    8   33   38                                             
CONECT    8    7    9   30                                                  
CONECT    9    8   10   11                                                  
CONECT   10    9                                                            
CONECT   11    9   12                                                       
CONECT   12   11   13   22                                                  
CONECT   13   12   14                                                       
CONECT   14   13   15   20                                                  
CONECT   15   14   16                                                       
CONECT   16   15   17                                                       
CONECT   17   16    1   18                                                  
CONECT   18   17   19                                                       
CONECT   19   18                                                            
CONECT   20   14   21                                                       
CONECT   21   20   22   23   27                                             
CONECT   22   21   12                                                       
CONECT   23   21   24                                                       
CONECT   24   23   25                                                       
CONECT   25   24   26   29                                                  
CONECT   26   25   27   28                                                  
CONECT   27   26   21                                                       
CONECT   28   26                                                            
CONECT   29   25                                                            
CONECT   30    8   31                                                       
CONECT   31   30   32   37                                                  
CONECT   32   31   33   36                                                  
CONECT   33   32    7   34                                                  
CONECT   34   33   35                                                       
CONECT   35   34    6                                                       
CONECT   36   32                                                            
CONECT   37   31                                                            
CONECT   38    7                                                            
CONECT   39    2                                                            
CONECT   40    1                                                            
MASTER        0    0    0    0    0    0    0    0   40    0   88    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₃₁H₄₄O₉

Average Mass

560.6840 Da

Monoisotopic Mass

560.29853 Da

IUPAC Name

(1'R,2R,4'S,5R,6S,8'S,10'E,12'R,13'R,14'E,16'E,20'S,21'R,24'S)-12',21',24'-trihydroxy-11'-(hydroxymethyl)-5,6,13',22'-tetramethyl-3',7',19'-trioxaspiro[oxane-2,6'-tetracyclo[15.6.1.1^{4,8}.0^{20,24}]pentacosane]-10',14',16',22'-tetraen-2'-one

Traditional Name

CAS Registry Number

Not Available

SMILES

C[C@@H]1CC[C@]2(C[C@@H]3C[C@H](C\C=C(CO)\[C@H](O)[C@H](C)\C=C\C=C4/CO[C@H]5[C@H](O)C(C)=C[C@@H](C(=O)O3)[C@]45O)O2)O[C@H]1C

InChI Identifier

InChI=1S/C31H44O9/c1-17-10-11-30(39-20(17)4)14-24-13-23(40-30)9-8-21(15-32)26(33)18(2)6-5-7-22-16-37-28-27(34)19(3)12-25(29(35)38-24)31(22,28)36/h5-8,12,17-18,20,23-28,32-34,36H,9-11,13-16H2,1-4H3/b6-5+,21-8+,22-7+/t17-,18-,20+,23+,24+,25+,26-,27-,28+,30+,31-/m1/s1

InChI Key

KYWVCYGVFODUCB-CVYFFTCRSA-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 cavourensis	LOTUS Database	35616633
Streptomyces cavourensis SANK 67386	Bacteria	KNApSAcK

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as milbemycins. These are a group of macrolides with a structure containing a 16-membered lactone ring fused to a 1,7-dioxaspiroundecane ring system and to either a benzofuran (or hydrogenated derivative thereof). In some cases (e.G. Milbemycin E), the tetrahydrofuranyl ring is missing. Milbemycins can be o-glycosylated at C13 to form Avermectins. Milbemycins are produced by Streptomyces species.

Kingdom

Organic compounds

Super Class

Phenylpropanoids and polyketides

Class

Macrolides and analogues

Sub Class

Milbemycins

Direct Parent

Milbemycins

Alternative Parents

Substituents

Milbemycin
Ketal
Oxane
Tetrahydrofuran
Tertiary alcohol
Secondary alcohol
Lactone
Carboxylic acid ester
Oxacycle
Organoheterocyclic compound
Polyol
Monocarboxylic acid or derivatives
Ether
Dialkyl ether
Carboxylic acid derivative
Acetal
Organic oxygen compound
Organic oxide
Hydrocarbon derivative
Primary alcohol
Organooxygen compound
Carbonyl group
Alcohol
Aliphatic heteropolycyclic compound

Molecular Framework

Aliphatic heteropolycyclic 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	2.75	ALOGPS
logP	1.57	ChemAxon
logS	-3.6	ALOGPS
pKa (Strongest Acidic)	12.54	ChemAxon
pKa (Strongest Basic)	-2.8	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	8	ChemAxon
Hydrogen Donor Count	4	ChemAxon
Polar Surface Area	134.91 Å²	ChemAxon
Rotatable Bond Count	1	ChemAxon
Refractivity	150.29 m³·mol⁻¹	ChemAxon
Polarizability	60.89 Å³	ChemAxon
Number of Rings	5	ChemAxon
Bioavailability	Yes	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

Not Available

METLIN ID

Not Available

PubChem Compound

163104819

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Not Available

Showing NP-Card for 13beta,29-Dihydroxymilbemycin A3 (NP0061626)

MOL for NP0061626 (13beta,29-Dihydroxymilbemycin A3)

3D MOL for NP0061626 (13beta,29-Dihydroxymilbemycin A3)

3D SDF for NP0061626 (13beta,29-Dihydroxymilbemycin A3)

3D-SDF for NP0061626 (13beta,29-Dihydroxymilbemycin A3)

PDB for NP0061626 (13beta,29-Dihydroxymilbemycin A3)

3D PDB for NP0061626 (13beta,29-Dihydroxymilbemycin A3)

SMILES for NP0061626 (13beta,29-Dihydroxymilbemycin A3)

INCHI for NP0061626 (13beta,29-Dihydroxymilbemycin A3)

Structure for NP0061626 (13beta,29-Dihydroxymilbemycin A3)

3D Structure for NP0061626 (13beta,29-Dihydroxymilbemycin A3)