NP-MRD: Showing NP-Card for milbemycin a3 (NP0214416)

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Record Information

Version

2.0

Created at

2022-09-05 13:42:45 UTC

Updated at

2022-09-05 13:42:46 UTC

NP-MRD ID

NP0214416

Secondary Accession Numbers

None

Natural Product Identification

Common Name

milbemycin a3

Description

Milbemycin A3, also known as milbemycin ALPHA1 or moxidectin, 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. milbemycin a3 is found in Streptomyces avermitilis and Streptomyces bingchenggensis. milbemycin a3 was first documented in 2018 (PMID: 30121749). Based on a literature review a small amount of articles have been published on milbemycin A3 (PMID: 34437755) (PMID: 33564920) (PMID: 32695892) (PMID: 32043186).

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652309052215422D          

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M  END

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M  END


  Mrv1652309052215422D          

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    4.9188    2.5665    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
    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
   11.3707    2.0901    0.0000 C   0  0  0  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
   11.1444    0.4557    0.0000 C   0  0  0  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
    8.4267    1.6648    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  2  0  0  0  0
  4  3  1  1  0  0  0
  4  5  1  0  0  0  0
  5  6  2  0  0  0  0
  5  7  1  0  0  0  0
  7  8  1  0  0  0  0
  8  9  1  6  0  0  0
 10  9  1  6  0  0  0
 10 11  1  0  0  0  0
 11 12  1  0  0  0  0
 12 13  2  0  0  0  0
 13 14  1  0  0  0  0
 13 15  1  0  0  0  0
 15 16  1  0  0  0  0
 16 17  1  1  0  0  0
 16 18  1  0  0  0  0
 18 19  2  0  0  0  0
 19 20  1  0  0  0  0
 20 21  2  0  0  0  0
 21 22  1  0  0  0  0
 22 23  1  0  0  0  0
 24 23  1  6  0  0  0
 24 25  1  0  0  0  0
  2 25  1  0  0  0  0
 25 26  1  6  0  0  0
 24 27  1  0  0  0  0
 21 27  1  0  0  0  0
  4 27  1  0  0  0  0
 27 28  1  1  0  0  0
 10 29  1  0  0  0  0
 30 29  1  6  0  0  0
 30 31  1  0  0  0  0
 31 32  1  0  0  0  0
 32 33  1  0  0  0  0
 33 34  1  6  0  0  0
 33 35  1  0  0  0  0
 35 36  1  1  0  0  0
 35 37  1  0  0  0  0
 30 37  1  0  0  0  0
 30 38  1  0  0  0  0
  8 38  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0214416

> <DATABASE_NAME>
NP-MRD

> <SMILES>
C[C@H]1CC[C@]2(C[C@@H]3C[C@@H](C\C=C(C)\C[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/C31H44O7/c1-18-7-6-8-23-17-35-28-27(32)21(4)14-26(31(23,28)34)29(33)36-25-15-24(10-9-19(2)13-18)38-30(16-25)12-11-20(3)22(5)37-30/h6-9,14,18,20,22,24-28,32,34H,10-13,15-17H2,1-5H3/b7-6+,19-9+,23-8+/t18-,20-,22+,24+,25-,26-,27+,28+,30-,31+/m0/s1

> <INCHI_KEY>
ZLBGSRMUSVULIE-GSMJGMFJSA-N

> <FORMULA>
C31H44O7

> <MOLECULAR_WEIGHT>
528.686

> <EXACT_MASS>
528.308703757

> <JCHEM_ACCEPTOR_COUNT>
6

> <JCHEM_ATOM_COUNT>
82

> <JCHEM_AVERAGE_POLARIZABILITY>
58.70278447689501

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(1'R,2R,4'S,5S,6R,8'R,10'E,13'R,14'E,16'E,20'R,21'R,24'S)-21',24'-dihydroxy-5,6,11',13',22'-pentamethyl-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_LOGP>
4.006861331

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
5

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
13.665894791669544

> <JCHEM_PKA_STRONGEST_ACIDIC>
12.553557465703225

> <JCHEM_PKA_STRONGEST_BASIC>
-3.449075134179056

> <JCHEM_POLAR_SURFACE_AREA>
94.45000000000002

> <JCHEM_REFRACTIVITY>
147.0723

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
0

> <JCHEM_TRADITIONAL_IUPAC>
(1'R,2R,4'S,5S,6R,8'R,10'E,13'R,14'E,16'E,20'R,21'R,24'S)-21',24'-dihydroxy-5,6,11',13',22'-pentamethyl-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                                 05-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   05-SEP-22         0                                  
HETATM    1  C   UNK     0       9.329   7.846   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       9.278   6.307   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      10.586   5.494   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      10.445   3.839   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      11.661   2.894   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0      11.450   1.368   0.000  0.00  0.00           O+0
HETATM    7  O   UNK     0      13.088   3.473   0.000  0.00  0.00           O+0
HETATM    8  C   UNK     0      14.303   2.528   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      14.092   1.002   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      15.307   0.057   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      15.096  -1.469   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      13.670  -2.049   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      13.458  -3.574   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      14.674  -4.520   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0      12.032  -4.154   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0      10.816  -3.208   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       9.390  -3.788   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0      11.027  -1.683   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       9.812  -0.737   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0      10.023   0.788   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0       8.808   1.734   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0       7.272   1.623   0.000  0.00  0.00           C+0
HETATM   23  O   UNK     0       6.692   3.050   0.000  0.00  0.00           O+0
HETATM   24  C   UNK     0       7.869   4.042   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0       7.920   5.582   0.000  0.00  0.00           C+0
HETATM   26  O   UNK     0       6.612   6.395   0.000  0.00  0.00           O+0
HETATM   27  C   UNK     0       9.019   3.259   0.000  0.00  0.00           C+0
HETATM   28  O   UNK     0       9.182   4.791   0.000  0.00  0.00           O+0
HETATM   29  O   UNK     0      16.734   0.637   0.000  0.00  0.00           O+0
HETATM   30  C   UNK     0      16.945   2.162   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0      17.156   3.687   0.000  0.00  0.00           C+0
HETATM   32  C   UNK     0      18.583   4.267   0.000  0.00  0.00           C+0
HETATM   33  C   UNK     0      19.799   3.322   0.000  0.00  0.00           C+0
HETATM   34  C   UNK     0      21.225   3.902   0.000  0.00  0.00           C+0
HETATM   35  C   UNK     0      19.587   1.796   0.000  0.00  0.00           C+0
HETATM   36  C   UNK     0      20.803   0.851   0.000  0.00  0.00           C+0
HETATM   37  O   UNK     0      18.161   1.216   0.000  0.00  0.00           O+0
HETATM   38  C   UNK     0      15.730   3.108   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3   25                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5   27                                                  
CONECT    5    4    6    7                                                  
CONECT    6    5                                                            
CONECT    7    5    8                                                       
CONECT    8    7    9   38                                                  
CONECT    9    8   10                                                       
CONECT   10    9   11   29                                                  
CONECT   11   10   12                                                       
CONECT   12   11   13                                                       
CONECT   13   12   14   15                                                  
CONECT   14   13                                                            
CONECT   15   13   16                                                       
CONECT   16   15   17   18                                                  
CONECT   17   16                                                            
CONECT   18   16   19                                                       
CONECT   19   18   20                                                       
CONECT   20   19   21                                                       
CONECT   21   20   22   27                                                  
CONECT   22   21   23                                                       
CONECT   23   22   24                                                       
CONECT   24   23   25   27                                                  
CONECT   25   24    2   26                                                  
CONECT   26   25                                                            
CONECT   27   24   21    4   28                                             
CONECT   28   27                                                            
CONECT   29   10   30                                                       
CONECT   30   29   31   37   38                                             
CONECT   31   30   32                                                       
CONECT   32   31   33                                                       
CONECT   33   32   34   35                                                  
CONECT   34   33                                                            
CONECT   35   33   36   37                                                  
CONECT   36   35                                                            
CONECT   37   35   30                                                       
CONECT   38   30    8                                                       
MASTER        0    0    0    0    0    0    0    0   38    0   84    0
END

View in JSmol

Synonyms

Value	Source
5-Hydroxymilbemycin beta7	MeSH
Milbemycin D	MeSH
Milbemycin alpha1	MeSH
Milbemycin alpha13	MeSH
Milbemycin alpha3	MeSH
Milbemycin alpha6	MeSH
Milbemycins	MeSH
Moxidectin	MeSH
Milbemycin alpha14	MeSH
Milbemycin alpha15	MeSH
Milbemycin alpha2	MeSH
Milbemycin alpha4	MeSH
Milbemycin alpha8	MeSH
Milbemycin beta2	MeSH
Milbemycin beta3	MeSH
Mixture OF milbemycins a3 and a4	MeSH
Milbeknock	MeSH
Milbemycin b	MeSH
Milbemycin alpha5	MeSH
Milbemycin alpha7	MeSH
Milbemycin beta12	MeSH
Cydectin	MeSH
Milbemectin	MeSH
Milbemycin a4	MeSH
Milbemycin alpha10	MeSH
Milbemycin alpha11	MeSH
Milbemycin alpha9	MeSH
Milbemycin beta1	MeSH

Chemical Formula

C₃₁H₄₄O₇

Average Mass

528.6860 Da

Monoisotopic Mass

528.30870 Da

IUPAC Name

(1'R,2R,4'S,5S,6R,8'R,10'E,13'R,14'E,16'E,20'R,21'R,24'S)-21',24'-dihydroxy-5,6,11',13',22'-pentamethyl-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(C)\C[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/C31H44O7/c1-18-7-6-8-23-17-35-28-27(32)21(4)14-26(31(23,28)34)29(33)36-25-15-24(10-9-19(2)13-18)38-30(16-25)12-11-20(3)22(5)37-30/h6-9,14,18,20,22,24-28,32,34H,10-13,15-17H2,1-5H3/b7-6+,19-9+,23-8+/t18-,20-,22+,24+,25-,26-,27+,28+,30-,31+/m0/s1

InChI Key

ZLBGSRMUSVULIE-GSMJGMFJSA-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, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 252 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 50 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 75 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 101 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 126 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 151 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 176 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 201 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 226 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, H₂O, 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 avermitilis	LOTUS Database	35616633
Streptomyces bingchenggensis	LOTUS Database	35616633

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
Carboxylic acid ester
Lactone
Secondary alcohol
Acetal
Carboxylic acid derivative
Dialkyl ether
Ether
Monocarboxylic acid or derivatives
Oxacycle
Organoheterocyclic compound
Carbonyl group
Organic oxide
Hydrocarbon derivative
Alcohol
Organooxygen compound
Organic oxygen compound
Aliphatic heteropolycyclic compound

Molecular Framework

Aliphatic heteropolycyclic compounds

External Descriptors

milbemycin (CHEBI:39228 )
Pesticides (C18557 )

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	4.01	ChemAxon
pKa (Strongest Acidic)	12.55	ChemAxon
pKa (Strongest Basic)	-3.4	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	6	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	94.45 Å²	ChemAxon
Rotatable Bond Count	0	ChemAxon
Refractivity	147.07 m³·mol⁻¹	ChemAxon
Polarizability	58.7 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

C00017118

Chemspider ID

8004083

KEGG Compound ID

C18557

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

9828343

PDB ID

Not Available

ChEBI ID

39228

Good Scents ID

Not Available

References

General References

Chu L, Li S, Dong Z, Zhang Y, Jin P, Ye L, Wang X, Xiang W: Mining and engineering exporters for titer improvement of macrolide biopesticides in Streptomyces. Microb Biotechnol. 2022 Apr;15(4):1120-1132. doi: 10.1111/1751-7915.13883. Epub 2021 Aug 26. [PubMed:34437755 ]
Liu Y, Wang H, Li S, Zhang Y, Cheng X, Xiang W, Wang X: Engineering of primary metabolic pathways for titer improvement of milbemycins in Streptomyces bingchenggensis. Appl Microbiol Biotechnol. 2021 Mar;105(5):1875-1887. doi: 10.1007/s00253-021-11164-7. Epub 2021 Feb 10. [PubMed:33564920 ]
Jin P, Li S, Zhang Y, Chu L, He H, Dong Z, Xiang W: Mining and fine-tuning sugar uptake system for titer improvement of milbemycins in Streptomyces bingchenggensis. Synth Syst Biotechnol. 2020 Jul 14;5(3):214-221. doi: 10.1016/j.synbio.2020.07.001. eCollection 2020 Sep. [PubMed:32695892 ]
Wang H, Cheng X, Liu Y, Li S, Zhang Y, Wang X, Xiang W: Improved milbemycin production by engineering two Cytochromes P450 in Streptomyces bingchenggensis. Appl Microbiol Biotechnol. 2020 Apr;104(7):2935-2946. doi: 10.1007/s00253-020-10410-8. Epub 2020 Feb 11. [PubMed:32043186 ]
Wei K, Wu Y, Li L, Jiang W, Hu J, Lu Y, Chen S: MilR2, a novel TetR family regulator involved in 5-oxomilbemycin A3/A4 biosynthesis in Streptomyces hygroscopicus. Appl Microbiol Biotechnol. 2018 Oct;102(20):8841-8853. doi: 10.1007/s00253-018-9280-2. Epub 2018 Aug 18. [PubMed:30121749 ]
LOTUS database [Link]

Showing NP-Card for milbemycin a3 (NP0214416)

MOL for NP0214416 (milbemycin a3)

3D MOL for NP0214416 (milbemycin a3)

3D SDF for NP0214416 (milbemycin a3)

3D-SDF for NP0214416 (milbemycin a3)

PDB for NP0214416 (milbemycin a3)

3D PDB for NP0214416 (milbemycin a3)

SMILES for NP0214416 (milbemycin a3)

INCHI for NP0214416 (milbemycin a3)

Structure for NP0214416 (milbemycin a3)

3D Structure for NP0214416 (milbemycin a3)