NP-MRD: Showing NP-Card for (1s,4e,6r,10r,12e,14s,15s,17r,18s,19s,20s)-20-benzyl-6,22-dihydroxy-10,17,18-trimethyl-2,16-dioxa-21-azatetracyclo[12.8.0.0¹,¹⁹.0¹⁵,¹⁷]docosa-4,12,21-trien-3-one (NP0229679)

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Record Information

Version

2.0

Created at

2022-09-06 09:51:03 UTC

Updated at

2022-09-06 09:51:03 UTC

NP-MRD ID

NP0229679

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(1s,4e,6r,10r,12e,14s,15s,17r,18s,19s,20s)-20-benzyl-6,22-dihydroxy-10,17,18-trimethyl-2,16-dioxa-21-azatetracyclo[12.8.0.0¹,¹⁹.0¹⁵,¹⁷]docosa-4,12,21-trien-3-one

Description

Cytochalasin F belongs to the class of organic compounds known as cytochalasins. These are cytochalasans in which the hydrogenated isoindolone bears a benzyl group. (1s,4e,6r,10r,12e,14s,15s,17r,18s,19s,20s)-20-benzyl-6,22-dihydroxy-10,17,18-trimethyl-2,16-dioxa-21-azatetracyclo[12.8.0.0¹,¹⁹.0¹⁵,¹⁷]docosa-4,12,21-trien-3-one is found in Boeremia exigua. (1s,4e,6r,10r,12e,14s,15s,17r,18s,19s,20s)-20-benzyl-6,22-dihydroxy-10,17,18-trimethyl-2,16-dioxa-21-azatetracyclo[12.8.0.0¹,¹⁹.0¹⁵,¹⁷]docosa-4,12,21-trien-3-one was first documented in 2003 (PMID: 14695792). Based on a literature review very few articles have been published on Cytochalasin F (PMID: 34846891).

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652309062211512D          

 35 39  0  0  1  0            999 V2000
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  2 34  1  0  0  0  0
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 34 35  1  1  0  0  0
M  END

     RDKit          3D

 72 76  0  0  0  0  0  0  0  0999 V2000
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M  END


  Mrv1652309062211512D          

 35 39  0  0  1  0            999 V2000
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  8  9  2  0  0  0  0
  9 10  1  0  0  0  0
 10 11  2  0  0  0  0
  6 11  1  0  0  0  0
  4 12  1  0  0  0  0
 12 13  2  0  0  0  0
 13 14  1  0  0  0  0
 15 13  1  1  0  0  0
  3 15  1  0  0  0  0
 15 16  1  0  0  0  0
 16 17  1  0  0  0  0
 17 18  2  0  0  0  0
 17 19  1  0  0  0  0
 19 20  2  0  0  0  0
 20 21  1  0  0  0  0
 21 22  1  6  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  1  0  0  0
 26 28  1  0  0  0  0
 28 29  1  0  0  0  0
 29 30  2  0  0  0  0
 31 30  1  1  0  0  0
 15 31  1  0  0  0  0
 31 32  1  0  0  0  0
 32 33  1  6  0  0  0
 33 34  1  0  0  0  0
  2 34  1  0  0  0  0
 32 34  1  0  0  0  0
 34 35  1  1  0  0  0
M  END
> <DATABASE_ID>
NP0229679

> <DATABASE_NAME>
NP-MRD

> <SMILES>
C[C@H]1[C@H]2[C@H](CC3=CC=CC=C3)N=C(O)[C@]22OC(=O)\C=C\[C@H](O)CCC[C@@H](C)C\C=C\[C@H]2[C@@H]2O[C@]12C

> <INCHI_IDENTIFIER>
InChI=1S/C29H37NO5/c1-18-9-7-13-21(31)15-16-24(32)34-29-22(14-8-10-18)26-28(3,35-26)19(2)25(29)23(30-27(29)33)17-20-11-5-4-6-12-20/h4-6,8,11-12,14-16,18-19,21-23,25-26,31H,7,9-10,13,17H2,1-3H3,(H,30,33)/b14-8+,16-15+/t18-,19+,21-,22+,23+,25+,26+,28-,29-/m1/s1

> <INCHI_KEY>
CXWYFIYZAZBQGQ-QJMMVEIUSA-N

> <FORMULA>
C29H37NO5

> <MOLECULAR_WEIGHT>
479.617

> <EXACT_MASS>
479.267173295

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_ATOM_COUNT>
72

> <JCHEM_AVERAGE_POLARIZABILITY>
52.64800823599222

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(1S,4E,6R,10R,12E,14S,15S,17R,18S,19S,20S)-20-benzyl-6,22-dihydroxy-10,17,18-trimethyl-2,16-dioxa-21-azatetracyclo[12.8.0.0^{1,19}.0^{15,17}]docosa-4,12,21-trien-3-one

> <JCHEM_LOGP>
3.871761576885553

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
5

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
14.833640716237184

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.9165589111834578

> <JCHEM_PKA_STRONGEST_BASIC>
4.810241162816906

> <JCHEM_POLAR_SURFACE_AREA>
91.65

> <JCHEM_REFRACTIVITY>
135.1792

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
(1S,4E,6R,10R,12E,14S,15S,17R,18S,19S,20S)-20-benzyl-6,22-dihydroxy-10,17,18-trimethyl-2,16-dioxa-21-azatetracyclo[12.8.0.0^{1,19}.0^{15,17}]docosa-4,12,21-trien-3-one

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 06-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   06-SEP-22         0                                  
HETATM    1  C   UNK     0       9.766  -3.932   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       8.902  -2.657   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       7.366  -2.768   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       6.421  -3.984   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       6.849  -5.463   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       5.781  -6.574   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       6.209  -8.053   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       5.142  -9.163   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       3.647  -8.794   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       3.219  -7.314   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       4.286  -6.204   0.000  0.00  0.00           C+0
HETATM   12  N   UNK     0       4.973  -3.460   0.000  0.00  0.00           N+0
HETATM   13  C   UNK     0       4.982  -2.135   0.000  0.00  0.00           C+0
HETATM   14  O   UNK     0       3.807  -0.976   0.000  0.00  0.00           O+0
HETATM   15  C   UNK     0       6.502  -1.494   0.000  0.00  0.00           C+0
HETATM   16  O   UNK     0       4.966  -1.604   0.000  0.00  0.00           O+0
HETATM   17  C   UNK     0       4.294  -2.990   0.000  0.00  0.00           C+0
HETATM   18  O   UNK     0       5.158  -4.265   0.000  0.00  0.00           O+0
HETATM   19  C   UNK     0       2.758  -3.101   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       1.894  -1.826   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0       0.358  -1.937   0.000  0.00  0.00           C+0
HETATM   22  O   UNK     0      -0.314  -3.323   0.000  0.00  0.00           O+0
HETATM   23  C   UNK     0      -0.506  -0.662   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0       0.166   0.724   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0       1.702   0.834   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0       2.374   2.220   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0       1.510   3.495   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0       3.910   2.331   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0       4.774   1.056   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0       6.310   1.167   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0       7.174  -0.108   0.000  0.00  0.00           C+0
HETATM   32  C   UNK     0       8.710   0.003   0.000  0.00  0.00           C+0
HETATM   33  O   UNK     0      10.246   0.114   0.000  0.00  0.00           O+0
HETATM   34  C   UNK     0       9.574  -1.272   0.000  0.00  0.00           C+0
HETATM   35  C   UNK     0      10.960  -1.944   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3   34                                                  
CONECT    3    2    4   15                                                  
CONECT    4    3    5   12                                                  
CONECT    5    4    6                                                       
CONECT    6    5    7   11                                                  
CONECT    7    6    8                                                       
CONECT    8    7    9                                                       
CONECT    9    8   10                                                       
CONECT   10    9   11                                                       
CONECT   11   10    6                                                       
CONECT   12    4   13                                                       
CONECT   13   12   14   15                                                  
CONECT   14   13                                                            
CONECT   15   13    3   16   31                                             
CONECT   16   15   17                                                       
CONECT   17   16   18   19                                                  
CONECT   18   17                                                            
CONECT   19   17   20                                                       
CONECT   20   19   21                                                       
CONECT   21   20   22   23                                                  
CONECT   22   21                                                            
CONECT   23   21   24                                                       
CONECT   24   23   25                                                       
CONECT   25   24   26                                                       
CONECT   26   25   27   28                                                  
CONECT   27   26                                                            
CONECT   28   26   29                                                       
CONECT   29   28   30                                                       
CONECT   30   29   31                                                       
CONECT   31   30   15   32                                                  
CONECT   32   31   33   34                                                  
CONECT   33   32   34                                                       
CONECT   34   33    2   32   35                                             
CONECT   35   34                                                            
MASTER        0    0    0    0    0    0    0    0   35    0   78    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₂₉H₃₇NO₅

Average Mass

479.6170 Da

Monoisotopic Mass

479.26717 Da

IUPAC Name

(1S,4E,6R,10R,12E,14S,15S,17R,18S,19S,20S)-20-benzyl-6,22-dihydroxy-10,17,18-trimethyl-2,16-dioxa-21-azatetracyclo[12.8.0.0^{1,19}.0^{15,17}]docosa-4,12,21-trien-3-one

Traditional Name

(1S,4E,6R,10R,12E,14S,15S,17R,18S,19S,20S)-20-benzyl-6,22-dihydroxy-10,17,18-trimethyl-2,16-dioxa-21-azatetracyclo[12.8.0.0^{1,19}.0^{15,17}]docosa-4,12,21-trien-3-one

CAS Registry Number

Not Available

SMILES

C[C@H]1[C@H]2[C@H](CC3=CC=CC=C3)N=C(O)[C@]22OC(=O)\C=C\[C@H](O)CCC[C@@H](C)C\C=C\[C@H]2[C@@H]2O[C@]12C

InChI Identifier

InChI=1S/C29H37NO5/c1-18-9-7-13-21(31)15-16-24(32)34-29-22(14-8-10-18)26-28(3,35-26)19(2)25(29)23(30-27(29)33)17-20-11-5-4-6-12-20/h4-6,8,11-12,14-16,18-19,21-23,25-26,31H,7,9-10,13,17H2,1-3H3,(H,30,33)/b14-8+,16-15+/t18-,19+,21-,22+,23+,25+,26+,28-,29-/m1/s1

InChI Key

CXWYFIYZAZBQGQ-QJMMVEIUSA-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
Phoma exigua	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as cytochalasins. These are cytochalasans in which the hydrogenated isoindolone bears a benzyl group.

Kingdom

Organic compounds

Super Class

Alkaloids and derivatives

Class

Cytochalasans

Sub Class

Cytochalasins

Direct Parent

Cytochalasins

Alternative Parents

Substituents

Lactone cytochalasin skeleton
Cytochalasin
Macrolide lactam
Macrolactam
Macrolide
Isoindolone
Isoindoline
Isoindole or derivatives
Oxepane
Monocyclic benzene moiety
Benzenoid
2-pyrrolidone
Pyrrolidone
Alpha,beta-unsaturated carboxylic ester
Enoate ester
Pyrrolidine
Carboxamide group
Carboxylic acid ester
Lactam
Lactone
Secondary carboxylic acid amide
Secondary alcohol
Monocarboxylic acid or derivatives
Carboxylic acid derivative
Azacycle
Oxacycle
Organoheterocyclic compound
Ether
Oxirane
Dialkyl ether
Organooxygen compound
Organic oxide
Organic oxygen compound
Hydrocarbon derivative
Alcohol
Organic nitrogen compound
Carbonyl group
Organonitrogen compound
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic 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	3.87	ChemAxon
pKa (Strongest Acidic)	1.92	ChemAxon
pKa (Strongest Basic)	4.81	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	5	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	91.65 Å²	ChemAxon
Rotatable Bond Count	2	ChemAxon
Refractivity	135.18 m³·mol⁻¹	ChemAxon
Polarizability	52.65 Å³	ChemAxon
Number of Rings	5	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

C00011325

Chemspider ID

10282675

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

21672263

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Evidente A, Andolfi A, Vurro M, Zonno MC, Motta A: Cytochalasins Z4, Z5, and Z6, three new 24-Oxa[14]cytochalasans produced by Phoma exigua var. heteromorpha. J Nat Prod. 2003 Dec;66(12):1540-4. doi: 10.1021/np030252o. [PubMed:14695792 ]
Hu XY, Wang CY, Li XM, Yang SQ, Li X, Wang BG, Si SY, Meng LH: Cytochalasin Derivatives from the Endozoic Curvularia verruculosa CS-129, a Fungus Isolated from the Deep-Sea Squat Lobster Shinkaia crosnieri Living in the Cold Seep Environment. J Nat Prod. 2021 Dec 24;84(12):3122-3130. doi: 10.1021/acs.jnatprod.1c00907. Epub 2021 Nov 30. [PubMed:34846891 ]
LOTUS database [Link]

Showing NP-Card for (1s,4e,6r,10r,12e,14s,15s,17r,18s,19s,20s)-20-benzyl-6,22-dihydroxy-10,17,18-trimethyl-2,16-dioxa-21-azatetracyclo[12.8.0.0¹,¹⁹.0¹⁵,¹⁷]docosa-4,12,21-trien-3-one (NP0229679)

MOL for NP0229679 ((1s,4e,6r,10r,12e,14s,15s,17r,18s,19s,20s)-20-benzyl-6,22-dihydroxy-10,17,18-trimethyl-2,16-dioxa-21-azatetracyclo[12.8.0.0¹,¹⁹.0¹⁵,¹⁷]docosa-4,12,21-trien-3-one)

3D MOL for NP0229679 ((1s,4e,6r,10r,12e,14s,15s,17r,18s,19s,20s)-20-benzyl-6,22-dihydroxy-10,17,18-trimethyl-2,16-dioxa-21-azatetracyclo[12.8.0.0¹,¹⁹.0¹⁵,¹⁷]docosa-4,12,21-trien-3-one)

3D SDF for NP0229679 ((1s,4e,6r,10r,12e,14s,15s,17r,18s,19s,20s)-20-benzyl-6,22-dihydroxy-10,17,18-trimethyl-2,16-dioxa-21-azatetracyclo[12.8.0.0¹,¹⁹.0¹⁵,¹⁷]docosa-4,12,21-trien-3-one)

3D-SDF for NP0229679 ((1s,4e,6r,10r,12e,14s,15s,17r,18s,19s,20s)-20-benzyl-6,22-dihydroxy-10,17,18-trimethyl-2,16-dioxa-21-azatetracyclo[12.8.0.0¹,¹⁹.0¹⁵,¹⁷]docosa-4,12,21-trien-3-one)

PDB for NP0229679 ((1s,4e,6r,10r,12e,14s,15s,17r,18s,19s,20s)-20-benzyl-6,22-dihydroxy-10,17,18-trimethyl-2,16-dioxa-21-azatetracyclo[12.8.0.0¹,¹⁹.0¹⁵,¹⁷]docosa-4,12,21-trien-3-one)

3D PDB for NP0229679 ((1s,4e,6r,10r,12e,14s,15s,17r,18s,19s,20s)-20-benzyl-6,22-dihydroxy-10,17,18-trimethyl-2,16-dioxa-21-azatetracyclo[12.8.0.0¹,¹⁹.0¹⁵,¹⁷]docosa-4,12,21-trien-3-one)

SMILES for NP0229679 ((1s,4e,6r,10r,12e,14s,15s,17r,18s,19s,20s)-20-benzyl-6,22-dihydroxy-10,17,18-trimethyl-2,16-dioxa-21-azatetracyclo[12.8.0.0¹,¹⁹.0¹⁵,¹⁷]docosa-4,12,21-trien-3-one)

INCHI for NP0229679 ((1s,4e,6r,10r,12e,14s,15s,17r,18s,19s,20s)-20-benzyl-6,22-dihydroxy-10,17,18-trimethyl-2,16-dioxa-21-azatetracyclo[12.8.0.0¹,¹⁹.0¹⁵,¹⁷]docosa-4,12,21-trien-3-one)

Structure for NP0229679 ((1s,4e,6r,10r,12e,14s,15s,17r,18s,19s,20s)-20-benzyl-6,22-dihydroxy-10,17,18-trimethyl-2,16-dioxa-21-azatetracyclo[12.8.0.0¹,¹⁹.0¹⁵,¹⁷]docosa-4,12,21-trien-3-one)

3D Structure for NP0229679 ((1s,4e,6r,10r,12e,14s,15s,17r,18s,19s,20s)-20-benzyl-6,22-dihydroxy-10,17,18-trimethyl-2,16-dioxa-21-azatetracyclo[12.8.0.0¹,¹⁹.0¹⁵,¹⁷]docosa-4,12,21-trien-3-one)