NP-MRD: Showing NP-Card for (3s,6r,9s,14ar)-1,4,7-trihydroxy-3,6-dimethyl-9-[6-(oxiran-2-yl)-6-oxohexyl]-3h,6h,9h,12h,13h,14h,14ah-pyrrolo[1,2-a]1,4,7,10-tetraazacyclododecan-10-one (NP0249477)

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Record Information

Version

2.0

Created at

2022-09-07 12:02:41 UTC

Updated at

2022-09-07 12:02:41 UTC

NP-MRD ID

NP0249477

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(3s,6r,9s,14ar)-1,4,7-trihydroxy-3,6-dimethyl-9-[6-(oxiran-2-yl)-6-oxohexyl]-3h,6h,9h,12h,13h,14h,14ah-pyrrolo[1,2-a]1,4,7,10-tetraazacyclododecan-10-one

Description

HC toxin, also known as HC-toxin, belongs to the class of organic compounds known as cyclic peptides. Cyclic peptides are compounds containing a cyclic moiety bearing a peptide backbone. HC toxin is a secondary metabolite. Secondary metabolites are metabolically or physiologically non-essential metabolites that may serve a role as defense or signalling molecules. In some cases they are simply molecules that arise from the incomplete metabolism of other secondary metabolites. (3s,6r,9s,14ar)-1,4,7-trihydroxy-3,6-dimethyl-9-[6-(oxiran-2-yl)-6-oxohexyl]-3h,6h,9h,12h,13h,14h,14ah-pyrrolo[1,2-a]1,4,7,10-tetraazacyclododecan-10-one is found in Alternaria jesenskae and Bipolaris zeicola. (3s,6r,9s,14ar)-1,4,7-trihydroxy-3,6-dimethyl-9-[6-(oxiran-2-yl)-6-oxohexyl]-3h,6h,9h,12h,13h,14h,14ah-pyrrolo[1,2-a]1,4,7,10-tetraazacyclododecan-10-one was first documented in 1992 (PMID: 12297630). Based on a literature review a small amount of articles have been published on HC toxin (PMID: 10671527) (PMID: 15283467) (PMID: 16839576) (PMID: 18074352).

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652309072214022D          

 31 33  0  0  1  0            999 V2000
   -1.2079    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4934    0.4125    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
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   -0.9059   -1.1270    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7309   -1.1270    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4934   -1.8414    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.7484   -2.6261    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0809   -3.1110    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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    1.0461   -2.2539    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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M  END

     RDKit          3D

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M  END


  Mrv1652309072214022D          

 31 33  0  0  1  0            999 V2000
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   -0.4934    0.4125    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
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M  END
> <DATABASE_ID>
NP0249477

> <DATABASE_NAME>
NP-MRD

> <SMILES>
C[C@@H]1N=C(O)[C@H]2CCCN2C(=O)[C@H](CCCCCC(=O)C2CO2)N=C(O)[C@@H](C)N=C1O

> <INCHI_IDENTIFIER>
InChI=1S/C21H32N4O6/c1-12-18(27)22-13(2)19(28)24-14(7-4-3-5-9-16(26)17-11-31-17)21(30)25-10-6-8-15(25)20(29)23-12/h12-15,17H,3-11H2,1-2H3,(H,22,27)(H,23,29)(H,24,28)/t12-,13+,14-,15+,17?/m0/s1

> <INCHI_KEY>
GNYCTMYOHGBSBI-KVUCBBCISA-N

> <FORMULA>
C21H32N4O6

> <MOLECULAR_WEIGHT>
436.509

> <EXACT_MASS>
436.232184766

> <JCHEM_ACCEPTOR_COUNT>
9

> <JCHEM_ATOM_COUNT>
63

> <JCHEM_AVERAGE_POLARIZABILITY>
45.174990706814796

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(3S,6R,9S,14aR)-1,4,7-trihydroxy-3,6-dimethyl-9-[6-(oxiran-2-yl)-6-oxohexyl]-3H,6H,9H,10H,12H,13H,14H,14aH-pyrrolo[1,2-a]1,4,7,10-tetraazacyclododecan-10-one

> <JCHEM_LOGP>
-2.533119659797667

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
0.5839727579141423

> <JCHEM_PKA_STRONGEST_ACIDIC>
-0.9499126814660759

> <JCHEM_PKA_STRONGEST_BASIC>
8.30356391968846

> <JCHEM_POLAR_SURFACE_AREA>
147.68

> <JCHEM_REFRACTIVITY>
110.818

> <JCHEM_ROTATABLE_BOND_COUNT>
7

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
(3S,6R,9S,14aR)-1,4,7-trihydroxy-3,6-dimethyl-9-[6-(oxiran-2-yl)-6-oxohexyl]-3H,6H,9H,12H,13H,14H,14aH-pyrrolo[1,2-a]1,4,7,10-tetraazacyclododecan-10-one

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 07-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   07-SEP-22         0                                  
HETATM    1  C   UNK     0      -2.255   1.540   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -0.921   0.770   0.000  0.00  0.00           C+0
HETATM    3  N   UNK     0      -0.921  -0.770   0.000  0.00  0.00           N+0
HETATM    4  C   UNK     0      -1.691  -2.104   0.000  0.00  0.00           C+0
HETATM    5  O   UNK     0      -3.231  -2.104   0.000  0.00  0.00           O+0
HETATM    6  C   UNK     0      -0.921  -3.437   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      -1.397  -4.902   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      -0.151  -5.807   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       1.095  -4.902   0.000  0.00  0.00           C+0
HETATM   10  N   UNK     0       0.619  -3.437   0.000  0.00  0.00           N+0
HETATM   11  C   UNK     0       1.953  -4.207   0.000  0.00  0.00           C+0
HETATM   12  O   UNK     0       1.953  -5.747   0.000  0.00  0.00           O+0
HETATM   13  C   UNK     0       3.286  -3.437   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       4.620  -4.207   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       5.954  -3.437   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       7.287  -4.207   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       8.621  -3.437   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       9.955  -4.207   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0      11.288  -3.437   0.000  0.00  0.00           C+0
HETATM   20  O   UNK     0      11.288  -1.897   0.000  0.00  0.00           O+0
HETATM   21  C   UNK     0      12.622  -4.207   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0      14.162  -4.207   0.000  0.00  0.00           C+0
HETATM   23  O   UNK     0      13.392  -5.541   0.000  0.00  0.00           O+0
HETATM   24  N   UNK     0       3.286  -1.897   0.000  0.00  0.00           N+0
HETATM   25  C   UNK     0       4.056  -0.564   0.000  0.00  0.00           C+0
HETATM   26  O   UNK     0       5.596  -0.564   0.000  0.00  0.00           O+0
HETATM   27  C   UNK     0       3.286   0.770   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0       4.056   2.104   0.000  0.00  0.00           C+0
HETATM   29  N   UNK     0       1.746   0.770   0.000  0.00  0.00           N+0
HETATM   30  C   UNK     0       0.413   1.540   0.000  0.00  0.00           C+0
HETATM   31  O   UNK     0       0.413   3.080   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3   30                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5    6                                                  
CONECT    5    4                                                            
CONECT    6    4    7   10                                                  
CONECT    7    6    8                                                       
CONECT    8    7    9                                                       
CONECT    9    8   10                                                       
CONECT   10    9    6   11                                                  
CONECT   11   10   12   13                                                  
CONECT   12   11                                                            
CONECT   13   11   14   24                                                  
CONECT   14   13   15                                                       
CONECT   15   14   16                                                       
CONECT   16   15   17                                                       
CONECT   17   16   18                                                       
CONECT   18   17   19                                                       
CONECT   19   18   20   21                                                  
CONECT   20   19                                                            
CONECT   21   19   22   23                                                  
CONECT   22   21   23                                                       
CONECT   23   22   21                                                       
CONECT   24   13   25                                                       
CONECT   25   24   26   27                                                  
CONECT   26   25                                                            
CONECT   27   25   28   29                                                  
CONECT   28   27                                                            
CONECT   29   27   30                                                       
CONECT   30   29    2   31                                                  
CONECT   31   30                                                            
MASTER        0    0    0    0    0    0    0    0   31    0   66    0
END

View in JSmol

Synonyms

Value	Source
Cyclo(2-amino-8-oxo-9,10-epoxydecanoic acid-prolyl-alanyl-alanine)	ChEBI
Cyclo(aoe-pro-ala-ala)	ChEBI
HC-Toxin	ChEBI
Cyclo(2-amino-8-oxo-9,10-epoxydecanoate-prolyl-alanyl-alanine)	Generator
Helminthosporium carbonum toxin	MeSH

Chemical Formula

C₂₁H₃₂N₄O₆

Average Mass

436.5090 Da

Monoisotopic Mass

436.23218 Da

IUPAC Name

(3S,6R,9S,14aR)-1,4,7-trihydroxy-3,6-dimethyl-9-[6-(oxiran-2-yl)-6-oxohexyl]-3H,6H,9H,10H,12H,13H,14H,14aH-pyrrolo[1,2-a]1,4,7,10-tetraazacyclododecan-10-one

Traditional Name

(3S,6R,9S,14aR)-1,4,7-trihydroxy-3,6-dimethyl-9-[6-(oxiran-2-yl)-6-oxohexyl]-3H,6H,9H,12H,13H,14H,14aH-pyrrolo[1,2-a]1,4,7,10-tetraazacyclododecan-10-one

CAS Registry Number

Not Available

SMILES

C[C@@H]1N=C(O)[C@H]2CCCN2C(=O)[C@H](CCCCCC(=O)C2CO2)N=C(O)[C@@H](C)N=C1O

InChI Identifier

InChI=1S/C21H32N4O6/c1-12-18(27)22-13(2)19(28)24-14(7-4-3-5-9-16(26)17-11-31-17)21(30)25-10-6-8-15(25)20(29)23-12/h12-15,17H,3-11H2,1-2H3,(H,22,27)(H,23,29)(H,24,28)/t12-,13+,14-,15+,17?/m0/s1

InChI Key

GNYCTMYOHGBSBI-KVUCBBCISA-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
Alternaria jesenskae	LOTUS Database	35616633
Bipolaris zeicola	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as cyclic peptides. Cyclic peptides are compounds containing a cyclic moiety bearing a peptide backbone.

Kingdom

Organic compounds

Super Class

Organic acids and derivatives

Class

Carboxylic acids and derivatives

Sub Class

Amino acids, peptides, and analogues

Direct Parent

Cyclic peptides

Alternative Parents

Substituents

Cyclic alpha peptide
Alpha-amino acid or derivatives
Monosaccharide
Pyrrolidine
Tertiary carboxylic acid amide
Cyclic carboximidic acid
Carboxamide group
Ketone
Lactam
Dialkyl ether
Oxirane
Ether
Oxacycle
Polyol
Azacycle
Organoheterocyclic compound
Propargyl-type 1,3-dipolar organic compound
Organic 1,3-dipolar compound
Hydrocarbon derivative
Organic oxygen compound
Organonitrogen compound
Organooxygen compound
Organopnictogen compound
Organic nitrogen compound
Carbonyl group
Organic oxide
Aliphatic heteropolycyclic compound

Molecular Framework

Aliphatic heteropolycyclic compounds

External Descriptors

tetrapeptide (CHEBI:48028 )
homodetic cyclic peptide (CHEBI:48028 )

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	-2.5	ChemAxon
pKa (Strongest Acidic)	-0.95	ChemAxon
pKa (Strongest Basic)	8.3	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	9	ChemAxon
Hydrogen Donor Count	3	ChemAxon
Polar Surface Area	147.68 Å²	ChemAxon
Rotatable Bond Count	7	ChemAxon
Refractivity	110.82 m³·mol⁻¹	ChemAxon
Polarizability	45.17 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	Yes	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

26330566

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

107864

PDB ID

Not Available

ChEBI ID

48028

Good Scents ID

Not Available

References

General References

Cheng YQ, Walton JD: A eukaryotic alanine racemase gene involved in cyclic peptide biosynthesis. J Biol Chem. 2000 Feb 18;275(7):4906-11. doi: 10.1074/jbc.275.7.4906. [PubMed:10671527 ]
Meeley RB, Johal GS, Briggs SP, Walton JD: A Biochemical Phenotype for a Disease Resistance Gene of Maize. Plant Cell. 1992 Jan;4(1):71-77. doi: 10.1105/tpc.4.1.71. [PubMed:12297630 ]
Joung KE, Kim DK, Sheen YY: Antiproliferative effect of trichostatin A and HC-toxin in T47D human breast cancer cells. Arch Pharm Res. 2004 Jun;27(6):640-5. doi: 10.1007/BF02980164. [PubMed:15283467 ]
Walton JD: HC-toxin. Phytochemistry. 2006 Jul;67(14):1406-13. doi: 10.1016/j.phytochem.2006.05.033. Epub 2006 Jul 12. [PubMed:16839576 ]
Deubzer HE, Ehemann V, Westermann F, Heinrich R, Mechtersheimer G, Kulozik AE, Schwab M, Witt O: Histone deacetylase inhibitor Helminthosporium carbonum (HC)-toxin suppresses the malignant phenotype of neuroblastoma cells. Int J Cancer. 2008 Apr 15;122(8):1891-900. doi: 10.1002/ijc.23295. [PubMed:18074352 ]
LOTUS database [Link]

Showing NP-Card for (3s,6r,9s,14ar)-1,4,7-trihydroxy-3,6-dimethyl-9-[6-(oxiran-2-yl)-6-oxohexyl]-3h,6h,9h,12h,13h,14h,14ah-pyrrolo[1,2-a]1,4,7,10-tetraazacyclododecan-10-one (NP0249477)

MOL for NP0249477 ((3s,6r,9s,14ar)-1,4,7-trihydroxy-3,6-dimethyl-9-[6-(oxiran-2-yl)-6-oxohexyl]-3h,6h,9h,12h,13h,14h,14ah-pyrrolo[1,2-a]1,4,7,10-tetraazacyclododecan-10-one)

3D MOL for NP0249477 ((3s,6r,9s,14ar)-1,4,7-trihydroxy-3,6-dimethyl-9-[6-(oxiran-2-yl)-6-oxohexyl]-3h,6h,9h,12h,13h,14h,14ah-pyrrolo[1,2-a]1,4,7,10-tetraazacyclododecan-10-one)

3D SDF for NP0249477 ((3s,6r,9s,14ar)-1,4,7-trihydroxy-3,6-dimethyl-9-[6-(oxiran-2-yl)-6-oxohexyl]-3h,6h,9h,12h,13h,14h,14ah-pyrrolo[1,2-a]1,4,7,10-tetraazacyclododecan-10-one)

3D-SDF for NP0249477 ((3s,6r,9s,14ar)-1,4,7-trihydroxy-3,6-dimethyl-9-[6-(oxiran-2-yl)-6-oxohexyl]-3h,6h,9h,12h,13h,14h,14ah-pyrrolo[1,2-a]1,4,7,10-tetraazacyclododecan-10-one)

PDB for NP0249477 ((3s,6r,9s,14ar)-1,4,7-trihydroxy-3,6-dimethyl-9-[6-(oxiran-2-yl)-6-oxohexyl]-3h,6h,9h,12h,13h,14h,14ah-pyrrolo[1,2-a]1,4,7,10-tetraazacyclododecan-10-one)

3D PDB for NP0249477 ((3s,6r,9s,14ar)-1,4,7-trihydroxy-3,6-dimethyl-9-[6-(oxiran-2-yl)-6-oxohexyl]-3h,6h,9h,12h,13h,14h,14ah-pyrrolo[1,2-a]1,4,7,10-tetraazacyclododecan-10-one)

SMILES for NP0249477 ((3s,6r,9s,14ar)-1,4,7-trihydroxy-3,6-dimethyl-9-[6-(oxiran-2-yl)-6-oxohexyl]-3h,6h,9h,12h,13h,14h,14ah-pyrrolo[1,2-a]1,4,7,10-tetraazacyclododecan-10-one)

INCHI for NP0249477 ((3s,6r,9s,14ar)-1,4,7-trihydroxy-3,6-dimethyl-9-[6-(oxiran-2-yl)-6-oxohexyl]-3h,6h,9h,12h,13h,14h,14ah-pyrrolo[1,2-a]1,4,7,10-tetraazacyclododecan-10-one)

Structure for NP0249477 ((3s,6r,9s,14ar)-1,4,7-trihydroxy-3,6-dimethyl-9-[6-(oxiran-2-yl)-6-oxohexyl]-3h,6h,9h,12h,13h,14h,14ah-pyrrolo[1,2-a]1,4,7,10-tetraazacyclododecan-10-one)

3D Structure for NP0249477 ((3s,6r,9s,14ar)-1,4,7-trihydroxy-3,6-dimethyl-9-[6-(oxiran-2-yl)-6-oxohexyl]-3h,6h,9h,12h,13h,14h,14ah-pyrrolo[1,2-a]1,4,7,10-tetraazacyclododecan-10-one)