NP-MRD: Showing NP-Card for (3r,14e,16s,18r)-6-[(3-bromo-4-hydroxyphenyl)methyl]-5,11-dihydroxy-3,7,12,14,16,18-hexamethyl-1-oxa-4,7,10-triazacyclooctadeca-4,10,14-triene-2,8-dione (NP0258218)

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Record Information

Version

2.0

Created at

2022-09-07 23:34:04 UTC

Updated at

2022-09-07 23:34:05 UTC

NP-MRD ID

NP0258218

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(3r,14e,16s,18r)-6-[(3-bromo-4-hydroxyphenyl)methyl]-5,11-dihydroxy-3,7,12,14,16,18-hexamethyl-1-oxa-4,7,10-triazacyclooctadeca-4,10,14-triene-2,8-dione

Description

Geodiamolide E belongs to the class of organic compounds known as cyclic depsipeptides. These are natural or synthetic compounds having sequences of amino and hydroxy carboxylic acid residues (usually α-amino and α-hydroxy acids) connected in a ring. The residues are commonly but not necessarily regularly alternating. Based on a literature review very few articles have been published on Geodiamolide E.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652309082201342D          

 37 38  0  0  1  0            999 V2000
    5.0013    4.5375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2868    4.9500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2868    5.7750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0013    6.1875    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    5.0013    7.0125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.7158    5.7750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.7158    4.9500    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    5.3802    4.1963    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.4302    4.5375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.4302    3.7125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.7158    3.3000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
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  2 37  1  0  0  0  0
M  END

     RDKit          3D

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M  END


  Mrv1652309082201342D          

 37 38  0  0  1  0            999 V2000
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 12 13  1  1  0  0  0
 12 14  1  0  0  0  0
 14 15  2  0  0  0  0
 15 16  1  4  0  0  0
 15 17  1  0  0  0  0
 17 18  1  0  0  0  0
 18 19  1  0  0  0  0
 19 20  2  0  0  0  0
 20 21  1  0  0  0  0
 21 22  2  0  0  0  0
 22 23  1  0  0  0  0
 22 24  1  0  0  0  0
 24 25  1  0  0  0  0
 24 26  2  0  0  0  0
 19 26  1  0  0  0  0
 17 27  1  0  0  0  0
 27 28  1  0  0  0  0
 27 29  1  0  0  0  0
 29 30  2  0  0  0  0
 29 31  1  0  0  0  0
 32 31  1  4  0  0  0
 32 33  2  0  0  0  0
 33 34  1  0  0  0  0
 33 35  1  0  0  0  0
 35 36  1  0  0  0  0
 35 37  1  0  0  0  0
  2 37  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0258218

> <DATABASE_NAME>
NP-MRD

> <SMILES>
C[C@@H]1C[C@H](C)\C=C(C)\CC(C)C(O)=NCC(=O)N(C)C(CC2=CC=C(O)C(Br)=C2)C(O)=N[C@H](C)C(=O)O1

> <INCHI_IDENTIFIER>
InChI=1S/C27H38BrN3O6/c1-15-9-16(2)11-18(4)37-27(36)19(5)30-26(35)22(13-20-7-8-23(32)21(28)12-20)31(6)24(33)14-29-25(34)17(3)10-15/h7-9,12,16-19,22,32H,10-11,13-14H2,1-6H3,(H,29,34)(H,30,35)/b15-9+/t16-,17?,18-,19-,22?/m1/s1

> <INCHI_KEY>
INYUFROKXKFBJE-DMRKTBTMSA-N

> <FORMULA>
C27H38BrN3O6

> <MOLECULAR_WEIGHT>
580.52

> <EXACT_MASS>
579.194399

> <JCHEM_ACCEPTOR_COUNT>
7

> <JCHEM_ATOM_COUNT>
75

> <JCHEM_AVERAGE_POLARIZABILITY>
56.7228810790293

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(3R,14E,16S,18R)-6-[(3-bromo-4-hydroxyphenyl)methyl]-5,11-dihydroxy-3,7,12,14,16,18-hexamethyl-1-oxa-4,7,10-triazacyclooctadeca-4,10,14-triene-2,8-dione

> <JCHEM_LOGP>
2.9452255315964226

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
3.9504670079168003

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.9695837160829708

> <JCHEM_PKA_STRONGEST_BASIC>
6.724226585009585

> <JCHEM_POLAR_SURFACE_AREA>
132.02

> <JCHEM_REFRACTIVITY>
145.21370000000005

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
0

> <JCHEM_TRADITIONAL_IUPAC>
(3R,14E,16S,18R)-6-[(3-bromo-4-hydroxyphenyl)methyl]-5,11-dihydroxy-3,7,12,14,16,18-hexamethyl-1-oxa-4,7,10-triazacyclooctadeca-4,10,14-triene-2,8-dione

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 08-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   08-SEP-22         0                                  
HETATM    1  C   UNK     0       9.336   8.470   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       8.002   9.240   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       8.002  10.780   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       9.336  11.550   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       9.336  13.090   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      10.669  10.780   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      10.669   9.240   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      10.043   7.833   0.000  0.00  0.00           C+0
HETATM    9  O   UNK     0      12.003   8.470   0.000  0.00  0.00           O+0
HETATM   10  C   UNK     0      12.003   6.930   0.000  0.00  0.00           C+0
HETATM   11  O   UNK     0      10.669   6.160   0.000  0.00  0.00           O+0
HETATM   12  C   UNK     0      13.337   6.160   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      14.670   6.930   0.000  0.00  0.00           C+0
HETATM   14  N   UNK     0      13.337   4.620   0.000  0.00  0.00           N+0
HETATM   15  C   UNK     0      12.003   3.850   0.000  0.00  0.00           C+0
HETATM   16  O   UNK     0      10.669   4.620   0.000  0.00  0.00           O+0
HETATM   17  C   UNK     0      12.003   2.310   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0      13.337   1.540   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0      13.337  -0.000   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0      14.670  -0.770   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0      14.670  -2.310   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0      13.337  -3.080   0.000  0.00  0.00           C+0
HETATM   23  O   UNK     0      13.337  -4.620   0.000  0.00  0.00           O+0
HETATM   24  C   UNK     0      12.003  -2.310   0.000  0.00  0.00           C+0
HETATM   25 Br   UNK     0      10.669  -3.080   0.000  0.00  0.00          Br+0
HETATM   26  C   UNK     0      12.003  -0.770   0.000  0.00  0.00           C+0
HETATM   27  N   UNK     0      10.669   1.540   0.000  0.00  0.00           N+0
HETATM   28  C   UNK     0      10.669  -0.000   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0       9.336   2.310   0.000  0.00  0.00           C+0
HETATM   30  O   UNK     0       8.002   1.540   0.000  0.00  0.00           O+0
HETATM   31  C   UNK     0       9.336   3.850   0.000  0.00  0.00           C+0
HETATM   32  N   UNK     0       8.002   4.620   0.000  0.00  0.00           N+0
HETATM   33  C   UNK     0       8.002   6.160   0.000  0.00  0.00           C+0
HETATM   34  O   UNK     0       9.336   6.930   0.000  0.00  0.00           O+0
HETATM   35  C   UNK     0       6.668   6.930   0.000  0.00  0.00           C+0
HETATM   36  C   UNK     0       5.335   6.160   0.000  0.00  0.00           C+0
HETATM   37  C   UNK     0       6.668   8.470   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3   37                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5    6                                                  
CONECT    5    4                                                            
CONECT    6    4    7                                                       
CONECT    7    6    8    9                                                  
CONECT    8    7                                                            
CONECT    9    7   10                                                       
CONECT   10    9   11   12                                                  
CONECT   11   10                                                            
CONECT   12   10   13   14                                                  
CONECT   13   12                                                            
CONECT   14   12   15                                                       
CONECT   15   14   16   17                                                  
CONECT   16   15                                                            
CONECT   17   15   18   27                                                  
CONECT   18   17   19                                                       
CONECT   19   18   20   26                                                  
CONECT   20   19   21                                                       
CONECT   21   20   22                                                       
CONECT   22   21   23   24                                                  
CONECT   23   22                                                            
CONECT   24   22   25   26                                                  
CONECT   25   24                                                            
CONECT   26   24   19                                                       
CONECT   27   17   28   29                                                  
CONECT   28   27                                                            
CONECT   29   27   30   31                                                  
CONECT   30   29                                                            
CONECT   31   29   32                                                       
CONECT   32   31   33                                                       
CONECT   33   32   34   35                                                  
CONECT   34   33                                                            
CONECT   35   33   36   37                                                  
CONECT   36   35                                                            
CONECT   37   35    2                                                       
MASTER        0    0    0    0    0    0    0    0   37    0   76    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₂₇H₃₈BrN₃O₆

Average Mass

580.5200 Da

Monoisotopic Mass

579.19440 Da

IUPAC Name

(3R,14E,16S,18R)-6-[(3-bromo-4-hydroxyphenyl)methyl]-5,11-dihydroxy-3,7,12,14,16,18-hexamethyl-1-oxa-4,7,10-triazacyclooctadeca-4,10,14-triene-2,8-dione

Traditional Name

(3R,14E,16S,18R)-6-[(3-bromo-4-hydroxyphenyl)methyl]-5,11-dihydroxy-3,7,12,14,16,18-hexamethyl-1-oxa-4,7,10-triazacyclooctadeca-4,10,14-triene-2,8-dione

CAS Registry Number

Not Available

SMILES

C[C@@H]1C[C@H](C)\C=C(C)\CC(C)C(O)=NCC(=O)N(C)C(CC2=CC=C(O)C(Br)=C2)C(O)=N[C@H](C)C(=O)O1

InChI Identifier

InChI=1S/C27H38BrN3O6/c1-15-9-16(2)11-18(4)37-27(36)19(5)30-26(35)22(13-20-7-8-23(32)21(28)12-20)31(6)24(33)14-29-25(34)17(3)10-15/h7-9,12,16-19,22,32H,10-11,13-14H2,1-6H3,(H,29,34)(H,30,35)/b15-9+/t16-,17?,18-,19-,22?/m1/s1

InChI Key

INYUFROKXKFBJE-DMRKTBTMSA-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

Not Available

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as cyclic depsipeptides. These are natural or synthetic compounds having sequences of amino and hydroxy carboxylic acid residues (usually α-amino and α-hydroxy acids) connected in a ring. The residues are commonly but not necessarily regularly alternating.

Kingdom

Organic compounds

Super Class

Organic acids and derivatives

Class

Peptidomimetics

Sub Class

Depsipeptides

Direct Parent

Cyclic depsipeptides

Alternative Parents

Substituents

Cyclic depsipeptide
Macrolide lactam
Macrolide
Macrolactam
Alpha-amino acid ester
Alpha-amino acid or derivatives
2-bromophenol
2-halophenol
1-hydroxy-2-unsubstituted benzenoid
Phenol
Halobenzene
Bromobenzene
Benzenoid
Monocyclic benzene moiety
Aryl halide
Aryl bromide
Tertiary carboxylic acid amide
Secondary carboxylic acid amide
Lactone
Lactam
Carboxylic acid ester
Carboxamide group
Oxacycle
Azacycle
Organoheterocyclic compound
Monocarboxylic acid or derivatives
Carboxylic acid derivative
Organic nitrogen compound
Organic oxygen compound
Organopnictogen compound
Organic oxide
Hydrocarbon derivative
Organooxygen compound
Organonitrogen compound
Organobromide
Organohalogen compound
Carbonyl group
Aromatic heteromonocyclic compound

Molecular Framework

Aromatic heteromonocyclic 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	2.95	ChemAxon
pKa (Strongest Acidic)	1.97	ChemAxon
pKa (Strongest Basic)	6.72	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	7	ChemAxon
Hydrogen Donor Count	3	ChemAxon
Polar Surface Area	132.02 Å²	ChemAxon
Rotatable Bond Count	2	ChemAxon
Refractivity	145.21 m³·mol⁻¹	ChemAxon
Polarizability	56.72 Å³	ChemAxon
Number of Rings	2	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

4579624

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

5469059

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

LOTUS database [Link]

Showing NP-Card for (3r,14e,16s,18r)-6-[(3-bromo-4-hydroxyphenyl)methyl]-5,11-dihydroxy-3,7,12,14,16,18-hexamethyl-1-oxa-4,7,10-triazacyclooctadeca-4,10,14-triene-2,8-dione (NP0258218)

MOL for NP0258218 ((3r,14e,16s,18r)-6-[(3-bromo-4-hydroxyphenyl)methyl]-5,11-dihydroxy-3,7,12,14,16,18-hexamethyl-1-oxa-4,7,10-triazacyclooctadeca-4,10,14-triene-2,8-dione)

3D MOL for NP0258218 ((3r,14e,16s,18r)-6-[(3-bromo-4-hydroxyphenyl)methyl]-5,11-dihydroxy-3,7,12,14,16,18-hexamethyl-1-oxa-4,7,10-triazacyclooctadeca-4,10,14-triene-2,8-dione)

3D SDF for NP0258218 ((3r,14e,16s,18r)-6-[(3-bromo-4-hydroxyphenyl)methyl]-5,11-dihydroxy-3,7,12,14,16,18-hexamethyl-1-oxa-4,7,10-triazacyclooctadeca-4,10,14-triene-2,8-dione)

3D-SDF for NP0258218 ((3r,14e,16s,18r)-6-[(3-bromo-4-hydroxyphenyl)methyl]-5,11-dihydroxy-3,7,12,14,16,18-hexamethyl-1-oxa-4,7,10-triazacyclooctadeca-4,10,14-triene-2,8-dione)

PDB for NP0258218 ((3r,14e,16s,18r)-6-[(3-bromo-4-hydroxyphenyl)methyl]-5,11-dihydroxy-3,7,12,14,16,18-hexamethyl-1-oxa-4,7,10-triazacyclooctadeca-4,10,14-triene-2,8-dione)

3D PDB for NP0258218 ((3r,14e,16s,18r)-6-[(3-bromo-4-hydroxyphenyl)methyl]-5,11-dihydroxy-3,7,12,14,16,18-hexamethyl-1-oxa-4,7,10-triazacyclooctadeca-4,10,14-triene-2,8-dione)

SMILES for NP0258218 ((3r,14e,16s,18r)-6-[(3-bromo-4-hydroxyphenyl)methyl]-5,11-dihydroxy-3,7,12,14,16,18-hexamethyl-1-oxa-4,7,10-triazacyclooctadeca-4,10,14-triene-2,8-dione)

INCHI for NP0258218 ((3r,14e,16s,18r)-6-[(3-bromo-4-hydroxyphenyl)methyl]-5,11-dihydroxy-3,7,12,14,16,18-hexamethyl-1-oxa-4,7,10-triazacyclooctadeca-4,10,14-triene-2,8-dione)

Structure for NP0258218 ((3r,14e,16s,18r)-6-[(3-bromo-4-hydroxyphenyl)methyl]-5,11-dihydroxy-3,7,12,14,16,18-hexamethyl-1-oxa-4,7,10-triazacyclooctadeca-4,10,14-triene-2,8-dione)

3D Structure for NP0258218 ((3r,14e,16s,18r)-6-[(3-bromo-4-hydroxyphenyl)methyl]-5,11-dihydroxy-3,7,12,14,16,18-hexamethyl-1-oxa-4,7,10-triazacyclooctadeca-4,10,14-triene-2,8-dione)