NP-MRD: Showing NP-Card for 9-benzyl-5,7-dihydroxy-6-methyl-3-(7-oxooctan-2-yl)-3h,4h,5h,6h,9h,12h,13h,14h,14ah-pyrrolo[2,1-c]1-oxa-4,7-diazacyclododecane-1,10-dione (NP0264173)

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Record Information

Version

2.0

Created at

2022-09-08 07:36:34 UTC

Updated at

2022-09-08 07:36:35 UTC

NP-MRD ID

NP0264173

Secondary Accession Numbers

None

Natural Product Identification

Common Name

9-benzyl-5,7-dihydroxy-6-methyl-3-(7-oxooctan-2-yl)-3h,4h,5h,6h,9h,12h,13h,14h,14ah-pyrrolo[2,1-c]1-oxa-4,7-diazacyclododecane-1,10-dione

Description

9-Benzyl-5,7-dihydroxy-6-methyl-3-(7-oxooctan-2-yl)-1H,3H,4H,5H,6H,9H,10H,12H,13H,14H,14aH-pyrrolo[2,1-c]1-oxa-4,7-diazacyclododecane-1,10-dione 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. 9-Benzyl-5,7-dihydroxy-6-methyl-3-(7-oxooctan-2-yl)-1H,3H,4H,5H,6H,9H,10H,12H,13H,14H,14aH-pyrrolo[2,1-c]1-oxa-4,7-diazacyclododecane-1,10-dione is an extremely weak basic (essentially neutral) compound (based on its pKa).

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1533004251508382D          

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M  END

     RDKit          3D

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M  END


  Mrv1533004251508382D          

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   -0.0000   -0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0000   -1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8205   -1.5638    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -2.0625    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  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  1  0  0  0  0
  7  8  2  0  0  0  0
  7  9  1  0  0  0  0
  2 10  1  0  0  0  0
 10 11  1  0  0  0  0
 11 12  1  0  0  0  0
 12 13  1  0  0  0  0
 12 14  1  0  0  0  0
 14 15  1  0  0  0  0
 14 16  1  0  0  0  0
 16 17  2  0  0  0  0
 16 18  1  0  0  0  0
 18 19  1  0  0  0  0
 19 20  1  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
 23 24  2  0  0  0  0
 24 25  1  0  0  0  0
 25 26  2  0  0  0  0
 21 26  1  0  0  0  0
 19 27  1  0  0  0  0
 27 28  2  0  0  0  0
 27 29  1  0  0  0  0
 29 30  1  0  0  0  0
 30 31  1  0  0  0  0
 31 32  1  0  0  0  0
 32 33  1  0  0  0  0
 29 33  1  0  0  0  0
 33 34  1  0  0  0  0
 34 35  2  0  0  0  0
 34 36  1  0  0  0  0
 10 36  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0264173

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CC(CCCCC(C)=O)C1CC(O)C(C)C(=O)NC(CC2=CC=CC=C2)C(=O)N2CCCC2C(=O)O1

> <INCHI_IDENTIFIER>
InChI=1S/C28H40N2O6/c1-18(10-7-8-11-19(2)31)25-17-24(32)20(3)26(33)29-22(16-21-12-5-4-6-13-21)27(34)30-15-9-14-23(30)28(35)36-25/h4-6,12-13,18,20,22-25,32H,7-11,14-17H2,1-3H3,(H,29,33)

> <INCHI_KEY>
AOQQOEQINNPMNK-UHFFFAOYSA-N

> <FORMULA>
C28H40N2O6

> <MOLECULAR_WEIGHT>
500.636

> <EXACT_MASS>
500.288637016

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_ATOM_COUNT>
76

> <JCHEM_AVERAGE_POLARIZABILITY>
55.11297408461519

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
9-benzyl-5-hydroxy-6-methyl-3-(7-oxooctan-2-yl)-dodecahydro-1H-pyrrolo[2,1-c]1-oxa-4,7-diazacyclododecane-1,7,10-trione

> <ALOGPS_LOGP>
2.46

> <JCHEM_LOGP>
2.781183790333331

> <ALOGPS_LOGS>
-4.21

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
14.838019501885999

> <JCHEM_PKA_STRONGEST_ACIDIC>
11.439854176730751

> <JCHEM_PKA_STRONGEST_BASIC>
-1.6914145845099307

> <JCHEM_POLAR_SURFACE_AREA>
113.01

> <JCHEM_REFRACTIVITY>
134.89329999999998

> <JCHEM_ROTATABLE_BOND_COUNT>
8

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
3.08e-02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
9-benzyl-5-hydroxy-6-methyl-3-(7-oxooctan-2-yl)-decahydropyrrolo[2,1-c]1-oxa-4,7-diazacyclododecane-1,7,10-trione

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 25-APR-15   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   25-APR-15         0                                  
HETATM    1  C   UNK     0       2.667  -7.700   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       2.667  -6.160   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       4.001  -5.390   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       5.335  -6.160   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       6.668  -5.390   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       8.002  -6.160   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       9.336  -5.390   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0      10.669  -6.160   0.000  0.00  0.00           O+0
HETATM    9  C   UNK     0       9.336  -3.850   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       1.334  -5.390   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      -0.000  -6.160   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      -1.334  -5.390   0.000  0.00  0.00           C+0
HETATM   13  O   UNK     0      -1.334  -3.850   0.000  0.00  0.00           O+0
HETATM   14  C   UNK     0      -2.667  -6.160   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0      -2.667  -7.700   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0      -4.001  -5.390   0.000  0.00  0.00           C+0
HETATM   17  O   UNK     0      -5.335  -6.160   0.000  0.00  0.00           O+0
HETATM   18  N   UNK     0      -4.001  -3.850   0.000  0.00  0.00           N+0
HETATM   19  C   UNK     0      -2.667  -3.080   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0      -4.001  -2.310   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0      -5.335  -3.080   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0      -5.335  -4.620   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0      -6.668  -5.390   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0      -8.002  -4.620   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0      -8.002  -3.080   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0      -6.668  -2.310   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0      -2.667  -1.540   0.000  0.00  0.00           C+0
HETATM   28  O   UNK     0      -4.001  -0.770   0.000  0.00  0.00           O+0
HETATM   29  N   UNK     0      -1.334  -0.770   0.000  0.00  0.00           N+0
HETATM   30  C   UNK     0      -1.013   0.736   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0       0.518   0.897   0.000  0.00  0.00           C+0
HETATM   32  C   UNK     0       1.144  -0.510   0.000  0.00  0.00           C+0
HETATM   33  C   UNK     0      -0.000  -1.540   0.000  0.00  0.00           C+0
HETATM   34  C   UNK     0      -0.000  -3.080   0.000  0.00  0.00           C+0
HETATM   35  O   UNK     0      -1.532  -2.919   0.000  0.00  0.00           O+0
HETATM   36  O   UNK     0       1.334  -3.850   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3   10                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4    6                                                       
CONECT    6    5    7                                                       
CONECT    7    6    8    9                                                  
CONECT    8    7                                                            
CONECT    9    7                                                            
CONECT   10    2   11   36                                                  
CONECT   11   10   12                                                       
CONECT   12   11   13   14                                                  
CONECT   13   12                                                            
CONECT   14   12   15   16                                                  
CONECT   15   14                                                            
CONECT   16   14   17   18                                                  
CONECT   17   16                                                            
CONECT   18   16   19                                                       
CONECT   19   18   20   27                                                  
CONECT   20   19   21                                                       
CONECT   21   20   22   26                                                  
CONECT   22   21   23                                                       
CONECT   23   22   24                                                       
CONECT   24   23   25                                                       
CONECT   25   24   26                                                       
CONECT   26   25   21                                                       
CONECT   27   19   28   29                                                  
CONECT   28   27                                                            
CONECT   29   27   30   33                                                  
CONECT   30   29   31                                                       
CONECT   31   30   32                                                       
CONECT   32   31   33                                                       
CONECT   33   32   29   34                                                  
CONECT   34   33   35   36                                                  
CONECT   35   34                                                            
CONECT   36   34   10                                                       
MASTER        0    0    0    0    0    0    0    0   36    0   76    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₂₈H₄₀N₂O₆

Average Mass

500.6360 Da

Monoisotopic Mass

500.28864 Da

IUPAC Name

9-benzyl-5-hydroxy-6-methyl-3-(7-oxooctan-2-yl)-dodecahydro-1H-pyrrolo[2,1-c]1-oxa-4,7-diazacyclododecane-1,7,10-trione

Traditional Name

9-benzyl-5-hydroxy-6-methyl-3-(7-oxooctan-2-yl)-decahydropyrrolo[2,1-c]1-oxa-4,7-diazacyclododecane-1,7,10-trione

CAS Registry Number

Not Available

SMILES

CC(CCCCC(C)=O)C1CC(O)C(C)C(=O)NC(CC2=CC=CC=C2)C(=O)N2CCCC2C(=O)O1

InChI Identifier

InChI=1S/C28H40N2O6/c1-18(10-7-8-11-19(2)31)25-17-24(32)20(3)26(33)29-22(16-21-12-5-4-6-13-21)27(34)30-15-9-14-23(30)28(35)36-25/h4-6,12-13,18,20,22-25,32H,7-11,14-17H2,1-3H3,(H,29,33)

InChI Key

AOQQOEQINNPMNK-UHFFFAOYSA-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
Alpha-amino acid ester
Macrolactam
Alpha-amino acid or derivatives
Monocyclic benzene moiety
Benzenoid
Pyrrolidine
Tertiary carboxylic acid amide
Cyclic carboximidic acid
Carboxamide group
Carboxylic acid ester
Ketone
Lactam
Lactone
Secondary alcohol
Propargyl-type 1,3-dipolar organic compound
Monocarboxylic acid or derivatives
Oxacycle
Organic 1,3-dipolar compound
Organoheterocyclic compound
Azacycle
Carboxylic acid derivative
Organonitrogen compound
Organic oxide
Organic nitrogen compound
Organic oxygen compound
Alcohol
Organooxygen compound
Carbonyl group
Organopnictogen compound
Hydrocarbon derivative
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	2.46	ALOGPS
logP	2.78	ChemAxon
logS	-4.2	ALOGPS
pKa (Strongest Acidic)	11.44	ChemAxon
pKa (Strongest Basic)	-1.7	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	5	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	113.01 Å²	ChemAxon
Rotatable Bond Count	8	ChemAxon
Refractivity	134.89 m³·mol⁻¹	ChemAxon
Polarizability	55.11 Å³	ChemAxon
Number of Rings	3	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	No	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

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

74333798

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

LOTUS database [Link]

Showing NP-Card for 9-benzyl-5,7-dihydroxy-6-methyl-3-(7-oxooctan-2-yl)-3h,4h,5h,6h,9h,12h,13h,14h,14ah-pyrrolo[2,1-c]1-oxa-4,7-diazacyclododecane-1,10-dione (NP0264173)

MOL for NP0264173 (9-benzyl-5,7-dihydroxy-6-methyl-3-(7-oxooctan-2-yl)-3h,4h,5h,6h,9h,12h,13h,14h,14ah-pyrrolo[2,1-c]1-oxa-4,7-diazacyclododecane-1,10-dione)

3D MOL for NP0264173 (9-benzyl-5,7-dihydroxy-6-methyl-3-(7-oxooctan-2-yl)-3h,4h,5h,6h,9h,12h,13h,14h,14ah-pyrrolo[2,1-c]1-oxa-4,7-diazacyclododecane-1,10-dione)

3D SDF for NP0264173 (9-benzyl-5,7-dihydroxy-6-methyl-3-(7-oxooctan-2-yl)-3h,4h,5h,6h,9h,12h,13h,14h,14ah-pyrrolo[2,1-c]1-oxa-4,7-diazacyclododecane-1,10-dione)

3D-SDF for NP0264173 (9-benzyl-5,7-dihydroxy-6-methyl-3-(7-oxooctan-2-yl)-3h,4h,5h,6h,9h,12h,13h,14h,14ah-pyrrolo[2,1-c]1-oxa-4,7-diazacyclododecane-1,10-dione)

PDB for NP0264173 (9-benzyl-5,7-dihydroxy-6-methyl-3-(7-oxooctan-2-yl)-3h,4h,5h,6h,9h,12h,13h,14h,14ah-pyrrolo[2,1-c]1-oxa-4,7-diazacyclododecane-1,10-dione)

3D PDB for NP0264173 (9-benzyl-5,7-dihydroxy-6-methyl-3-(7-oxooctan-2-yl)-3h,4h,5h,6h,9h,12h,13h,14h,14ah-pyrrolo[2,1-c]1-oxa-4,7-diazacyclododecane-1,10-dione)

SMILES for NP0264173 (9-benzyl-5,7-dihydroxy-6-methyl-3-(7-oxooctan-2-yl)-3h,4h,5h,6h,9h,12h,13h,14h,14ah-pyrrolo[2,1-c]1-oxa-4,7-diazacyclododecane-1,10-dione)

INCHI for NP0264173 (9-benzyl-5,7-dihydroxy-6-methyl-3-(7-oxooctan-2-yl)-3h,4h,5h,6h,9h,12h,13h,14h,14ah-pyrrolo[2,1-c]1-oxa-4,7-diazacyclododecane-1,10-dione)

Structure for NP0264173 (9-benzyl-5,7-dihydroxy-6-methyl-3-(7-oxooctan-2-yl)-3h,4h,5h,6h,9h,12h,13h,14h,14ah-pyrrolo[2,1-c]1-oxa-4,7-diazacyclododecane-1,10-dione)

3D Structure for NP0264173 (9-benzyl-5,7-dihydroxy-6-methyl-3-(7-oxooctan-2-yl)-3h,4h,5h,6h,9h,12h,13h,14h,14ah-pyrrolo[2,1-c]1-oxa-4,7-diazacyclododecane-1,10-dione)