NP-MRD: Showing NP-Card for n-[7,10-dimethyl-12-(2-methylpropyl)-2,5,9,11-tetraoxo-3-(sec-butyl)-1,4,8-trioxacyclododecan-6-yl]-2-hydroxy-3-[(hydroxymethylidene)amino]benzenecarboximidic acid (NP0304118)

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Record Information

Version

2.0

Created at

2022-09-10 18:58:31 UTC

Updated at

2022-09-10 18:58:31 UTC

NP-MRD ID

NP0304118

Secondary Accession Numbers

None

Natural Product Identification

Common Name

n-[7,10-dimethyl-12-(2-methylpropyl)-2,5,9,11-tetraoxo-3-(sec-butyl)-1,4,8-trioxacyclododecan-6-yl]-2-hydroxy-3-[(hydroxymethylidene)amino]benzenecarboximidic acid

Description

JBIR-52, also known as JBIR 52, 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. n-[7,10-dimethyl-12-(2-methylpropyl)-2,5,9,11-tetraoxo-3-(sec-butyl)-1,4,8-trioxacyclododecan-6-yl]-2-hydroxy-3-[(hydroxymethylidene)amino]benzenecarboximidic acid was first documented in 2009 (PMID: 19662084). Based on a literature review very few articles have been published on JBIR-52.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652309102220582D          

 39 40  0  0  0  0            999 V2000
    0.7145    7.8375    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


  Mrv1652309102220582D          

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   -2.1434   11.1375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4289    9.9000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145    9.4875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3789   10.2412    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
  3  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
 10  9  1  4  0  0  0
 10 11  2  0  0  0  0
 11 12  1  0  0  0  0
 11 13  1  0  0  0  0
 13 14  2  0  0  0  0
 14 15  1  0  0  0  0
 15 16  2  0  0  0  0
 16 17  1  0  0  0  0
 17 18  1  0  0  0  0
 18 19  2  0  0  0  0
 19 20  1  4  0  0  0
 17 21  2  0  0  0  0
 13 21  1  0  0  0  0
 21 22  1  0  0  0  0
  9 23  1  0  0  0  0
 23 24  1  0  0  0  0
 23 25  1  0  0  0  0
 25 26  1  0  0  0  0
 26 27  2  0  0  0  0
 26 28  1  0  0  0  0
 28 29  1  0  0  0  0
 28 30  1  0  0  0  0
 30 31  2  0  0  0  0
 30 32  1  0  0  0  0
 32 33  1  0  0  0  0
 33 34  1  0  0  0  0
 34 35  1  0  0  0  0
 34 36  1  0  0  0  0
 32 37  1  0  0  0  0
 37 38  1  0  0  0  0
  5 38  1  0  0  0  0
 38 39  2  0  0  0  0
M  END
> <DATABASE_ID>
NP0304118

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CCC(C)C1OC(=O)C(N=C(O)C2=CC=CC(N=CO)=C2O)C(C)OC(=O)C(C)C(=O)C(CC(C)C)OC1=O

> <INCHI_IDENTIFIER>
InChI=1S/C27H36N2O10/c1-7-14(4)23-27(36)38-19(11-13(2)3)21(31)15(5)25(34)37-16(6)20(26(35)39-23)29-24(33)17-9-8-10-18(22(17)32)28-12-30/h8-10,12-16,19-20,23,32H,7,11H2,1-6H3,(H,28,30)(H,29,33)

> <INCHI_KEY>
ZQPBRVQLPNZKAB-UHFFFAOYSA-N

> <FORMULA>
C27H36N2O10

> <MOLECULAR_WEIGHT>
548.589

> <EXACT_MASS>
548.236995367

> <JCHEM_ACCEPTOR_COUNT>
9

> <JCHEM_ATOM_COUNT>
75

> <JCHEM_AVERAGE_POLARIZABILITY>
56.51300386095022

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
N-[3-(butan-2-yl)-7,10-dimethyl-12-(2-methylpropyl)-2,5,9,11-tetraoxo-1,4,8-trioxacyclododecan-6-yl]-2-hydroxy-3-[(hydroxymethylidene)amino]benzene-1-carboximidic acid

> <JCHEM_LOGP>
6.597250547333333

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
7.408280353067691

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.2877500472364374

> <JCHEM_PKA_STRONGEST_BASIC>
0.025153478184113176

> <JCHEM_POLAR_SURFACE_AREA>
181.37999999999997

> <JCHEM_REFRACTIVITY>
139.14720000000003

> <JCHEM_ROTATABLE_BOND_COUNT>
7

> <JCHEM_RULE_OF_FIVE>
0

> <JCHEM_TRADITIONAL_IUPAC>
N-[7,10-dimethyl-12-(2-methylpropyl)-2,5,9,11-tetraoxo-3-(sec-butyl)-1,4,8-trioxacyclododecan-6-yl]-2-hydroxy-3-[(hydroxymethylidene)amino]benzenecarboximidic acid

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 10-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   10-SEP-22         0                                  
HETATM    1  C   UNK     0       1.334  14.630   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       1.334  16.170   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -0.000  16.940   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -0.000  18.480   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      -1.334  16.170   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0      -0.000  15.400   0.000  0.00  0.00           O+0
HETATM    7  C   UNK     0      -0.000  13.860   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0       1.334  13.090   0.000  0.00  0.00           O+0
HETATM    9  C   UNK     0      -1.334  13.090   0.000  0.00  0.00           C+0
HETATM   10  N   UNK     0      -1.334  11.550   0.000  0.00  0.00           N+0
HETATM   11  C   UNK     0      -0.000  10.780   0.000  0.00  0.00           C+0
HETATM   12  O   UNK     0       1.334  11.550   0.000  0.00  0.00           O+0
HETATM   13  C   UNK     0      -0.000   9.240   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      -1.334   8.470   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0      -1.334   6.930   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0      -0.000   6.160   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       1.334   6.930   0.000  0.00  0.00           C+0
HETATM   18  N   UNK     0       2.667   6.160   0.000  0.00  0.00           N+0
HETATM   19  C   UNK     0       4.001   6.930   0.000  0.00  0.00           C+0
HETATM   20  O   UNK     0       5.335   6.160   0.000  0.00  0.00           O+0
HETATM   21  C   UNK     0       1.334   8.470   0.000  0.00  0.00           C+0
HETATM   22  O   UNK     0       2.667   9.240   0.000  0.00  0.00           O+0
HETATM   23  C   UNK     0      -2.667  13.860   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0      -2.667  15.400   0.000  0.00  0.00           C+0
HETATM   25  O   UNK     0      -4.001  13.090   0.000  0.00  0.00           O+0
HETATM   26  C   UNK     0      -5.335  13.860   0.000  0.00  0.00           C+0
HETATM   27  O   UNK     0      -6.668  13.090   0.000  0.00  0.00           O+0
HETATM   28  C   UNK     0      -5.335  15.400   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0      -6.668  16.170   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0      -4.001  16.170   0.000  0.00  0.00           C+0
HETATM   31  O   UNK     0      -2.469  16.331   0.000  0.00  0.00           O+0
HETATM   32  C   UNK     0      -4.001  17.710   0.000  0.00  0.00           C+0
HETATM   33  C   UNK     0      -5.335  18.480   0.000  0.00  0.00           C+0
HETATM   34  C   UNK     0      -5.335  20.020   0.000  0.00  0.00           C+0
HETATM   35  C   UNK     0      -6.668  20.790   0.000  0.00  0.00           C+0
HETATM   36  C   UNK     0      -4.001  20.790   0.000  0.00  0.00           C+0
HETATM   37  O   UNK     0      -2.667  18.480   0.000  0.00  0.00           O+0
HETATM   38  C   UNK     0      -1.334  17.710   0.000  0.00  0.00           C+0
HETATM   39  O   UNK     0      -0.707  19.117   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4    5                                                  
CONECT    4    3                                                            
CONECT    5    3    6   38                                                  
CONECT    6    5    7                                                       
CONECT    7    6    8    9                                                  
CONECT    8    7                                                            
CONECT    9    7   10   23                                                  
CONECT   10    9   11                                                       
CONECT   11   10   12   13                                                  
CONECT   12   11                                                            
CONECT   13   11   14   21                                                  
CONECT   14   13   15                                                       
CONECT   15   14   16                                                       
CONECT   16   15   17                                                       
CONECT   17   16   18   21                                                  
CONECT   18   17   19                                                       
CONECT   19   18   20                                                       
CONECT   20   19                                                            
CONECT   21   17   13   22                                                  
CONECT   22   21                                                            
CONECT   23    9   24   25                                                  
CONECT   24   23                                                            
CONECT   25   23   26                                                       
CONECT   26   25   27   28                                                  
CONECT   27   26                                                            
CONECT   28   26   29   30                                                  
CONECT   29   28                                                            
CONECT   30   28   31   32                                                  
CONECT   31   30                                                            
CONECT   32   30   33   37                                                  
CONECT   33   32   34                                                       
CONECT   34   33   35   36                                                  
CONECT   35   34                                                            
CONECT   36   34                                                            
CONECT   37   32   38                                                       
CONECT   38   37    5   39                                                  
CONECT   39   38                                                            
MASTER        0    0    0    0    0    0    0    0   39    0   80    0
END

View in JSmol

Synonyms

Value	Source
JBIR 52	MeSH

Chemical Formula

C₂₇H₃₆N₂O₁₀

Average Mass

548.5890 Da

Monoisotopic Mass

548.23700 Da

IUPAC Name

N-[3-(butan-2-yl)-7,10-dimethyl-12-(2-methylpropyl)-2,5,9,11-tetraoxo-1,4,8-trioxacyclododecan-6-yl]-2-hydroxy-3-[(hydroxymethylidene)amino]benzene-1-carboximidic acid

Traditional Name

N-[7,10-dimethyl-12-(2-methylpropyl)-2,5,9,11-tetraoxo-3-(sec-butyl)-1,4,8-trioxacyclododecan-6-yl]-2-hydroxy-3-[(hydroxymethylidene)amino]benzenecarboximidic acid

CAS Registry Number

Not Available

SMILES

CCC(C)C1OC(=O)C(N=C(O)C2=CC=CC(N=CO)=C2O)C(C)OC(=O)C(C)C(=O)C(CC(C)C)OC1=O

InChI Identifier

InChI=1S/C27H36N2O10/c1-7-14(4)23-27(36)38-19(11-13(2)3)21(31)15(5)25(34)37-16(6)20(26(35)39-23)29-24(33)17-9-8-10-18(22(17)32)28-12-30/h8-10,12-16,19-20,23,32H,7,11H2,1-6H3,(H,28,30)(H,29,33)

InChI Key

ZQPBRVQLPNZKAB-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
Macrolactam
Alpha-amino acid ester
N-acyl-alpha amino acid or derivatives
Acylaminobenzoic acid or derivatives
Salicylamide
Salicylic acid or derivatives
Alpha-amino acid or derivatives
Benzoic acid or derivatives
Anilide
Tricarboxylic acid or derivatives
Benzamide
Benzoyl
N-arylamide
Phenol
Alpha-acyloxy ketone
1-hydroxy-4-unsubstituted benzenoid
Monocyclic benzene moiety
1,3-dicarbonyl compound
Benzenoid
Vinylogous acid
Carboxamide group
Carboxylic acid ester
Ketone
Lactone
Cyclic ketone
Secondary carboxylic acid amide
Organoheterocyclic compound
Carboxylic acid derivative
Oxacycle
Organic oxygen compound
Organic nitrogen compound
Carbonyl group
Organopnictogen compound
Organic oxide
Hydrocarbon derivative
Organooxygen compound
Organonitrogen compound
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	6.6	ChemAxon
pKa (Strongest Acidic)	3.29	ChemAxon
pKa (Strongest Basic)	0.025	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	9	ChemAxon
Hydrogen Donor Count	3	ChemAxon
Polar Surface Area	181.38 Å²	ChemAxon
Rotatable Bond Count	7	ChemAxon
Refractivity	139.15 m³·mol⁻¹	ChemAxon
Polarizability	56.51 Å³	ChemAxon
Number of Rings	2	ChemAxon
Bioavailability	No	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

28286915

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

44542737

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Kozone I, Ueda JY, Takagi M, Shin-Ya K: JBIR-52, a new antimycin-like compound, from Streptomyces sp. ML55. J Antibiot (Tokyo). 2009 Oct;62(10):593-5. doi: 10.1038/ja.2009.79. Epub 2009 Aug 7. [PubMed:19662084 ]
LOTUS database [Link]

Showing NP-Card for n-[7,10-dimethyl-12-(2-methylpropyl)-2,5,9,11-tetraoxo-3-(sec-butyl)-1,4,8-trioxacyclododecan-6-yl]-2-hydroxy-3-[(hydroxymethylidene)amino]benzenecarboximidic acid (NP0304118)

MOL for NP0304118 (n-[7,10-dimethyl-12-(2-methylpropyl)-2,5,9,11-tetraoxo-3-(sec-butyl)-1,4,8-trioxacyclododecan-6-yl]-2-hydroxy-3-[(hydroxymethylidene)amino]benzenecarboximidic acid)

3D MOL for NP0304118 (n-[7,10-dimethyl-12-(2-methylpropyl)-2,5,9,11-tetraoxo-3-(sec-butyl)-1,4,8-trioxacyclododecan-6-yl]-2-hydroxy-3-[(hydroxymethylidene)amino]benzenecarboximidic acid)

3D SDF for NP0304118 (n-[7,10-dimethyl-12-(2-methylpropyl)-2,5,9,11-tetraoxo-3-(sec-butyl)-1,4,8-trioxacyclododecan-6-yl]-2-hydroxy-3-[(hydroxymethylidene)amino]benzenecarboximidic acid)

3D-SDF for NP0304118 (n-[7,10-dimethyl-12-(2-methylpropyl)-2,5,9,11-tetraoxo-3-(sec-butyl)-1,4,8-trioxacyclododecan-6-yl]-2-hydroxy-3-[(hydroxymethylidene)amino]benzenecarboximidic acid)

PDB for NP0304118 (n-[7,10-dimethyl-12-(2-methylpropyl)-2,5,9,11-tetraoxo-3-(sec-butyl)-1,4,8-trioxacyclododecan-6-yl]-2-hydroxy-3-[(hydroxymethylidene)amino]benzenecarboximidic acid)

3D PDB for NP0304118 (n-[7,10-dimethyl-12-(2-methylpropyl)-2,5,9,11-tetraoxo-3-(sec-butyl)-1,4,8-trioxacyclododecan-6-yl]-2-hydroxy-3-[(hydroxymethylidene)amino]benzenecarboximidic acid)

SMILES for NP0304118 (n-[7,10-dimethyl-12-(2-methylpropyl)-2,5,9,11-tetraoxo-3-(sec-butyl)-1,4,8-trioxacyclododecan-6-yl]-2-hydroxy-3-[(hydroxymethylidene)amino]benzenecarboximidic acid)

INCHI for NP0304118 (n-[7,10-dimethyl-12-(2-methylpropyl)-2,5,9,11-tetraoxo-3-(sec-butyl)-1,4,8-trioxacyclododecan-6-yl]-2-hydroxy-3-[(hydroxymethylidene)amino]benzenecarboximidic acid)

Structure for NP0304118 (n-[7,10-dimethyl-12-(2-methylpropyl)-2,5,9,11-tetraoxo-3-(sec-butyl)-1,4,8-trioxacyclododecan-6-yl]-2-hydroxy-3-[(hydroxymethylidene)amino]benzenecarboximidic acid)

3D Structure for NP0304118 (n-[7,10-dimethyl-12-(2-methylpropyl)-2,5,9,11-tetraoxo-3-(sec-butyl)-1,4,8-trioxacyclododecan-6-yl]-2-hydroxy-3-[(hydroxymethylidene)amino]benzenecarboximidic acid)