NP-MRD: Showing NP-Card for 1,5,11,15,21,25-hexahydroxy-1,6,11,16,21,26-hexaazacyclohentriaconta-5,15,25-triene-2,12,22-trione (NP0245180)

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Record Information

Version

1.0

Created at

2022-09-07 06:09:44 UTC

Updated at

2022-09-07 06:09:45 UTC

NP-MRD ID

NP0245180

Secondary Accession Numbers

None

Natural Product Identification

Common Name

1,5,11,15,21,25-hexahydroxy-1,6,11,16,21,26-hexaazacyclohentriaconta-5,15,25-triene-2,12,22-trione

Description

Desferrioxamine X1 belongs to the class of organic compounds known as macrolactams. These are cyclic amides of amino carboxylic acids, having a 1-azacycloalkan-2-one structure, or analogues having unsaturation or heteroatoms replacing one or more carbon atoms of the ring. They are nitrogen analogues (the a nitrogen atom replacing the o atom of the cyclic carboxylic acid group ) of the naturally occurring macrolides. 1,5,11,15,21,25-hexahydroxy-1,6,11,16,21,26-hexaazacyclohentriaconta-5,15,25-triene-2,12,22-trione is found in Streptomyces olivaceus. It was first documented in 2006 (PMID: 17473886). Based on a literature review a significant number of articles have been published on Desferrioxamine X1 (PMID: 36088123) (PMID: 36088122) (PMID: 36088121) (PMID: 24317070).

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652309072208092D          

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M  END

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M  END


  Mrv1652309072208092D          

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    4.7357   -4.2741    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9114   -4.2411    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5277   -3.5107    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.7034   -3.4778    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.9685   -2.8133    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.7928   -2.8463    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.5848   -2.0829    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0256   -1.3855    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6420   -0.6551    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8176   -0.6222    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.0827    0.0423    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.6991    0.7727    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.1398    1.4701    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7562    2.2005    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.1969    2.8979    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.8133    3.6283    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2540    4.3257    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.8546    5.0476    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  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
  5  7  2  0  0  0  0
  7  8  1  4  0  0  0
  8  9  1  0  0  0  0
  9 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  2  0  0  0  0
 14 16  1  0  0  0  0
 16 17  1  0  0  0  0
 17 18  1  0  0  0  0
 18 19  1  0  0  0  0
 18 20  2  0  0  0  0
 20 21  1  4  0  0  0
 21 22  1  0  0  0  0
 22 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
 25 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
 31 33  2  0  0  0  0
 33 34  1  4  0  0  0
 34 35  1  0  0  0  0
 35 36  1  0  0  0  0
 36 37  1  0  0  0  0
 37 38  1  0  0  0  0
 38 39  1  0  0  0  0
  2 39  1  0  0  0  0
 39 40  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0245180

> <DATABASE_NAME>
NP-MRD

> <SMILES>
ON1CCCCCN=C(O)CCC(=O)N(O)CCCCN=C(O)CCC(=O)N(O)CCCCN=C(O)CCC1=O

> <INCHI_IDENTIFIER>
InChI=1S/C25H44N6O9/c32-20-8-12-24(36)30(39)18-6-4-16-28-22(34)10-13-25(37)31(40)19-7-3-15-27-21(33)9-11-23(35)29(38)17-5-1-2-14-26-20/h38-40H,1-19H2,(H,26,32)(H,27,33)(H,28,34)

> <INCHI_KEY>
YEUGMACLLZSLDG-UHFFFAOYSA-N

> <FORMULA>
C25H44N6O9

> <MOLECULAR_WEIGHT>
572.66

> <EXACT_MASS>
572.316977021

> <JCHEM_ACCEPTOR_COUNT>
12

> <JCHEM_ATOM_COUNT>
84

> <JCHEM_AVERAGE_POLARIZABILITY>
59.66481417835958

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
6

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
1,5,11,15,21,25-hexahydroxy-1,6,11,16,21,26-hexaazacyclohentriaconta-5,15,25-triene-2,12,22-trione

> <JCHEM_LOGP>
-2.19946660651805

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
4.38966863433174

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.8044518277074464

> <JCHEM_PKA_STRONGEST_BASIC>
6.656601956234343

> <JCHEM_POLAR_SURFACE_AREA>
219.38999999999996

> <JCHEM_REFRACTIVITY>
145.00730000000004

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
0

> <JCHEM_TRADITIONAL_IUPAC>
1,5,11,15,21,25-hexahydroxy-1,6,11,16,21,26-hexaazacyclohentriaconta-5,15,25-triene-2,12,22-trione

> <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  O   UNK     0      10.152   6.633   0.000  0.00  0.00           O+0
HETATM    2  C   UNK     0       9.626   8.080   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      10.811   9.064   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      12.113   8.242   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      11.732   6.749   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0      13.265   6.896   0.000  0.00  0.00           O+0
HETATM    7  N   UNK     0      12.451   5.225   0.000  0.00  0.00           N+0
HETATM    8  C   UNK     0      11.628   3.923   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      12.344   2.560   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      11.521   1.258   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      12.237  -0.106   0.000  0.00  0.00           C+0
HETATM   12  N   UNK     0      11.415  -1.408   0.000  0.00  0.00           N+0
HETATM   13  O   UNK     0       9.876  -1.346   0.000  0.00  0.00           O+0
HETATM   14  C   UNK     0      12.131  -2.771   0.000  0.00  0.00           C+0
HETATM   15  O   UNK     0      13.669  -2.832   0.000  0.00  0.00           O+0
HETATM   16  C   UNK     0      11.308  -4.073   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0      12.024  -5.436   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0      11.201  -6.738   0.000  0.00  0.00           C+0
HETATM   19  O   UNK     0       9.663  -6.676   0.000  0.00  0.00           O+0
HETATM   20  N   UNK     0      11.918  -8.101   0.000  0.00  0.00           N+0
HETATM   21  C   UNK     0      11.095  -9.403   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0       9.556  -9.342   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0       8.840  -7.978   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0       7.301  -7.917   0.000  0.00  0.00           C+0
HETATM   25  N   UNK     0       6.585  -6.553   0.000  0.00  0.00           N+0
HETATM   26  O   UNK     0       5.046  -6.492   0.000  0.00  0.00           O+0
HETATM   27  C   UNK     0       7.408  -5.252   0.000  0.00  0.00           C+0
HETATM   28  O   UNK     0       8.947  -5.313   0.000  0.00  0.00           O+0
HETATM   29  C   UNK     0       6.692  -3.888   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0       7.514  -2.586   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0       6.798  -1.223   0.000  0.00  0.00           C+0
HETATM   32  O   UNK     0       5.260  -1.161   0.000  0.00  0.00           O+0
HETATM   33  N   UNK     0       7.621   0.079   0.000  0.00  0.00           N+0
HETATM   34  C   UNK     0       6.905   1.442   0.000  0.00  0.00           C+0
HETATM   35  C   UNK     0       7.728   2.744   0.000  0.00  0.00           C+0
HETATM   36  C   UNK     0       7.012   4.108   0.000  0.00  0.00           C+0
HETATM   37  C   UNK     0       7.834   5.409   0.000  0.00  0.00           C+0
HETATM   38  C   UNK     0       7.118   6.773   0.000  0.00  0.00           C+0
HETATM   39  N   UNK     0       7.941   8.075   0.000  0.00  0.00           N+0
HETATM   40  O   UNK     0       7.195   9.422   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3   39                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4    6    7                                                  
CONECT    6    5                                                            
CONECT    7    5    8                                                       
CONECT    8    7    9                                                       
CONECT    9    8   10                                                       
CONECT   10    9   11                                                       
CONECT   11   10   12                                                       
CONECT   12   11   13   14                                                  
CONECT   13   12                                                            
CONECT   14   12   15   16                                                  
CONECT   15   14                                                            
CONECT   16   14   17                                                       
CONECT   17   16   18                                                       
CONECT   18   17   19   20                                                  
CONECT   19   18                                                            
CONECT   20   18   21                                                       
CONECT   21   20   22                                                       
CONECT   22   21   23                                                       
CONECT   23   22   24                                                       
CONECT   24   23   25                                                       
CONECT   25   24   26   27                                                  
CONECT   26   25                                                            
CONECT   27   25   28   29                                                  
CONECT   28   27                                                            
CONECT   29   27   30                                                       
CONECT   30   29   31                                                       
CONECT   31   30   32   33                                                  
CONECT   32   31                                                            
CONECT   33   31   34                                                       
CONECT   34   33   35                                                       
CONECT   35   34   36                                                       
CONECT   36   35   37                                                       
CONECT   37   36   38                                                       
CONECT   38   37   39                                                       
CONECT   39   38    2   40                                                  
CONECT   40   39                                                            
MASTER        0    0    0    0    0    0    0    0   40    0   80    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₂₅H₄₄N₆O₉

Average Mass

572.6600 Da

Monoisotopic Mass

572.31698 Da

IUPAC Name

1,5,11,15,21,25-hexahydroxy-1,6,11,16,21,26-hexaazacyclohentriaconta-5,15,25-triene-2,12,22-trione

Traditional Name

1,5,11,15,21,25-hexahydroxy-1,6,11,16,21,26-hexaazacyclohentriaconta-5,15,25-triene-2,12,22-trione

CAS Registry Number

Not Available

SMILES

ON1CCCCCN=C(O)CCC(=O)N(O)CCCCN=C(O)CCC(=O)N(O)CCCCN=C(O)CCC1=O

InChI Identifier

InChI=1S/C25H44N6O9/c32-20-8-12-24(36)30(39)18-6-4-16-28-22(34)10-13-25(37)31(40)19-7-3-15-27-21(33)9-11-23(35)29(38)17-5-1-2-14-26-20/h38-40H,1-19H2,(H,26,32)(H,27,33)(H,28,34)

InChI Key

YEUGMACLLZSLDG-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

Species Name	Source	Reference
Streptomyces olivaceus	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as macrolactams. These are cyclic amides of amino carboxylic acids, having a 1-azacycloalkan-2-one structure, or analogues having unsaturation or heteroatoms replacing one or more carbon atoms of the ring. They are nitrogen analogues (the a nitrogen atom replacing the o atom of the cyclic carboxylic acid group ) of the naturally occurring macrolides.

Kingdom

Organic compounds

Super Class

Phenylpropanoids and polyketides

Class

Macrolactams

Sub Class

Not Available

Direct Parent

Macrolactams

Alternative Parents

Substituents

Macrolactam
Carboxamide group
Hydroxamic acid
Lactam
Secondary carboxylic acid amide
Carboxylic acid derivative
Polyol
Azacycle
Organoheterocyclic compound
Organonitrogen compound
Hydrocarbon derivative
Organic oxide
Organic oxygen compound
Organooxygen compound
Carbonyl group
Organic nitrogen compound
Aliphatic heteromonocyclic compound

Molecular Framework

Aliphatic 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	-2.2	ChemAxon
pKa (Strongest Acidic)	3.8	ChemAxon
pKa (Strongest Basic)	6.66	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	12	ChemAxon
Hydrogen Donor Count	6	ChemAxon
Polar Surface Area	219.39 Å²	ChemAxon
Rotatable Bond Count	0	ChemAxon
Refractivity	145.01 m³·mol⁻¹	ChemAxon
Polarizability	59.66 Å³	ChemAxon
Number of Rings	1	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

22369709

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

14671619

PDB ID

Not Available

ChEBI ID

182834

Good Scents ID

Not Available

References

General References

Xu X, Rothrock MJ Jr, Reeves J, Kumar GD, Mishra A: Using E. coli population to predict foodborne pathogens in pastured poultry farms. Food Microbiol. 2022 Dec;108:104092. doi: 10.1016/j.fm.2022.104092. Epub 2022 Jul 14. [PubMed:36088123 ]
Lanzl MI, Zwietering MH, Abee T, den Besten HMW: Combining enrichment with multiplex real-time PCR leads to faster detection and identification of Campylobacter spp. in food compared to ISO 10272-1:2017. Food Microbiol. 2022 Dec;108:104117. doi: 10.1016/j.fm.2022.104117. Epub 2022 Aug 19. [PubMed:36088122 ]
Cacciatore FA, Maders C, Alexandre B, Barreto Pinilla CM, Brandelli A, da Silva Malheiros P: Carvacrol encapsulation into nanoparticles produced from chia and flaxseed mucilage: Characterization, stability and antimicrobial activity against Salmonella and Listeria monocytogenes. Food Microbiol. 2022 Dec;108:104116. doi: 10.1016/j.fm.2022.104116. Epub 2022 Aug 18. [PubMed:36088121 ]
Fujita MJ, Sakai R: Heterologous production of desferrioxamines with a fusion biosynthetic gene cluster. Biosci Biotechnol Biochem. 2013;77(12):2467-72. doi: 10.1271/bbb.130597. Epub 2013 Dec 7. [PubMed:24317070 ]
Zawadzka AM, Vandecasteele FP, Crawford RL, Paszczynski AJ: Identification of siderophores of Pseudomonas stutzeri. Can J Microbiol. 2006 Dec;52(12):1164-76. doi: 10.1139/w06-077. [PubMed:17473886 ]
LOTUS database [Link]

Showing NP-Card for 1,5,11,15,21,25-hexahydroxy-1,6,11,16,21,26-hexaazacyclohentriaconta-5,15,25-triene-2,12,22-trione (NP0245180)

MOL for NP0245180 (1,5,11,15,21,25-hexahydroxy-1,6,11,16,21,26-hexaazacyclohentriaconta-5,15,25-triene-2,12,22-trione)

3D MOL for NP0245180 (1,5,11,15,21,25-hexahydroxy-1,6,11,16,21,26-hexaazacyclohentriaconta-5,15,25-triene-2,12,22-trione)

3D SDF for NP0245180 (1,5,11,15,21,25-hexahydroxy-1,6,11,16,21,26-hexaazacyclohentriaconta-5,15,25-triene-2,12,22-trione)

3D-SDF for NP0245180 (1,5,11,15,21,25-hexahydroxy-1,6,11,16,21,26-hexaazacyclohentriaconta-5,15,25-triene-2,12,22-trione)

PDB for NP0245180 (1,5,11,15,21,25-hexahydroxy-1,6,11,16,21,26-hexaazacyclohentriaconta-5,15,25-triene-2,12,22-trione)

3D PDB for NP0245180 (1,5,11,15,21,25-hexahydroxy-1,6,11,16,21,26-hexaazacyclohentriaconta-5,15,25-triene-2,12,22-trione)

SMILES for NP0245180 (1,5,11,15,21,25-hexahydroxy-1,6,11,16,21,26-hexaazacyclohentriaconta-5,15,25-triene-2,12,22-trione)

INCHI for NP0245180 (1,5,11,15,21,25-hexahydroxy-1,6,11,16,21,26-hexaazacyclohentriaconta-5,15,25-triene-2,12,22-trione)

Structure for NP0245180 (1,5,11,15,21,25-hexahydroxy-1,6,11,16,21,26-hexaazacyclohentriaconta-5,15,25-triene-2,12,22-trione)

3D Structure for NP0245180 (1,5,11,15,21,25-hexahydroxy-1,6,11,16,21,26-hexaazacyclohentriaconta-5,15,25-triene-2,12,22-trione)