NP-MRD: Showing NP-Card for 2-hydroxy-3-({3-[(2e)-n-hydroxydec-2-enamido]propyl}-c-hydroxycarbonimidoyl)-2-({[3-(n-hydroxyacetamido)propyl]-c-hydroxycarbonimidoyl}methyl)propanoic acid (NP0309012)

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Record Information

Version

1.0

Created at

2022-09-11 03:15:27 UTC

Updated at

2022-09-11 03:15:27 UTC

NP-MRD ID

NP0309012

Secondary Accession Numbers

None

Natural Product Identification

Common Name

2-hydroxy-3-({3-[(2e)-n-hydroxydec-2-enamido]propyl}-c-hydroxycarbonimidoyl)-2-({[3-(n-hydroxyacetamido)propyl]-c-hydroxycarbonimidoyl}methyl)propanoic acid

Description

Rhizobactin 1021 belongs to the class of organic compounds known as hydroxy fatty acids. These are fatty acids in which the chain bears a hydroxyl group. It was first documented in 2006 (PMID: 16549659). Based on a literature review a significant number of articles have been published on rhizobactin 1021 (PMID: 25887945) (PMID: 23378574) (PMID: 22328673) (PMID: 20210991).

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652309112205152D          

 37 36  0  0  0  0            999 V2000
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    6.0474    1.8414    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


  Mrv1652309112205152D          

 37 36  0  0  0  0            999 V2000
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   11.5717   -2.3941    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  1  0  0  0  0
  8  9  2  0  0  0  0
  9 10  1  0  0  0  0
 10 11  2  0  0  0  0
 10 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
 15 16  1  0  0  0  0
 17 16  1  4  0  0  0
 17 18  2  0  0  0  0
 18 19  1  0  0  0  0
 18 20  1  0  0  0  0
 20 21  1  0  0  0  0
 21 22  1  0  0  0  0
 21 23  1  0  0  0  0
 23 24  1  0  0  0  0
 24 25  1  0  0  0  0
 24 26  2  0  0  0  0
 26 27  1  4  0  0  0
 27 28  1  0  0  0  0
 28 29  1  0  0  0  0
 29 30  1  0  0  0  0
 30 31  1  0  0  0  0
 30 32  1  0  0  0  0
 32 33  1  0  0  0  0
 32 34  2  0  0  0  0
 21 35  1  0  0  0  0
 35 36  2  0  0  0  0
 35 37  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0309012

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CCCCCCC\C=C\C(=O)N(O)CCCN=C(O)CC(O)(CC(O)=NCCCN(O)C(C)=O)C(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C24H42N4O9/c1-3-4-5-6-7-8-9-12-22(32)28(37)16-11-14-26-21(31)18-24(35,23(33)34)17-20(30)25-13-10-15-27(36)19(2)29/h9,12,35-37H,3-8,10-11,13-18H2,1-2H3,(H,25,30)(H,26,31)(H,33,34)/b12-9+

> <INCHI_KEY>
WRSKPFYPBJAAEG-FMIVXFBMSA-N

> <FORMULA>
C24H42N4O9

> <MOLECULAR_WEIGHT>
530.619

> <EXACT_MASS>
530.295178948

> <JCHEM_ACCEPTOR_COUNT>
11

> <JCHEM_ATOM_COUNT>
79

> <JCHEM_AVERAGE_POLARIZABILITY>
56.7334851572699

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
6

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
2-hydroxy-3-({3-[(2E)-N-hydroxydec-2-enamido]propyl}-C-hydroxycarbonimidoyl)-2-({[3-(N-hydroxyacetamido)propyl]-C-hydroxycarbonimidoyl}methyl)propanoic acid

> <JCHEM_LOGP>
-1.6415955396820454

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
3.6410015414314363

> <JCHEM_PKA_STRONGEST_ACIDIC>
2.9897763486451083

> <JCHEM_PKA_STRONGEST_BASIC>
6.353844098712359

> <JCHEM_POLAR_SURFACE_AREA>
203.78999999999996

> <JCHEM_REFRACTIVITY>
136.0795

> <JCHEM_ROTATABLE_BOND_COUNT>
20

> <JCHEM_RULE_OF_FIVE>
0

> <JCHEM_TRADITIONAL_IUPAC>
2-hydroxy-3-({3-[(2E)-N-hydroxydec-2-enamido]propyl}-C-hydroxycarbonimidoyl)-2-({[3-(N-hydroxyacetamido)propyl]-C-hydroxycarbonimidoyl}methyl)propanoic acid

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 11-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   11-SEP-22         0                                  
HETATM    1  C   UNK     0       1.953   2.667   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       3.286   3.437   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       4.620   2.667   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       5.954   3.437   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       7.287   2.667   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       8.621   3.437   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       9.955   2.667   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      11.288   3.437   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      12.622   2.667   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      13.956   3.437   0.000  0.00  0.00           C+0
HETATM   11  O   UNK     0      13.956   4.977   0.000  0.00  0.00           O+0
HETATM   12  N   UNK     0      15.289   2.667   0.000  0.00  0.00           N+0
HETATM   13  O   UNK     0      16.623   3.437   0.000  0.00  0.00           O+0
HETATM   14  C   UNK     0      15.289   1.127   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0      16.623   0.357   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0      16.623  -1.183   0.000  0.00  0.00           C+0
HETATM   17  N   UNK     0      17.957  -1.953   0.000  0.00  0.00           N+0
HETATM   18  C   UNK     0      17.957  -3.493   0.000  0.00  0.00           C+0
HETATM   19  O   UNK     0      16.623  -4.263   0.000  0.00  0.00           O+0
HETATM   20  C   UNK     0      19.290  -4.263   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0      19.290  -5.803   0.000  0.00  0.00           C+0
HETATM   22  O   UNK     0      17.750  -5.803   0.000  0.00  0.00           O+0
HETATM   23  C   UNK     0      19.290  -7.343   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0      17.957  -8.113   0.000  0.00  0.00           C+0
HETATM   25  O   UNK     0      16.623  -7.343   0.000  0.00  0.00           O+0
HETATM   26  N   UNK     0      17.957  -9.653   0.000  0.00  0.00           N+0
HETATM   27  C   UNK     0      19.290 -10.423   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0      20.624  -9.653   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0      21.958 -10.423   0.000  0.00  0.00           C+0
HETATM   30  N   UNK     0      23.292  -9.653   0.000  0.00  0.00           N+0
HETATM   31  O   UNK     0      23.292  -8.113   0.000  0.00  0.00           O+0
HETATM   32  C   UNK     0      24.625 -10.423   0.000  0.00  0.00           C+0
HETATM   33  C   UNK     0      25.959  -9.653   0.000  0.00  0.00           C+0
HETATM   34  O   UNK     0      24.625 -11.963   0.000  0.00  0.00           O+0
HETATM   35  C   UNK     0      20.830  -5.803   0.000  0.00  0.00           C+0
HETATM   36  O   UNK     0      21.600  -7.136   0.000  0.00  0.00           O+0
HETATM   37  O   UNK     0      21.600  -4.469   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4    6                                                       
CONECT    6    5    7                                                       
CONECT    7    6    8                                                       
CONECT    8    7    9                                                       
CONECT    9    8   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                                                       
CONECT   16   15   17                                                       
CONECT   17   16   18                                                       
CONECT   18   17   19   20                                                  
CONECT   19   18                                                            
CONECT   20   18   21                                                       
CONECT   21   20   22   23   35                                             
CONECT   22   21                                                            
CONECT   23   21   24                                                       
CONECT   24   23   25   26                                                  
CONECT   25   24                                                            
CONECT   26   24   27                                                       
CONECT   27   26   28                                                       
CONECT   28   27   29                                                       
CONECT   29   28   30                                                       
CONECT   30   29   31   32                                                  
CONECT   31   30                                                            
CONECT   32   30   33   34                                                  
CONECT   33   32                                                            
CONECT   34   32                                                            
CONECT   35   21   36   37                                                  
CONECT   36   35                                                            
CONECT   37   35                                                            
MASTER        0    0    0    0    0    0    0    0   37    0   72    0
END

View in JSmol

Synonyms

Value	Source
Rhizobactin-1021	ChEBI

Chemical Formula

C₂₄H₄₂N₄O₉

Average Mass

530.6190 Da

Monoisotopic Mass

530.29518 Da

IUPAC Name

2-hydroxy-3-({3-[(2E)-N-hydroxydec-2-enamido]propyl}-C-hydroxycarbonimidoyl)-2-({[3-(N-hydroxyacetamido)propyl]-C-hydroxycarbonimidoyl}methyl)propanoic acid

Traditional Name

2-hydroxy-3-({3-[(2E)-N-hydroxydec-2-enamido]propyl}-C-hydroxycarbonimidoyl)-2-({[3-(N-hydroxyacetamido)propyl]-C-hydroxycarbonimidoyl}methyl)propanoic acid

CAS Registry Number

Not Available

SMILES

CCCCCCC\C=C\C(=O)N(O)CCCN=C(O)CC(O)(CC(O)=NCCCN(O)C(C)=O)C(O)=O

InChI Identifier

InChI=1S/C24H42N4O9/c1-3-4-5-6-7-8-9-12-22(32)28(37)16-11-14-26-21(31)18-24(35,23(33)34)17-20(30)25-13-10-15-27(36)19(2)29/h9,12,35-37H,3-8,10-11,13-18H2,1-2H3,(H,25,30)(H,26,31)(H,33,34)/b12-9+

InChI Key

WRSKPFYPBJAAEG-FMIVXFBMSA-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 hydroxy fatty acids. These are fatty acids in which the chain bears a hydroxyl group.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Fatty Acyls

Sub Class

Fatty acids and conjugates

Direct Parent

Hydroxy fatty acids

Alternative Parents

Substituents

Branched fatty acid
Hydroxy fatty acid
Alpha-hydroxy acid
Fatty amide
Hydroxy acid
N-acyl-amine
Acetohydroxamic acid
Acetamide
Tertiary alcohol
Carboxamide group
Hydroxamic acid
Secondary carboxylic acid amide
Carboxylic acid derivative
Carboxylic acid
Monocarboxylic acid or derivatives
Hydrocarbon derivative
Organic oxide
Alcohol
Organopnictogen compound
Carbonyl group
Organic oxygen compound
Organooxygen compound
Organonitrogen compound
Organic nitrogen compound
Aliphatic acyclic compound

Molecular Framework

Aliphatic acyclic compounds

External Descriptors

tertiary alcohol (CHEBI:74252 )
hydroxamic acid (CHEBI:74252 )
hydroxy monocarboxylic acid (CHEBI:74252 )

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	-1.6	ChemAxon
pKa (Strongest Acidic)	2.99	ChemAxon
pKa (Strongest Basic)	6.35	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	11	ChemAxon
Hydrogen Donor Count	6	ChemAxon
Polar Surface Area	203.79 Å²	ChemAxon
Rotatable Bond Count	20	ChemAxon
Refractivity	136.08 m³·mol⁻¹	ChemAxon
Polarizability	56.73 Å³	ChemAxon
Number of Rings	0	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

29368224

KEGG Compound ID

Not Available

BioCyc ID

CPD-1021

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

71581041

PDB ID

Not Available

ChEBI ID

74252

Good Scents ID

Not Available

References

General References

Amaya-Gomez CV, Hirsch AM, Soto MJ: Biofilm formation assessment in Sinorhizobium meliloti reveals interlinked control with surface motility. BMC Microbiol. 2015 Mar 3;15:58. doi: 10.1186/s12866-015-0390-z. [PubMed:25887945 ]
Funahashi T, Tanabe T, Maki J, Miyamoto K, Tsujibo H, Yamamoto S: Identification and characterization of a cluster of genes involved in biosynthesis and transport of acinetoferrin, a siderophore produced by Acinetobacter haemolyticus ATCC 17906T. Microbiology (Reading). 2013 Apr;159(Pt 4):678-690. doi: 10.1099/mic.0.065177-0. Epub 2013 Feb 1. [PubMed:23378574 ]
Nogales J, Bernabeu-Roda L, Cuellar V, Soto MJ: ExpR is not required for swarming but promotes sliding in Sinorhizobium meliloti. J Bacteriol. 2012 Apr;194(8):2027-35. doi: 10.1128/JB.06524-11. Epub 2012 Feb 10. [PubMed:22328673 ]
Nogales J, Dominguez-Ferreras A, Amaya-Gomez CV, van Dillewijn P, Cuellar V, Sanjuan J, Olivares J, Soto MJ: Transcriptome profiling of a Sinorhizobium meliloti fadD mutant reveals the role of rhizobactin 1021 biosynthesis and regulation genes in the control of swarming. BMC Genomics. 2010 Mar 8;11:157. doi: 10.1186/1471-2164-11-157. [PubMed:20210991 ]
Cuiv PO, Clarke P, O'Connell M: Identification and characterization of an iron-regulated gene, chtA, required for the utilization of the xenosiderophores aerobactin, rhizobactin 1021 and schizokinen by Pseudomonas aeruginosa. Microbiology (Reading). 2006 Apr;152(Pt 4):945-954. doi: 10.1099/mic.0.28552-0. [PubMed:16549659 ]
LOTUS database [Link]

Showing NP-Card for 2-hydroxy-3-({3-[(2e)-n-hydroxydec-2-enamido]propyl}-c-hydroxycarbonimidoyl)-2-({[3-(n-hydroxyacetamido)propyl]-c-hydroxycarbonimidoyl}methyl)propanoic acid (NP0309012)

MOL for NP0309012 (2-hydroxy-3-({3-[(2e)-n-hydroxydec-2-enamido]propyl}-c-hydroxycarbonimidoyl)-2-({[3-(n-hydroxyacetamido)propyl]-c-hydroxycarbonimidoyl}methyl)propanoic acid)

3D MOL for NP0309012 (2-hydroxy-3-({3-[(2e)-n-hydroxydec-2-enamido]propyl}-c-hydroxycarbonimidoyl)-2-({[3-(n-hydroxyacetamido)propyl]-c-hydroxycarbonimidoyl}methyl)propanoic acid)

3D SDF for NP0309012 (2-hydroxy-3-({3-[(2e)-n-hydroxydec-2-enamido]propyl}-c-hydroxycarbonimidoyl)-2-({[3-(n-hydroxyacetamido)propyl]-c-hydroxycarbonimidoyl}methyl)propanoic acid)

3D-SDF for NP0309012 (2-hydroxy-3-({3-[(2e)-n-hydroxydec-2-enamido]propyl}-c-hydroxycarbonimidoyl)-2-({[3-(n-hydroxyacetamido)propyl]-c-hydroxycarbonimidoyl}methyl)propanoic acid)

PDB for NP0309012 (2-hydroxy-3-({3-[(2e)-n-hydroxydec-2-enamido]propyl}-c-hydroxycarbonimidoyl)-2-({[3-(n-hydroxyacetamido)propyl]-c-hydroxycarbonimidoyl}methyl)propanoic acid)

3D PDB for NP0309012 (2-hydroxy-3-({3-[(2e)-n-hydroxydec-2-enamido]propyl}-c-hydroxycarbonimidoyl)-2-({[3-(n-hydroxyacetamido)propyl]-c-hydroxycarbonimidoyl}methyl)propanoic acid)

SMILES for NP0309012 (2-hydroxy-3-({3-[(2e)-n-hydroxydec-2-enamido]propyl}-c-hydroxycarbonimidoyl)-2-({[3-(n-hydroxyacetamido)propyl]-c-hydroxycarbonimidoyl}methyl)propanoic acid)

INCHI for NP0309012 (2-hydroxy-3-({3-[(2e)-n-hydroxydec-2-enamido]propyl}-c-hydroxycarbonimidoyl)-2-({[3-(n-hydroxyacetamido)propyl]-c-hydroxycarbonimidoyl}methyl)propanoic acid)

Structure for NP0309012 (2-hydroxy-3-({3-[(2e)-n-hydroxydec-2-enamido]propyl}-c-hydroxycarbonimidoyl)-2-({[3-(n-hydroxyacetamido)propyl]-c-hydroxycarbonimidoyl}methyl)propanoic acid)

3D Structure for NP0309012 (2-hydroxy-3-({3-[(2e)-n-hydroxydec-2-enamido]propyl}-c-hydroxycarbonimidoyl)-2-({[3-(n-hydroxyacetamido)propyl]-c-hydroxycarbonimidoyl}methyl)propanoic acid)