NP-MRD: Showing NP-Card for Imidacin B1 (NP0333740)

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Record Information

Version

2.0

Created at

2024-08-22 11:12:57 UTC

Updated at

2024-09-16 10:47:05 UTC

NP-MRD ID

NP0333740

Natural Product DOI

https://doi.org/10.57994/3219

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Imidacin B1

Description

Imidacin B1 belongs to the class of organic compounds known as heterocyclic fatty acids. These are fatty acids containing a heterocyclic attached to the acyl chain. Imidacin B1 was first documented in 2024 (PMID: 39037587). Based on a literature review very few articles have been published on Imidacin B1.

Structure

MOL SDF PDB SMILES InChI


  Mrv2104 05062313452D          

 23 24  0  0  0  0            999 V2000
    4.5077   -9.0098    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.5077   -8.1848    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7932   -7.7723    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.2221   -7.7723    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.2221   -6.9473    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.8096   -6.2328    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.6346   -6.2328    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.3491   -5.8203    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.0636   -6.2328    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.7781   -5.8203    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.4925   -6.2328    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.2070   -5.8203    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.9215   -6.2328    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.6359   -5.8203    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.3504   -6.2328    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.0649   -5.8203    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.7794   -6.2328    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   13.4938   -5.8203    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   14.2083   -6.2328    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   14.9620   -5.8972    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   15.5140   -6.5103    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   15.1015   -7.2248    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   14.2945   -7.0533    0.0000 N   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
  2  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  5  7  1  0  0  0  0
  6  7  1  0  0  0  0
  7  8  1  0  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
 13 14  1  0  0  0  0
 14 15  1  0  0  0  0
 15 16  1  0  0  0  0
 16 17  1  0  0  0  0
 17 18  2  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  1  0  0  0  0
 22 23  2  0  0  0  0
 19 23  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0333740

> <DATABASE_NAME>
NP-MRD

> <SMILES>
OC(=O)CC1CC1CCCCCCCCC\C=C\C1=CNC=N1

> <INCHI_IDENTIFIER>
InChI=1/C19H30N2O2/c22-19(23)13-17-12-16(17)10-8-6-4-2-1-3-5-7-9-11-18-14-20-15-21-18/h9,11,14-17H,1-8,10,12-13H2,(H,20,21)(H,22,23)/b11-9+

> <INCHI_KEY>
IFDUXXGMQRRBFE-PKNBQFBNNA-N

> <FORMULA>
C19H30N2O2

> <MOLECULAR_WEIGHT>
318.461

> <EXACT_MASS>
318.230728214

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_ATOM_COUNT>
53

> <JCHEM_AVERAGE_POLARIZABILITY>
39.095784695796745

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
2-{2-[(10E)-11-(1H-imidazol-4-yl)undec-10-en-1-yl]cyclopropyl}acetic acid

> <JCHEM_LOGP>
3.8402994867668037

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
13.938227229888515

> <JCHEM_PKA_STRONGEST_ACIDIC>
4.7905370252143955

> <JCHEM_PKA_STRONGEST_BASIC>
6.146491828910105

> <JCHEM_POLAR_SURFACE_AREA>
65.97999999999999

> <JCHEM_REFRACTIVITY>
93.4969

> <JCHEM_ROTATABLE_BOND_COUNT>
13

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
{2-[(10E)-11-(1H-imidazol-4-yl)undec-10-en-1-yl]cyclopropyl}acetic acid

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 06-MAY-23   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   06-MAY-23         0                                  
HETATM    1  O   UNK     0       8.414 -16.818   0.000  0.00  0.00           O+0
HETATM    2  C   UNK     0       8.414 -15.278   0.000  0.00  0.00           C+0
HETATM    3  O   UNK     0       7.081 -14.508   0.000  0.00  0.00           O+0
HETATM    4  C   UNK     0       9.748 -14.508   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       9.748 -12.968   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       8.978 -11.635   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      10.518 -11.635   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      11.852 -10.865   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      13.185 -11.635   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      14.519 -10.865   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      15.853 -11.635   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      17.186 -10.865   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      18.520 -11.635   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      19.854 -10.865   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0      21.187 -11.635   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0      22.521 -10.865   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0      23.855 -11.635   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0      25.188 -10.865   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0      26.522 -11.635   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0      27.929 -11.008   0.000  0.00  0.00           C+0
HETATM   21  N   UNK     0      28.959 -12.153   0.000  0.00  0.00           N+0
HETATM   22  C   UNK     0      28.189 -13.486   0.000  0.00  0.00           C+0
HETATM   23  N   UNK     0      26.683 -13.166   0.000  0.00  0.00           N+0
CONECT    1    2                                                            
CONECT    2    1    3    4                                                  
CONECT    3    2                                                            
CONECT    4    2    5                                                       
CONECT    5    4    6    7                                                  
CONECT    6    5    7                                                       
CONECT    7    5    6    8                                                  
CONECT    8    7    9                                                       
CONECT    9    8   10                                                       
CONECT   10    9   11                                                       
CONECT   11   10   12                                                       
CONECT   12   11   13                                                       
CONECT   13   12   14                                                       
CONECT   14   13   15                                                       
CONECT   15   14   16                                                       
CONECT   16   15   17                                                       
CONECT   17   16   18                                                       
CONECT   18   17   19                                                       
CONECT   19   18   20   23                                                  
CONECT   20   19   21                                                       
CONECT   21   20   22                                                       
CONECT   22   21   23                                                       
CONECT   23   22   19                                                       
MASTER        0    0    0    0    0    0    0    0   23    0   48    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₁₉H₃₀N₂O₂

Average Mass

318.4610 Da

Monoisotopic Mass

318.23073 Da

IUPAC Name

2-{2-[(10E)-11-(1H-imidazol-4-yl)undec-10-en-1-yl]cyclopropyl}acetic acid

Traditional Name

{2-[(10E)-11-(1H-imidazol-4-yl)undec-10-en-1-yl]cyclopropyl}acetic acid

CAS Registry Number

Not Available

SMILES

OC(=O)CC1CC1CCCCCCCCC\C=C\C1=CNC=N1

InChI Identifier

InChI=1/C19H30N2O2/c22-19(23)13-17-12-16(17)10-8-6-4-2-1-3-5-7-9-11-18-14-20-15-21-18/h9,11,14-17H,1-8,10,12-13H2,(H,20,21)(H,22,23)/b11-9+

InChI Key

IFDUXXGMQRRBFE-PKNBQFBNNA-N

Experimental Spectra

Spectrum Type	Description	Depositor Email	Depositor Organization	Depositor	Deposition Date	View
1D NMR	¹³C NMR Spectrum (1D, 151 MHz, CD3OD, experimental)	stefan.schulz@tu-bs.de	Technische Universität Braunschweig	Stefan Schulz	2024-08-22	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 151 MHz, CD3OD, experimental)	stefan.schulz@tu-bs.de	Technische Universität Braunschweig	Stefan Schulz	2024-08-22	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, CD3OD, experimental)	stefan.schulz@tu-bs.de	Technische Universität Braunschweig	Stefan Schulz	2024-08-22	View Spectrum

Predicted Spectra

Spectrum Type	Description	Depositor ID	Depositor Organization	Depositor	Deposition Date	View

Chemical Shift Submissions

Not Available

Species

Species of Origin

Species Name	Source	Reference
aurantiaca		Not Available

Chemical Taxonomy

Description

This compound belongs to the class of organic compounds known as heterocyclic fatty acids. These are fatty acids containing a heterocyclic attached to the acyl chain.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Fatty Acyls

Sub Class

Fatty acids and conjugates

Direct Parent

Heterocyclic fatty acids

Alternative Parents

Substituents

Heterocyclic fatty acid
Branched fatty acid
Heteroaromatic compound
Imidazole
Azole
Formamidine
Azacycle
Organoheterocyclic compound
Organic 1,3-dipolar compound
Propargyl-type 1,3-dipolar organic compound
Carboximidamide
Monocarboxylic acid or derivatives
Carboxylic acid
Carboxylic acid derivative
Amidine
Organic nitrogen compound
Organic oxygen compound
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	3.84	ChemAxon
pKa (Strongest Acidic)	4.79	ChemAxon
pKa (Strongest Basic)	6.15	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	3	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	65.98 Å²	ChemAxon
Rotatable Bond Count	13	ChemAxon
Refractivity	93.5 m³·mol⁻¹	ChemAxon
Polarizability	39.1 Å³	ChemAxon
Number of Rings	2	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	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

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

Not Available

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Kostka M, Krug D, Herrmann J, Dickschat JS, Meyer J, Muller R, Schulz S: Identification by Synthesis: Imidacins, Urocanate-Derived Alkaloids from the Myxobacterium Stigmatella aurantiaca. Org Lett. 2024 Aug 2;26(30):6359-6363. doi: 10.1021/acs.orglett.4c02036. Epub 2024 Jul 22. [PubMed:39037587 ]

Showing NP-Card for Imidacin B1 (NP0333740)

MOL for NP0333740 (Imidacin B1)

3D MOL for NP0333740 (Imidacin B1)

3D SDF for NP0333740 (Imidacin B1)

3D-SDF for NP0333740 (Imidacin B1)

PDB for NP0333740 (Imidacin B1)

3D PDB for NP0333740 (Imidacin B1)

SMILES for NP0333740 (Imidacin B1)

INCHI for NP0333740 (Imidacin B1)

Structure for NP0333740 (Imidacin B1)

3D Structure for NP0333740 (Imidacin B1)