NP-MRD: Showing NP-Card for n-[(2e)-3-(2-imino-1,3-dihydroimidazol-4-yl)prop-2-en-1-yl]-1h-pyrrole-2-carboxamide (NP0263930)

Jump To Section:

Identification Spectra BioTaxonomy ChemoTaxonomy Physical properties Links References XML

Record Information

Version

2.0

Created at

2022-09-08 07:16:44 UTC

Updated at

2022-09-08 07:16:44 UTC

NP-MRD ID

NP0263930

Secondary Accession Numbers

None

Natural Product Identification

Common Name

n-[(2e)-3-(2-imino-1,3-dihydroimidazol-4-yl)prop-2-en-1-yl]-1h-pyrrole-2-carboxamide

Description

Clathrodin belongs to the class of organic compounds known as 2-heteroaryl carboxamides. 2-Heteroaryl carboxamides are compounds containing a heteroaromatic ring that carries a carboxamide group. n-[(2e)-3-(2-imino-1,3-dihydroimidazol-4-yl)prop-2-en-1-yl]-1h-pyrrole-2-carboxamide is found in Agelas clathrodes. n-[(2e)-3-(2-imino-1,3-dihydroimidazol-4-yl)prop-2-en-1-yl]-1h-pyrrole-2-carboxamide was first documented in 2014 (PMID: 24714127). Based on a literature review a small amount of articles have been published on Clathrodin (PMID: 28802123) (PMID: 28580714) (PMID: 26709468) (PMID: 24534840).

Structure

MOL 3D MOL SDF PDB SMILES InChI

     RDKit          3D

 30 31  0  0  0  0  0  0  0  0999 V2000
    5.0684    1.3564   -3.0268 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.5150    1.2392   -2.1061 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.8904    0.7204   -1.0862 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.4023    0.5347    0.1431 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.4872   -0.0218    0.9486 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3503   -0.1947    0.1975 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0675   -0.7738    0.6474 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0542   -0.8773   -0.1934 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2084   -1.4551    0.2760 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3044   -0.5347    0.1557 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6057   -0.9360    0.5674 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8039   -2.1089    1.0429 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7566   -0.0601    0.4747 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0472   -0.3378    0.8384 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.8575    0.7649    0.5927 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0066    1.7124    0.0691 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7440    1.1939    0.0066 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.6274    0.2670   -1.0380 N   0  0  0  0  0  0  0  0  0  0  0  0
    6.3937    0.8068    0.3881 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.6331   -0.2731    1.9697 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9955   -1.1027    1.6747 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1866   -0.5275   -1.2204 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1275   -1.7130    1.3487 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4188   -2.3537   -0.3528 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1344    0.4109   -0.2297 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.4308   -1.2651    1.2601 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.9169    0.8165    0.7874 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.3241    2.6890   -0.2294 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9374    1.7522   -0.3636 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.9526    0.2710   -1.8444 H   0  0  0  0  0  0  0  0  0  0  0  0
  2  3  2  0
  3  4  1  0
  4  5  1  0
  5  6  2  0
  6 18  1  0
  6  7  1  0
  7  8  2  0
  8  9  1  0
  9 10  1  0
 10 11  1  0
 11 12  2  0
 11 13  1  0
 13 14  2  0
 14 15  1  0
 15 16  2  0
 16 17  1  0
 18  3  1  0
 17 13  1  0
  2  1  1  0
  4 19  1  0
  5 20  1  0
 18 30  1  0
  7 21  1  0
  8 22  1  0
  9 23  1  0
  9 24  1  0
 10 25  1  0
 14 26  1  0
 15 27  1  0
 16 28  1  0
 17 29  1  0
M  END


  Mrv1652309082209162D          

 17 18  0  0  0  0            999 V2000
    4.6568   -1.7425    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.6568   -2.5675    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.3242   -3.0524    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    5.0693   -3.8371    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2443   -3.8371    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7594   -4.5045    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9389   -4.4183    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4540   -5.0857    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6335   -4.9995    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.1486   -5.6669    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4841   -6.4206    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.3281   -5.5807    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2239   -6.1938    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9776   -5.8582    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8914   -5.0377    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0844   -4.8662    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.9894   -3.0524    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
  3  4  1  0  0  0  0
  4  5  2  0  0  0  0
  5  6  1  0  0  0  0
  6  7  2  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  2  0  0  0  0
 10 12  1  0  0  0  0
 12 13  2  0  0  0  0
 13 14  1  0  0  0  0
 14 15  2  0  0  0  0
 15 16  1  0  0  0  0
 12 16  1  0  0  0  0
  5 17  1  0  0  0  0
  2 17  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0263930

> <DATABASE_NAME>
NP-MRD

> <SMILES>
N=C1NC=C(N1)\C=C\CNC(=O)C1=CC=CN1

> <INCHI_IDENTIFIER>
InChI=1S/C11H13N5O/c12-11-15-7-8(16-11)3-1-6-14-10(17)9-4-2-5-13-9/h1-5,7,13H,6H2,(H,14,17)(H3,12,15,16)/b3-1+

> <INCHI_KEY>
PJKFCZYTTBYEHL-HNQUOIGGSA-N

> <FORMULA>
C11H13N5O

> <MOLECULAR_WEIGHT>
231.259

> <EXACT_MASS>
231.112010059

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_ATOM_COUNT>
30

> <JCHEM_AVERAGE_POLARIZABILITY>
24.413055708197973

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
5

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
N-[(2E)-3-(2-imino-2,3-dihydro-1H-imidazol-4-yl)prop-2-en-1-yl]-1H-pyrrole-2-carboxamide

> <JCHEM_LOGP>
-0.246477436

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
1

> <JCHEM_PKA>
15.221674041421863

> <JCHEM_PKA_STRONGEST_ACIDIC>
14.973332210385426

> <JCHEM_PKA_STRONGEST_BASIC>
7.258305507811379

> <JCHEM_POLAR_SURFACE_AREA>
92.80000000000001

> <JCHEM_REFRACTIVITY>
76.90610000000001

> <JCHEM_ROTATABLE_BOND_COUNT>
4

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
N-[(2E)-3-(2-imino-1,3-dihydroimidazol-4-yl)prop-2-en-1-yl]-1H-pyrrole-2-carboxamide

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 08-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   08-SEP-22         0                                  
HETATM    1  N   UNK     0       8.693  -3.253   0.000  0.00  0.00           N+0
HETATM    2  C   UNK     0       8.693  -4.793   0.000  0.00  0.00           C+0
HETATM    3  N   UNK     0       9.939  -5.698   0.000  0.00  0.00           N+0
HETATM    4  C   UNK     0       9.463  -7.162   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       7.923  -7.162   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       7.018  -8.408   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       5.486  -8.247   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       4.581  -9.493   0.000  0.00  0.00           C+0
HETATM    9  N   UNK     0       3.049  -9.332   0.000  0.00  0.00           N+0
HETATM   10  C   UNK     0       2.144 -10.578   0.000  0.00  0.00           C+0
HETATM   11  O   UNK     0       2.770 -11.985   0.000  0.00  0.00           O+0
HETATM   12  C   UNK     0       0.612 -10.417   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      -0.418 -11.562   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      -1.825 -10.935   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0      -1.664  -9.404   0.000  0.00  0.00           C+0
HETATM   16  N   UNK     0      -0.158  -9.084   0.000  0.00  0.00           N+0
HETATM   17  N   UNK     0       7.447  -5.698   0.000  0.00  0.00           N+0
CONECT    1    2                                                            
CONECT    2    1    3   17                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4    6   17                                                  
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   16                                                  
CONECT   13   12   14                                                       
CONECT   14   13   15                                                       
CONECT   15   14   16                                                       
CONECT   16   15   12                                                       
CONECT   17    5    2                                                       
MASTER        0    0    0    0    0    0    0    0   17    0   36    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₁₁H₁₃N₅O

Average Mass

231.2590 Da

Monoisotopic Mass

231.11201 Da

IUPAC Name

N-[(2E)-3-(2-imino-2,3-dihydro-1H-imidazol-4-yl)prop-2-en-1-yl]-1H-pyrrole-2-carboxamide

Traditional Name

N-[(2E)-3-(2-imino-1,3-dihydroimidazol-4-yl)prop-2-en-1-yl]-1H-pyrrole-2-carboxamide

CAS Registry Number

Not Available

SMILES

N=C1NC=C(N1)\C=C\CNC(=O)C1=CC=CN1

InChI Identifier

InChI=1S/C11H13N5O/c12-11-15-7-8(16-11)3-1-6-14-10(17)9-4-2-5-13-9/h1-5,7,13H,6H2,(H,14,17)(H3,12,15,16)/b3-1+

InChI Key

PJKFCZYTTBYEHL-HNQUOIGGSA-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
Agelas clathrodes	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as 2-heteroaryl carboxamides. 2-Heteroaryl carboxamides are compounds containing a heteroaromatic ring that carries a carboxamide group.

Kingdom

Organic compounds

Super Class

Organic acids and derivatives

Class

Carboxylic acids and derivatives

Sub Class

Carboxylic acid derivatives

Direct Parent

2-heteroaryl carboxamides

Alternative Parents

Substituents

2-heteroaryl carboxamide
Pyrrole-2-carboxamide
Pyrrole-2-carboxylic acid or derivatives
Aminoimidazole
Substituted pyrrole
Azole
Imidazole
Pyrrole
Heteroaromatic compound
Secondary carboxylic acid amide
Amino acid or derivatives
Organoheterocyclic compound
Azacycle
Organic oxide
Organic nitrogen compound
Organopnictogen compound
Organic oxygen compound
Primary amine
Organooxygen compound
Organonitrogen compound
Amine
Hydrocarbon derivative
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	-0.25	ChemAxon
pKa (Strongest Acidic)	14.97	ChemAxon
pKa (Strongest Basic)	7.26	ChemAxon
Physiological Charge	1	ChemAxon
Hydrogen Acceptor Count	4	ChemAxon
Hydrogen Donor Count	5	ChemAxon
Polar Surface Area	92.8 Å²	ChemAxon
Rotatable Bond Count	4	ChemAxon
Refractivity	76.91 m³·mol⁻¹	ChemAxon
Polarizability	24.41 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

4534846

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

5388709

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Zidar N, Zula A, Tomasic T, Rogers M, Kirby RW, Tytgat J, Peigneur S, Kikelj D, Ilas J, Masic LP: Clathrodin, hymenidin and oroidin, and their synthetic analogues as inhibitors of the voltage-gated potassium channels. Eur J Med Chem. 2017 Oct 20;139:232-241. doi: 10.1016/j.ejmech.2017.08.015. Epub 2017 Aug 7. [PubMed:28802123 ]
Lillsunde KE, Tomasic T, Kikelj D, Tammela P: Marine alkaloid oroidin analogues with antiviral potential: A novel class of synthetic compounds targeting the cellular chaperone Hsp90. Chem Biol Drug Des. 2017 Dec;90(6):1147-1154. doi: 10.1111/cbdd.13034. Epub 2017 Jul 3. [PubMed:28580714 ]
Montalvao S, Leino TO, Kiuru PS, Lillsunde KE, Yli-Kauhaluoma J, Tammela P: Synthesis and Biological Evaluation of 2-Aminobenzothiazole and Benzimidazole Analogs Based on the Clathrodin Structure. Arch Pharm (Weinheim). 2016 Feb;349(2):137-49. doi: 10.1002/ardp.201500365. Epub 2015 Dec 28. [PubMed:26709468 ]
Peigneur S, Zula A, Zidar N, Chan-Porter F, Kirby R, Madge D, Ilas J, Kikelj D, Tytgat J: Action of clathrodin and analogues on voltage-gated sodium channels. Mar Drugs. 2014 Apr 4;12(4):2132-43. doi: 10.3390/md12042132. [PubMed:24714127 ]
Zidar N, Montalvao S, Hodnik Z, Nawrot DA, Zula A, Ilas J, Kikelj D, Tammela P, Masic LP: Antimicrobial activity of the marine alkaloids, clathrodin and oroidin, and their synthetic analogues. Mar Drugs. 2014 Feb 14;12(2):940-63. doi: 10.3390/md12020940. [PubMed:24534840 ]
LOTUS database [Link]

Showing NP-Card for n-[(2e)-3-(2-imino-1,3-dihydroimidazol-4-yl)prop-2-en-1-yl]-1h-pyrrole-2-carboxamide (NP0263930)

MOL for NP0263930 (n-[(2e)-3-(2-imino-1,3-dihydroimidazol-4-yl)prop-2-en-1-yl]-1h-pyrrole-2-carboxamide)

3D MOL for NP0263930 (n-[(2e)-3-(2-imino-1,3-dihydroimidazol-4-yl)prop-2-en-1-yl]-1h-pyrrole-2-carboxamide)

3D SDF for NP0263930 (n-[(2e)-3-(2-imino-1,3-dihydroimidazol-4-yl)prop-2-en-1-yl]-1h-pyrrole-2-carboxamide)

3D-SDF for NP0263930 (n-[(2e)-3-(2-imino-1,3-dihydroimidazol-4-yl)prop-2-en-1-yl]-1h-pyrrole-2-carboxamide)

PDB for NP0263930 (n-[(2e)-3-(2-imino-1,3-dihydroimidazol-4-yl)prop-2-en-1-yl]-1h-pyrrole-2-carboxamide)

3D PDB for NP0263930 (n-[(2e)-3-(2-imino-1,3-dihydroimidazol-4-yl)prop-2-en-1-yl]-1h-pyrrole-2-carboxamide)

SMILES for NP0263930 (n-[(2e)-3-(2-imino-1,3-dihydroimidazol-4-yl)prop-2-en-1-yl]-1h-pyrrole-2-carboxamide)

INCHI for NP0263930 (n-[(2e)-3-(2-imino-1,3-dihydroimidazol-4-yl)prop-2-en-1-yl]-1h-pyrrole-2-carboxamide)

Structure for NP0263930 (n-[(2e)-3-(2-imino-1,3-dihydroimidazol-4-yl)prop-2-en-1-yl]-1h-pyrrole-2-carboxamide)

3D Structure for NP0263930 (n-[(2e)-3-(2-imino-1,3-dihydroimidazol-4-yl)prop-2-en-1-yl]-1h-pyrrole-2-carboxamide)