NP-MRD: Showing NP-Card for [(1s)-2-(2-{[(1s,2s,3s,7as)-1,7-dihydroxy-3,7a-dimethyl-5-[(3-methylbut-2-enoyl)imino]-2,3-dihydro-1h-pyrrolizin-2-yl]sulfanyl}-3h-imidazol-4-yl)-1-carboxyethyl]trimethylazanium (NP0326760)

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Record Information

Version

2.0

Created at

2022-09-12 08:40:08 UTC

Updated at

2022-09-12 08:40:09 UTC

NP-MRD ID

NP0326760

Secondary Accession Numbers

None

Natural Product Identification

Common Name

[(1s)-2-(2-{[(1s,2s,3s,7as)-1,7-dihydroxy-3,7a-dimethyl-5-[(3-methylbut-2-enoyl)imino]-2,3-dihydro-1h-pyrrolizin-2-yl]sulfanyl}-3h-imidazol-4-yl)-1-carboxyethyl]trimethylazanium

Description

[(1S)-2-(2-{[(1S,2S,3S,7aS)-1,7-dihydroxy-3,7a-dimethyl-5-[(3-methylbut-2-enoyl)imino]-2,3,5,7a-tetrahydro-1H-pyrrolizin-2-yl]sulfanyl}-1H-imidazol-5-yl)-1-carboxyethyl]trimethylazanium belongs to the class of organic compounds known as histidine and derivatives. Histidine and derivatives are compounds containing cysteine or a derivative thereof resulting from reaction of cysteine at the amino group or the carboxy group, or from the replacement of any hydrogen of glycine by a heteroatom. [(1s)-2-(2-{[(1s,2s,3s,7as)-1,7-dihydroxy-3,7a-dimethyl-5-[(3-methylbut-2-enoyl)imino]-2,3-dihydro-1h-pyrrolizin-2-yl]sulfanyl}-3h-imidazol-4-yl)-1-carboxyethyl]trimethylazanium is found in Streptomyces spinoverrucosus. Based on a literature review very few articles have been published on [(1S)-2-(2-{[(1S,2S,3S,7aS)-1,7-dihydroxy-3,7a-dimethyl-5-[(3-methylbut-2-enoyl)imino]-2,3,5,7a-tetrahydro-1H-pyrrolizin-2-yl]sulfanyl}-1H-imidazol-5-yl)-1-carboxyethyl]trimethylazanium.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652309122210402D          

 34 36  0  0  1  0            999 V2000
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  8 34  1  0  0  0  0
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M  CHG  1  27   1
M  END

     RDKit          3D

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M  CHG  1  27   1
M  END


  Mrv1652309122210402D          

 34 36  0  0  1  0            999 V2000
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 18 31  1  0  0  0  0
 16 32  1  0  0  0  0
 32 33  1  6  0  0  0
 32 34  1  0  0  0  0
  8 34  1  0  0  0  0
 12 34  1  0  0  0  0
M  CHG  1  27   1
M  END
> <DATABASE_ID>
NP0326760

> <DATABASE_NAME>
NP-MRD

> <SMILES>
C[C@H]1[C@H](SC2=NC=C(C[C@@H](C(O)=O)[N+](C)(C)C)N2)[C@@H](O)[C@]2(C)N1C(C=C2O)=NC(=O)C=C(C)C

> <INCHI_IDENTIFIER>
InChI=1S/C23H33N5O5S/c1-12(2)8-18(30)26-17-10-16(29)23(4)20(31)19(13(3)27(17)23)34-22-24-11-14(25-22)9-15(21(32)33)28(5,6)7/h8,10-11,13,15,19-20,31H,9H2,1-7H3,(H2-,24,25,26,29,30,32,33)/p+1/t13-,15-,19-,20+,23+/m0/s1

> <INCHI_KEY>
SAPJXBIMTXJROH-HVUPQINQSA-O

> <FORMULA>
C23H34N5O5S

> <MOLECULAR_WEIGHT>
492.61

> <EXACT_MASS>
492.227516809

> <JCHEM_ACCEPTOR_COUNT>
8

> <JCHEM_ATOM_COUNT>
68

> <JCHEM_AVERAGE_POLARIZABILITY>
52.68644690774484

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
1

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
[(1S)-2-(2-{[(1S,2S,3S,7aS)-1,7-dihydroxy-3,7a-dimethyl-5-[(3-methylbut-2-enoyl)imino]-2,3,5,7a-tetrahydro-1H-pyrrolizin-2-yl]sulfanyl}-1H-imidazol-5-yl)-1-carboxyethyl]trimethylazanium

> <JCHEM_LOGP>
-3.783128089063743

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
6.7362862679562845

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.6413371790157032

> <JCHEM_PKA_STRONGEST_BASIC>
5.068567893052943

> <JCHEM_POLAR_SURFACE_AREA>
139.11

> <JCHEM_REFRACTIVITY>
143.33699999999996

> <JCHEM_ROTATABLE_BOND_COUNT>
7

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
[(1S)-2-(2-{[(1S,2S,3S,7aS)-1,7-dihydroxy-3,7a-dimethyl-5-[(3-methylbut-2-enoyl)imino]-2,3-dihydro-1H-pyrrolizin-2-yl]sulfanyl}-3H-imidazol-4-yl)-1-carboxyethyl]trimethylazanium

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 12-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   12-SEP-22         0                                  
HETATM    1  C   UNK     0       0.466  -7.580   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       0.942  -6.116   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -0.088  -4.971   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       2.449  -5.795   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       2.924  -4.331   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0       4.431  -4.011   0.000  0.00  0.00           O+0
HETATM    7  N   UNK     0       1.894  -3.186   0.000  0.00  0.00           N+0
HETATM    8  C   UNK     0       2.370  -1.722   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       1.465  -0.476   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       2.370   0.770   0.000  0.00  0.00           C+0
HETATM   11  O   UNK     0       1.894   2.235   0.000  0.00  0.00           O+0
HETATM   12  C   UNK     0       3.834   0.294   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       3.834   1.834   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       5.299   0.770   0.000  0.00  0.00           C+0
HETATM   15  O   UNK     0       5.775   2.235   0.000  0.00  0.00           O+0
HETATM   16  C   UNK     0       6.204  -0.476   0.000  0.00  0.00           C+0
HETATM   17  S   UNK     0       7.744  -0.476   0.000  0.00  0.00           S+0
HETATM   18  C   UNK     0       8.514   0.858   0.000  0.00  0.00           C+0
HETATM   19  N   UNK     0       7.888   2.265   0.000  0.00  0.00           N+0
HETATM   20  C   UNK     0       9.032   3.295   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0      10.366   2.525   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0      11.773   3.151   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0      11.934   4.683   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0      13.341   5.309   0.000  0.00  0.00           C+0
HETATM   25  O   UNK     0      13.502   6.841   0.000  0.00  0.00           O+0
HETATM   26  O   UNK     0      14.587   4.404   0.000  0.00  0.00           O+0
HETATM   27  N   UNK     0      10.688   5.588   0.000  0.00  0.00           N+1
HETATM   28  C   UNK     0       9.442   6.493   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0      11.593   6.834   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0       9.783   4.342   0.000  0.00  0.00           C+0
HETATM   31  N   UNK     0      10.046   1.019   0.000  0.00  0.00           N+0
HETATM   32  C   UNK     0       5.299  -1.722   0.000  0.00  0.00           C+0
HETATM   33  C   UNK     0       5.775  -3.186   0.000  0.00  0.00           C+0
HETATM   34  N   UNK     0       3.834  -1.246   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                                                            
CONECT    7    5    8                                                       
CONECT    8    7    9   34                                                  
CONECT    9    8   10                                                       
CONECT   10    9   11   12                                                  
CONECT   11   10                                                            
CONECT   12   10   13   14   34                                             
CONECT   13   12                                                            
CONECT   14   12   15   16                                                  
CONECT   15   14                                                            
CONECT   16   14   17   32                                                  
CONECT   17   16   18                                                       
CONECT   18   17   19   31                                                  
CONECT   19   18   20                                                       
CONECT   20   19   21                                                       
CONECT   21   20   22   31                                                  
CONECT   22   21   23                                                       
CONECT   23   22   24   27                                                  
CONECT   24   23   25   26                                                  
CONECT   25   24                                                            
CONECT   26   24                                                            
CONECT   27   23   28   29   30                                             
CONECT   28   27                                                            
CONECT   29   27                                                            
CONECT   30   27                                                            
CONECT   31   21   18                                                       
CONECT   32   16   33   34                                                  
CONECT   33   32                                                            
CONECT   34   32    8   12                                                  
MASTER        0    0    0    0    0    0    0    0   34    0   72    0
END

View in JSmol

Synonyms

Value	Source
[(1S)-2-(2-{[(1S,2S,3S,7as)-1,7-dihydroxy-3,7a-dimethyl-5-[(3-methylbut-2-enoyl)imino]-2,3,5,7a-tetrahydro-1H-pyrrolizin-2-yl]sulphanyl}-1H-imidazol-5-yl)-1-carboxyethyl]trimethylazanium	Generator

Chemical Formula

C₂₃H₃₄N₅O₅S

Average Mass

492.6100 Da

Monoisotopic Mass

492.22752 Da

IUPAC Name

[(1S)-2-(2-{[(1S,2S,3S,7aS)-1,7-dihydroxy-3,7a-dimethyl-5-[(3-methylbut-2-enoyl)imino]-2,3,5,7a-tetrahydro-1H-pyrrolizin-2-yl]sulfanyl}-1H-imidazol-5-yl)-1-carboxyethyl]trimethylazanium

Traditional Name

[(1S)-2-(2-{[(1S,2S,3S,7aS)-1,7-dihydroxy-3,7a-dimethyl-5-[(3-methylbut-2-enoyl)imino]-2,3-dihydro-1H-pyrrolizin-2-yl]sulfanyl}-3H-imidazol-4-yl)-1-carboxyethyl]trimethylazanium

CAS Registry Number

Not Available

SMILES

C[C@H]1[C@H](SC2=NC=C(C[C@@H](C(O)=O)[N+](C)(C)C)N2)[C@@H](O)[C@]2(C)N1C(C=C2O)=NC(=O)C=C(C)C

InChI Identifier

InChI=1S/C23H33N5O5S/c1-12(2)8-18(30)26-17-10-16(29)23(4)20(31)19(13(3)27(17)23)34-22-24-11-14(25-22)9-15(21(32)33)28(5,6)7/h8,10-11,13,15,19-20,31H,9H2,1-7H3,(H2-,24,25,26,29,30,32,33)/p+1/t13-,15-,19-,20+,23+/m0/s1

InChI Key

SAPJXBIMTXJROH-HVUPQINQSA-O

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 spinoverrucosus	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as histidine and derivatives. Histidine and derivatives are compounds containing cysteine or a derivative thereof resulting from reaction of cysteine at the amino group or the carboxy group, or from the replacement of any hydrogen of glycine by a heteroatom.

Kingdom

Organic compounds

Super Class

Organic acids and derivatives

Class

Carboxylic acids and derivatives

Sub Class

Amino acids, peptides, and analogues

Direct Parent

Histidine and derivatives

Alternative Parents

Substituents

Histidine or derivatives
L-alpha-amino acid
Alpha-amino acid
Aryl thioether
Pyrrolizine
Aralkylamine
Alkylarylthioether
Tetraalkylammonium salt
Heteroaromatic compound
Quaternary ammonium salt
Pyrroline
Pyrrolidine
Imidazole
Azole
N-acylimine
Secondary alcohol
Azacycle
Organoheterocyclic compound
Sulfenyl compound
Carboximidamide
Thioether
Monocarboxylic acid or derivatives
Enol
Carboxylic acid
Carboxylic acid amidine
Amidine
Organic nitrogen compound
Organic oxygen compound
Organopnictogen compound
Organic oxide
Hydrocarbon derivative
Organic salt
Organosulfur compound
Organooxygen compound
Organonitrogen compound
Carbonyl group
Amine
Alcohol
Organic cation
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic heteropolycyclic 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	-3.8	ChemAxon
pKa (Strongest Acidic)	1.64	ChemAxon
pKa (Strongest Basic)	5.07	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	8	ChemAxon
Hydrogen Donor Count	4	ChemAxon
Polar Surface Area	139.11 Å²	ChemAxon
Rotatable Bond Count	7	ChemAxon
Refractivity	143.34 m³·mol⁻¹	ChemAxon
Polarizability	52.69 Å³	ChemAxon
Number of Rings	3	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	Yes	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

122376923

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

LOTUS database [Link]

Showing NP-Card for [(1s)-2-(2-{[(1s,2s,3s,7as)-1,7-dihydroxy-3,7a-dimethyl-5-[(3-methylbut-2-enoyl)imino]-2,3-dihydro-1h-pyrrolizin-2-yl]sulfanyl}-3h-imidazol-4-yl)-1-carboxyethyl]trimethylazanium (NP0326760)

MOL for NP0326760 ([(1s)-2-(2-{[(1s,2s,3s,7as)-1,7-dihydroxy-3,7a-dimethyl-5-[(3-methylbut-2-enoyl)imino]-2,3-dihydro-1h-pyrrolizin-2-yl]sulfanyl}-3h-imidazol-4-yl)-1-carboxyethyl]trimethylazanium)

3D MOL for NP0326760 ([(1s)-2-(2-{[(1s,2s,3s,7as)-1,7-dihydroxy-3,7a-dimethyl-5-[(3-methylbut-2-enoyl)imino]-2,3-dihydro-1h-pyrrolizin-2-yl]sulfanyl}-3h-imidazol-4-yl)-1-carboxyethyl]trimethylazanium)

3D SDF for NP0326760 ([(1s)-2-(2-{[(1s,2s,3s,7as)-1,7-dihydroxy-3,7a-dimethyl-5-[(3-methylbut-2-enoyl)imino]-2,3-dihydro-1h-pyrrolizin-2-yl]sulfanyl}-3h-imidazol-4-yl)-1-carboxyethyl]trimethylazanium)

3D-SDF for NP0326760 ([(1s)-2-(2-{[(1s,2s,3s,7as)-1,7-dihydroxy-3,7a-dimethyl-5-[(3-methylbut-2-enoyl)imino]-2,3-dihydro-1h-pyrrolizin-2-yl]sulfanyl}-3h-imidazol-4-yl)-1-carboxyethyl]trimethylazanium)

PDB for NP0326760 ([(1s)-2-(2-{[(1s,2s,3s,7as)-1,7-dihydroxy-3,7a-dimethyl-5-[(3-methylbut-2-enoyl)imino]-2,3-dihydro-1h-pyrrolizin-2-yl]sulfanyl}-3h-imidazol-4-yl)-1-carboxyethyl]trimethylazanium)

3D PDB for NP0326760 ([(1s)-2-(2-{[(1s,2s,3s,7as)-1,7-dihydroxy-3,7a-dimethyl-5-[(3-methylbut-2-enoyl)imino]-2,3-dihydro-1h-pyrrolizin-2-yl]sulfanyl}-3h-imidazol-4-yl)-1-carboxyethyl]trimethylazanium)

SMILES for NP0326760 ([(1s)-2-(2-{[(1s,2s,3s,7as)-1,7-dihydroxy-3,7a-dimethyl-5-[(3-methylbut-2-enoyl)imino]-2,3-dihydro-1h-pyrrolizin-2-yl]sulfanyl}-3h-imidazol-4-yl)-1-carboxyethyl]trimethylazanium)

INCHI for NP0326760 ([(1s)-2-(2-{[(1s,2s,3s,7as)-1,7-dihydroxy-3,7a-dimethyl-5-[(3-methylbut-2-enoyl)imino]-2,3-dihydro-1h-pyrrolizin-2-yl]sulfanyl}-3h-imidazol-4-yl)-1-carboxyethyl]trimethylazanium)

Structure for NP0326760 ([(1s)-2-(2-{[(1s,2s,3s,7as)-1,7-dihydroxy-3,7a-dimethyl-5-[(3-methylbut-2-enoyl)imino]-2,3-dihydro-1h-pyrrolizin-2-yl]sulfanyl}-3h-imidazol-4-yl)-1-carboxyethyl]trimethylazanium)

3D Structure for NP0326760 ([(1s)-2-(2-{[(1s,2s,3s,7as)-1,7-dihydroxy-3,7a-dimethyl-5-[(3-methylbut-2-enoyl)imino]-2,3-dihydro-1h-pyrrolizin-2-yl]sulfanyl}-3h-imidazol-4-yl)-1-carboxyethyl]trimethylazanium)