NP-MRD: Showing NP-Card for (2r,5e)-7-hydroxy-2-[(4r)-2-iminoimidazolidin-4-yl]-6-methylhept-5-enoic acid (NP0259735)

Jump To Section:

Identification Spectra BioTaxonomy ChemoTaxonomy Physical properties Links References XML

Record Information

Version

2.0

Created at

2022-09-08 01:42:19 UTC

Updated at

2022-09-08 01:42:19 UTC

NP-MRD ID

NP0259735

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(2r,5e)-7-hydroxy-2-[(4r)-2-iminoimidazolidin-4-yl]-6-methylhept-5-enoic acid

Description

(2R,5E)-7-hydroxy-2-[(4R)-2-iminoimidazolidin-4-yl]-6-methylhept-5-enoic acid belongs to the class of organic compounds known as medium-chain hydroxy acids and derivatives. These are hydroxy acids with a 6 to 12 carbon atoms long side chain. (2r,5e)-7-hydroxy-2-[(4r)-2-iminoimidazolidin-4-yl]-6-methylhept-5-enoic acid is found in Plumbago zeylanica. Based on a literature review very few articles have been published on (2R,5E)-7-hydroxy-2-[(4R)-2-iminoimidazolidin-4-yl]-6-methylhept-5-enoic acid.

Structure

MOL 3D MOL SDF PDB SMILES InChI

     RDKit          3D

 36 36  0  0  0  0  0  0  0  0999 V2000
   -4.0135   -2.9778   -0.7815 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1067   -2.5338   -0.9567 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9908   -1.2500   -0.9292 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0259   -0.3143   -0.6706 N   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4080    0.8950   -0.1545 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9056    0.6898   -0.3679 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.2428    0.7815    0.9466 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.2230    0.5892    1.0391 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8111   -0.7084    0.6376 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3191   -0.6991    0.8386 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1698   -0.8835   -0.1502 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6456   -1.1065   -1.4994 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.6465   -0.8734    0.0610 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.1659    0.1632   -0.7336 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4941    2.1886    1.4546 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5005    2.8291    1.8568 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7047    2.8057    1.5077 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7895   -0.4771   -1.1552 N   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0481   -0.5026   -0.8338 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7425    1.7976   -0.6848 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6735    0.8917    0.9299 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5553    1.6162   -0.9486 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7841    0.0652    1.6558 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5758    0.7651    2.1108 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7725    1.4164    0.4821 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4732   -1.5467    1.3163 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5905   -1.0015   -0.3730 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.7195   -0.5351    1.8316 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.4695   -0.9857   -2.2299 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9210   -0.2973   -1.7424 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2261   -2.1185   -1.6620 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.1151   -1.8100   -0.2928 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.8849   -0.7056    1.1261 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.2957    0.9806   -0.1904 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9857    3.6354    1.0407 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0535   -0.7834   -1.8019 H   0  0  0  0  0  0  0  0  0  0  0  0
 12 11  1  0
 11 13  1  0
 13 14  1  0
 11 10  2  0
 10  9  1  0
  9  8  1  0
  8  7  1  0
  7  6  1  0
  6  5  1  0
  5  4  1  0
  4  3  1  0
  3  2  2  0
  3 18  1  0
  7 15  1  0
 15 17  1  0
 15 16  2  0
 18  6  1  0
 12 29  1  0
 12 30  1  0
 12 31  1  0
 13 32  1  0
 13 33  1  0
 14 34  1  0
 10 28  1  0
  9 26  1  0
  9 27  1  0
  8 24  1  0
  8 25  1  0
  7 23  1  1
  6 22  1  6
  5 20  1  0
  5 21  1  0
  4 19  1  0
  2  1  1  0
 18 36  1  0
 17 35  1  0
M  END


  Mrv1652309082203422D          

 17 17  0  0  1  0            999 V2000
    1.8465    1.2639    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1321    0.8514    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1321    0.0264    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8465   -0.3861    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8465   -1.2111    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5610   -1.6236    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    3.2755   -1.2111    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2755   -0.3861    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.9899   -1.6236    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.5610   -2.4486    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    3.2284   -2.9335    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9735   -3.7181    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.1485   -3.7181    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6636   -4.3856    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.8936   -2.9335    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.4176    1.2639    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2969    0.8514    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  2  0  0  0  0
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  6  5  1  1  0  0  0
  6  7  1  0  0  0  0
  7  8  2  0  0  0  0
  7  9  1  0  0  0  0
 10  6  1  6  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  2  0  0  0  0
 13 15  1  0  0  0  0
 10 15  1  0  0  0  0
  2 16  1  0  0  0  0
 16 17  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0259735

> <DATABASE_NAME>
NP-MRD

> <SMILES>
C\C(CO)=C/CC[C@H]([C@@H]1CNC(=N)N1)C(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C11H19N3O3/c1-7(6-15)3-2-4-8(10(16)17)9-5-13-11(12)14-9/h3,8-9,15H,2,4-6H2,1H3,(H,16,17)(H3,12,13,14)/b7-3+/t8-,9+/m1/s1

> <INCHI_KEY>
MKVOYTACJBMDBA-UEXUUTQISA-N

> <FORMULA>
C11H19N3O3

> <MOLECULAR_WEIGHT>
241.291

> <EXACT_MASS>
241.142641484

> <JCHEM_ACCEPTOR_COUNT>
6

> <JCHEM_ATOM_COUNT>
36

> <JCHEM_AVERAGE_POLARIZABILITY>
25.663803736343276

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
5

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2R,5E)-7-hydroxy-2-[(4R)-2-iminoimidazolidin-4-yl]-6-methylhept-5-enoic acid

> <JCHEM_LOGP>
-1.8014890164741792

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
16.644029829586547

> <JCHEM_PKA_STRONGEST_ACIDIC>
4.068133267775434

> <JCHEM_PKA_STRONGEST_BASIC>
11.797949636269161

> <JCHEM_POLAR_SURFACE_AREA>
105.44000000000001

> <JCHEM_REFRACTIVITY>
74.04499999999999

> <JCHEM_ROTATABLE_BOND_COUNT>
6

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
(2R,5E)-7-hydroxy-2-[(4R)-2-iminoimidazolidin-4-yl]-6-methylhept-5-enoic acid

> <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  C   UNK     0       3.447   2.359   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       2.113   1.589   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       2.113   0.049   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       3.447  -0.721   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       3.447  -2.261   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       4.781  -3.031   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       6.114  -2.261   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0       6.114  -0.721   0.000  0.00  0.00           O+0
HETATM    9  O   UNK     0       7.448  -3.031   0.000  0.00  0.00           O+0
HETATM   10  C   UNK     0       4.781  -4.571   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       6.026  -5.476   0.000  0.00  0.00           C+0
HETATM   12  N   UNK     0       5.551  -6.941   0.000  0.00  0.00           N+0
HETATM   13  C   UNK     0       4.011  -6.941   0.000  0.00  0.00           C+0
HETATM   14  N   UNK     0       3.105  -8.186   0.000  0.00  0.00           N+0
HETATM   15  N   UNK     0       3.535  -5.476   0.000  0.00  0.00           N+0
HETATM   16  C   UNK     0       0.780   2.359   0.000  0.00  0.00           C+0
HETATM   17  O   UNK     0      -0.554   1.589   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3   16                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4    6                                                       
CONECT    6    5    7   10                                                  
CONECT    7    6    8    9                                                  
CONECT    8    7                                                            
CONECT    9    7                                                            
CONECT   10    6   11   15                                                  
CONECT   11   10   12                                                       
CONECT   12   11   13                                                       
CONECT   13   12   14   15                                                  
CONECT   14   13                                                            
CONECT   15   13   10                                                       
CONECT   16    2   17                                                       
CONECT   17   16                                                            
MASTER        0    0    0    0    0    0    0    0   17    0   34    0
END

View in JSmol

Synonyms

Value	Source
(2R,5E)-7-Hydroxy-2-[(4R)-2-iminoimidazolidin-4-yl]-6-methylhept-5-enoate	Generator

Chemical Formula

C₁₁H₁₉N₃O₃

Average Mass

241.2910 Da

Monoisotopic Mass

241.14264 Da

IUPAC Name

Not Available

Traditional Name

Not Available

CAS Registry Number

Not Available

SMILES

C\C(CO)=C/CC[C@H]([C@@H]1CNC(=N)N1)C(O)=O

InChI Identifier

InChI=1S/C11H19N3O3/c1-7(6-15)3-2-4-8(10(16)17)9-5-13-11(12)14-9/h3,8-9,15H,2,4-6H2,1H3,(H,16,17)(H3,12,13,14)/b7-3+/t8-,9+/m1/s1

InChI Key

MKVOYTACJBMDBA-UEXUUTQISA-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
Plumbago zeylanica	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as medium-chain hydroxy acids and derivatives. These are hydroxy acids with a 6 to 12 carbon atoms long side chain.

Kingdom

Organic compounds

Super Class

Organic acids and derivatives

Class

Hydroxy acids and derivatives

Sub Class

Medium-chain hydroxy acids and derivatives

Direct Parent

Medium-chain hydroxy acids and derivatives

Alternative Parents

Substituents

Medium-chain hydroxy acid
Imidazolyl carboxylic acid derivative
Medium-chain fatty acid
Amino fatty acid
Branched fatty acid
Heterocyclic fatty acid
Hydroxy fatty acid
Methyl-branched fatty acid
Fatty acyl
Fatty acid
Unsaturated fatty acid
2-imidazoline
Guanidine
Carboxylic acid derivative
Carboxylic acid
Azacycle
Organoheterocyclic compound
Organic 1,3-dipolar compound
Propargyl-type 1,3-dipolar organic compound
Monocarboxylic acid or derivatives
Carboximidamide
Amine
Hydrocarbon derivative
Organic oxide
Organic nitrogen compound
Organic oxygen compound
Carbonyl group
Alcohol
Organonitrogen compound
Organooxygen compound
Primary alcohol
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

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

30821892

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

73346000

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

LOTUS database [Link]

Showing NP-Card for (2r,5e)-7-hydroxy-2-[(4r)-2-iminoimidazolidin-4-yl]-6-methylhept-5-enoic acid (NP0259735)

MOL for NP0259735 ((2r,5e)-7-hydroxy-2-[(4r)-2-iminoimidazolidin-4-yl]-6-methylhept-5-enoic acid)

3D MOL for NP0259735 ((2r,5e)-7-hydroxy-2-[(4r)-2-iminoimidazolidin-4-yl]-6-methylhept-5-enoic acid)

3D SDF for NP0259735 ((2r,5e)-7-hydroxy-2-[(4r)-2-iminoimidazolidin-4-yl]-6-methylhept-5-enoic acid)

3D-SDF for NP0259735 ((2r,5e)-7-hydroxy-2-[(4r)-2-iminoimidazolidin-4-yl]-6-methylhept-5-enoic acid)

PDB for NP0259735 ((2r,5e)-7-hydroxy-2-[(4r)-2-iminoimidazolidin-4-yl]-6-methylhept-5-enoic acid)

3D PDB for NP0259735 ((2r,5e)-7-hydroxy-2-[(4r)-2-iminoimidazolidin-4-yl]-6-methylhept-5-enoic acid)

SMILES for NP0259735 ((2r,5e)-7-hydroxy-2-[(4r)-2-iminoimidazolidin-4-yl]-6-methylhept-5-enoic acid)

INCHI for NP0259735 ((2r,5e)-7-hydroxy-2-[(4r)-2-iminoimidazolidin-4-yl]-6-methylhept-5-enoic acid)

Structure for NP0259735 ((2r,5e)-7-hydroxy-2-[(4r)-2-iminoimidazolidin-4-yl]-6-methylhept-5-enoic acid)

3D Structure for NP0259735 ((2r,5e)-7-hydroxy-2-[(4r)-2-iminoimidazolidin-4-yl]-6-methylhept-5-enoic acid)