NP-MRD: Showing NP-Card for {[5-hydroxy-5-(hydroxymethyl)-2-methoxy-3-[(1z)-prop-1-en-1-ylamino]cyclohex-2-en-1-ylidene]amino}acetic acid (NP0246901)

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Record Information

Version

1.0

Created at

2022-09-07 08:31:09 UTC

Updated at

2022-09-07 08:31:09 UTC

NP-MRD ID

NP0246901

Secondary Accession Numbers

None

Natural Product Identification

Common Name

{[5-hydroxy-5-(hydroxymethyl)-2-methoxy-3-[(1z)-prop-1-en-1-ylamino]cyclohex-2-en-1-ylidene]amino}acetic acid

Description

Usujirene belongs to the class of organic compounds known as alpha amino acids and derivatives. These are amino acids in which the amino group is attached to the carbon atom immediately adjacent to the carboxylate group (alpha carbon), or a derivative thereof. {[5-hydroxy-5-(hydroxymethyl)-2-methoxy-3-[(1z)-prop-1-en-1-ylamino]cyclohex-2-en-1-ylidene]amino}acetic acid is found in Lamellodysidea herbacea. Based on a literature review very few articles have been published on Usujirene.

Structure

MOL 3D MOL SDF PDB SMILES InChI

     RDKit          3D

 40 40  0  0  0  0  0  0  0  0999 V2000
   -4.3952   -1.4171    0.8520 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2251   -0.3873   -0.2106 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0321    0.1334   -0.4081 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9219   -0.2787    0.3787 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6500    0.2964    0.1237 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4006   -0.5064   -0.0139 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2960   -1.8906    0.0832 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3189   -2.5536   -1.0207 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7215    0.0489   -0.2762 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7590   -0.6103    0.0363 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.8028   -1.8951    0.6446 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2205   -2.1463    1.0807 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.1271   -1.3036    0.8925 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.4519   -3.3780    1.7062 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.7642    1.3996   -0.9145 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8125    2.2957   -0.1757 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.4309    2.6153    1.0526 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7128    3.5946   -0.9513 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0639    4.4767   -0.1820 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5465    1.7513    0.0228 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3403   -0.8771    1.8324 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6289   -2.2035    0.7988 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.4060   -1.8304    0.7558 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0493   -0.0528   -0.8256 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9273    0.8787   -1.1828 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0228   -0.9853    1.1289 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2324   -2.3809   -1.9652 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3648   -2.1750   -1.1378 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3857   -3.6391   -0.8740 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.1281   -2.0097    1.5240 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4954   -2.6465   -0.1141 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.3250   -3.8325    1.4781 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.7764    1.8137   -0.8177 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4649    1.3270   -1.9821 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7401    2.5942    1.7578 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6928    4.0117   -1.2051 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1021    3.3796   -1.8712 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9710    4.1136   -0.1830 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9752    2.1884    0.9589 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2322    2.0808   -0.7960 H   0  0  0  0  0  0  0  0  0  0  0  0
  8  7  1  0
  7  6  1  0
  6  5  2  0
  5 20  1  0
 20 16  1  0
 16 17  1  1
 16 18  1  0
 18 19  1  0
 16 15  1  0
 15  9  1  0
  9 10  2  0
 10 11  1  0
 11 12  1  0
 12 14  1  0
 12 13  2  0
  5  4  1  0
  4  3  1  0
  3  2  2  0
  2  1  1  0
  9  6  1  0
  8 27  1  0
  8 28  1  0
  8 29  1  0
 20 39  1  0
 20 40  1  0
 17 35  1  0
 18 36  1  0
 18 37  1  0
 19 38  1  0
 15 33  1  0
 15 34  1  0
 11 30  1  0
 11 31  1  0
 14 32  1  0
  4 26  1  0
  3 25  1  0
  2 24  1  0
  1 21  1  0
  1 22  1  0
  1 23  1  0
M  END


  Mrv1652309072210312D          

 20 20  0  0  0  0            999 V2000
    3.5724   -1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -0.4125    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0000   -1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145   -0.4125    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145   -1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4289   -1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4289   -2.4750    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1434   -1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1842    1.8695    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.2448    1.8695    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0572    1.7262    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.8250    0.0000 C   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
  5  6  2  0  0  0  0
  6  7  1  0  0  0  0
  7  8  1  0  0  0  0
  6  9  1  0  0  0  0
  9 10  2  0  0  0  0
 10 11  1  4  0  0  0
 11 12  1  0  0  0  0
 12 13  2  0  0  0  0
 12 14  1  0  0  0  0
  9 15  1  0  0  0  0
 15 16  1  0  0  0  0
 16 17  1  0  0  0  0
 16 18  1  0  0  0  0
 18 19  1  0  0  0  0
 16 20  1  0  0  0  0
  5 20  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0246901

> <DATABASE_NAME>
NP-MRD

> <SMILES>
COC1=C(CC(O)(CO)CC1=NCC(O)=O)N\C=C/C

> <INCHI_IDENTIFIER>
InChI=1S/C13H20N2O5/c1-3-4-14-9-5-13(19,8-16)6-10(12(9)20-2)15-7-11(17)18/h3-4,14,16,19H,5-8H2,1-2H3,(H,17,18)/b4-3-,15-10?

> <INCHI_KEY>
NJNSCDPJAXLFPB-RVLQVYQRSA-N

> <FORMULA>
C13H20N2O5

> <MOLECULAR_WEIGHT>
284.312

> <EXACT_MASS>
284.137221752

> <JCHEM_ACCEPTOR_COUNT>
7

> <JCHEM_ATOM_COUNT>
40

> <JCHEM_AVERAGE_POLARIZABILITY>
29.598444298568403

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
2-{[5-hydroxy-5-(hydroxymethyl)-2-methoxy-3-{[(1Z)-prop-1-en-1-yl]amino}cyclohex-2-en-1-ylidene]amino}acetic acid

> <JCHEM_LOGP>
-3.9084939406052985

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
13.660567820508575

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.9752095457275471

> <JCHEM_PKA_STRONGEST_BASIC>
6.900015474311341

> <JCHEM_POLAR_SURFACE_AREA>
111.38000000000001

> <JCHEM_REFRACTIVITY>
74.5956

> <JCHEM_ROTATABLE_BOND_COUNT>
6

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
{[5-hydroxy-5-(hydroxymethyl)-2-methoxy-3-[(1Z)-prop-1-en-1-ylamino]cyclohex-2-en-1-ylidene]amino}acetic acid

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 07-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   07-SEP-22         0                                  
HETATM    1  C   UNK     0       6.668  -2.310   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       6.668  -0.770   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       5.335   0.000   0.000  0.00  0.00           C+0
HETATM    4  N   UNK     0       4.001  -0.770   0.000  0.00  0.00           N+0
HETATM    5  C   UNK     0       2.667   0.000   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0       1.334  -2.310   0.000  0.00  0.00           O+0
HETATM    8  C   UNK     0      -0.000  -3.080   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      -0.000   0.000   0.000  0.00  0.00           C+0
HETATM   10  N   UNK     0      -1.334  -0.770   0.000  0.00  0.00           N+0
HETATM   11  C   UNK     0      -1.334  -2.310   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      -2.667  -3.080   0.000  0.00  0.00           C+0
HETATM   13  O   UNK     0      -2.667  -4.620   0.000  0.00  0.00           O+0
HETATM   14  O   UNK     0      -4.001  -2.310   0.000  0.00  0.00           O+0
HETATM   15  C   UNK     0       0.000   1.540   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       1.334   2.310   0.000  0.00  0.00           C+0
HETATM   17  O   UNK     0       0.344   3.490   0.000  0.00  0.00           O+0
HETATM   18  C   UNK     0       2.324   3.490   0.000  0.00  0.00           C+0
HETATM   19  O   UNK     0       3.840   3.222   0.000  0.00  0.00           O+0
HETATM   20  C   UNK     0       2.667   1.540   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4    6   20                                                  
CONECT    6    5    7    9                                                  
CONECT    7    6    8                                                       
CONECT    8    7                                                            
CONECT    9    6   10   15                                                  
CONECT   10    9   11                                                       
CONECT   11   10   12                                                       
CONECT   12   11   13   14                                                  
CONECT   13   12                                                            
CONECT   14   12                                                            
CONECT   15    9   16                                                       
CONECT   16   15   17   18   20                                             
CONECT   17   16                                                            
CONECT   18   16   19                                                       
CONECT   19   18                                                            
CONECT   20   16    5                                                       
MASTER        0    0    0    0    0    0    0    0   20    0   40    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₁₃H₂₀N₂O₅

Average Mass

284.3120 Da

Monoisotopic Mass

284.13722 Da

IUPAC Name

Not Available

Traditional Name

Not Available

CAS Registry Number

Not Available

SMILES

COC1=C(CC(O)(CO)CC1=NCC(O)=O)N\C=C/C

InChI Identifier

InChI=1S/C13H20N2O5/c1-3-4-14-9-5-13(19,8-16)6-10(12(9)20-2)15-7-11(17)18/h3-4,14,16,19H,5-8H2,1-2H3,(H,17,18)/b4-3-,15-10?

InChI Key

NJNSCDPJAXLFPB-RVLQVYQRSA-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
Lamellodysidea herbacea	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as alpha amino acids and derivatives. These are amino acids in which the amino group is attached to the carbon atom immediately adjacent to the carboxylate group (alpha carbon), or a derivative thereof.

Kingdom

Organic compounds

Super Class

Organic acids and derivatives

Class

Carboxylic acids and derivatives

Sub Class

Amino acids, peptides, and analogues

Direct Parent

Alpha amino acids and derivatives

Alternative Parents

Substituents

Alpha-amino acid or derivatives
Tertiary alcohol
Secondary ketimine
Azomethine
Amino acid
Ketimine
1,2-diol
Allylamine
Organic 1,3-dipolar compound
Propargyl-type 1,3-dipolar organic compound
Secondary amine
Monocarboxylic acid or derivatives
Enamine
Secondary aliphatic amine
Carboxylic acid
Organic nitrogen compound
Organic oxygen compound
Organopnictogen compound
Organic oxide
Hydrocarbon derivative
Primary alcohol
Organooxygen compound
Organonitrogen compound
Imine
Carbonyl group
Amine
Alcohol
Aliphatic homomonocyclic compound

Molecular Framework

Aliphatic homomonocyclic 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

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

15847474

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

LOTUS database [Link]

Showing NP-Card for {[5-hydroxy-5-(hydroxymethyl)-2-methoxy-3-[(1z)-prop-1-en-1-ylamino]cyclohex-2-en-1-ylidene]amino}acetic acid (NP0246901)

MOL for NP0246901 ({[5-hydroxy-5-(hydroxymethyl)-2-methoxy-3-[(1z)-prop-1-en-1-ylamino]cyclohex-2-en-1-ylidene]amino}acetic acid)

3D MOL for NP0246901 ({[5-hydroxy-5-(hydroxymethyl)-2-methoxy-3-[(1z)-prop-1-en-1-ylamino]cyclohex-2-en-1-ylidene]amino}acetic acid)

3D SDF for NP0246901 ({[5-hydroxy-5-(hydroxymethyl)-2-methoxy-3-[(1z)-prop-1-en-1-ylamino]cyclohex-2-en-1-ylidene]amino}acetic acid)

3D-SDF for NP0246901 ({[5-hydroxy-5-(hydroxymethyl)-2-methoxy-3-[(1z)-prop-1-en-1-ylamino]cyclohex-2-en-1-ylidene]amino}acetic acid)

PDB for NP0246901 ({[5-hydroxy-5-(hydroxymethyl)-2-methoxy-3-[(1z)-prop-1-en-1-ylamino]cyclohex-2-en-1-ylidene]amino}acetic acid)

3D PDB for NP0246901 ({[5-hydroxy-5-(hydroxymethyl)-2-methoxy-3-[(1z)-prop-1-en-1-ylamino]cyclohex-2-en-1-ylidene]amino}acetic acid)

SMILES for NP0246901 ({[5-hydroxy-5-(hydroxymethyl)-2-methoxy-3-[(1z)-prop-1-en-1-ylamino]cyclohex-2-en-1-ylidene]amino}acetic acid)

INCHI for NP0246901 ({[5-hydroxy-5-(hydroxymethyl)-2-methoxy-3-[(1z)-prop-1-en-1-ylamino]cyclohex-2-en-1-ylidene]amino}acetic acid)

Structure for NP0246901 ({[5-hydroxy-5-(hydroxymethyl)-2-methoxy-3-[(1z)-prop-1-en-1-ylamino]cyclohex-2-en-1-ylidene]amino}acetic acid)

3D Structure for NP0246901 ({[5-hydroxy-5-(hydroxymethyl)-2-methoxy-3-[(1z)-prop-1-en-1-ylamino]cyclohex-2-en-1-ylidene]amino}acetic acid)