NP-MRD: Showing NP-Card for Cycasthioamide (NP0069759)

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Record Information

Version

2.0

Created at

2022-04-28 15:06:11 UTC

Updated at

2022-04-28 15:06:11 UTC

NP-MRD ID

NP0069759

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Cycasthioamide

Description

(2S)-1-[(2R)-2-amino-2-[(carboxymethyl)thio(carbonoimidyl)]ethyl]-5-oxopiperidine-2-carboxylic acid belongs to the class of organic compounds known as l-alpha-amino acids. These are alpha amino acids which have the L-configuration of the alpha-carbon atom. Cycasthioamide is found in Cycas revoluta . Based on a literature review very few articles have been published on (2S)-1-[(2R)-2-amino-2-[(carboxymethyl)thio(carbonoimidyl)]ethyl]-5-oxopiperidine-2-carboxylic acid.

Structure

MOL 3D MOL SDF PDB SMILES InChI

     RDKit          3D

 37 37  0  0  0  0  0  0  0  0999 V2000
    0.7803   -0.6430   -1.8318 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.0054   -1.0904   -0.5289 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.1540   -1.2836    0.3618 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0162   -0.1885    0.6558 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8678   -0.5670    1.7910 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2397   -0.0802    1.7206 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7644    0.4136    2.6934 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0578   -0.1642    0.4669 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0706   -0.5999   -0.6069 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8444    0.2619   -0.4470 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.3243    1.6426   -0.1341 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9951    2.2475    0.9166 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1681    2.3046   -1.0218 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1915   -0.5183    0.1589 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6969   -1.1745    1.5965 S   0  0  0  0  0  0  0  0  0  0  0  0
    2.8963    0.5646   -0.3632 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.0648    1.1568    0.2661 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.2290    0.2500    0.2321 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.1094   -0.9285   -0.2435 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.4959    0.5962    0.6969 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.2850   -1.2652   -2.4612 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9265    0.3309   -2.0560 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3777   -2.2064   -0.6953 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1878   -1.7255    1.3343 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7802   -2.1118   -0.0977 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3791   -0.1820    2.7004 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8964   -1.6962    1.8599 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4326    0.8496    0.2460 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8802   -0.8910    0.5431 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7691   -1.6396   -0.3094 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5097   -0.5807   -1.6063 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2728    0.2809   -1.3719 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7744    3.0630   -0.7488 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5655    0.9896   -1.2791 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.8611    1.4258    1.3268 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.3267    2.1052   -0.2384 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.1971    1.0538    0.1117 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  1  0
  4  5  1  0
  5  6  1  0
  6  7  2  0
  6  8  1  0
  8  9  1  0
  9 10  1  0
 10 11  1  0
 11 13  1  0
 11 12  2  0
  2 14  1  0
 14 15  2  0
 14 16  1  0
 16 17  1  0
 17 18  1  0
 18 20  1  0
 18 19  2  0
 10  4  1  0
  1 21  1  0
  1 22  1  0
  2 23  1  6
  3 24  1  0
  3 25  1  0
  5 26  1  0
  5 27  1  0
  8 28  1  0
  8 29  1  0
  9 30  1  0
  9 31  1  0
 10 32  1  6
 13 33  1  0
 16 34  1  0
 17 35  1  0
 17 36  1  0
 20 37  1  0
M  END


  Mrv1652304282217062D          

 20 20  0  0  1  0            999 V2000
    0.7145    4.5375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    4.9500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434    4.5375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579    4.9500    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434    3.7125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    3.3000    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    3.7125    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.0000    3.3000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145    3.7125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0000    2.4750    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434    2.0625    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.8579    2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579    3.3000    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724    2.0625    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.2868    2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0013    2.0625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0013    1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.7158    2.4750    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434    1.2375    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  3  4  2  0  0  0  0
  3  5  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  1  0  0  0  0
  1  7  1  0  0  0  0
  7  8  1  6  0  0  0
  8  9  2  0  0  0  0
  8 10  1  0  0  0  0
  6 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
 15 16  1  0  0  0  0
 16 17  1  0  0  0  0
 17 18  2  0  0  0  0
 17 19  1  0  0  0  0
 12 20  1  6  0  0  0
M  END
> <DATABASE_ID>
NP0069759

> <DATABASE_NAME>
NP-MRD

> <SMILES>
N[C@H](CN1CC(=O)CC[C@H]1C(O)=O)C(=S)NCC(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C11H17N3O5S/c12-7(10(20)13-3-9(16)17)5-14-4-6(15)1-2-8(14)11(18)19/h7-8H,1-5,12H2,(H,13,20)(H,16,17)(H,18,19)/t7-,8+/m1/s1

> <INCHI_KEY>
AWUZUPCVMWGRIB-SFYZADRCSA-N

> <FORMULA>
C11H17N3O5S

> <MOLECULAR_WEIGHT>
303.33

> <EXACT_MASS>
303.088891833

> <JCHEM_ACCEPTOR_COUNT>
7

> <JCHEM_ATOM_COUNT>
37

> <JCHEM_AVERAGE_POLARIZABILITY>
29.272579542045108

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2S)-1-[(2R)-2-amino-2-[(carboxymethyl)carbamothioyl]ethyl]-5-oxopiperidine-2-carboxylic acid

> <ALOGPS_LOGP>
-2.14

> <JCHEM_LOGP>
-3.918038679716788

> <ALOGPS_LOGS>
-2.46

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
4.2671980893098285

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.345752616672371

> <JCHEM_PKA_STRONGEST_BASIC>
8.670229714107016

> <JCHEM_POLAR_SURFACE_AREA>
132.96

> <JCHEM_REFRACTIVITY>
72.92309999999999

> <JCHEM_ROTATABLE_BOND_COUNT>
6

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.06e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(2S)-1-[(2R)-2-amino-2-(carboxymethylcarbamothioyl)ethyl]-5-oxopiperidine-2-carboxylic acid

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 28-APR-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   28-APR-22         0                                  
HETATM    1  C   UNK     0       1.334   8.470   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       2.667   9.240   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       4.001   8.470   0.000  0.00  0.00           C+0
HETATM    4  O   UNK     0       5.335   9.240   0.000  0.00  0.00           O+0
HETATM    5  C   UNK     0       4.001   6.930   0.000  0.00  0.00           C+0
HETATM    6  N   UNK     0       2.667   6.160   0.000  0.00  0.00           N+0
HETATM    7  C   UNK     0       1.334   6.930   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      -0.000   6.160   0.000  0.00  0.00           C+0
HETATM    9  O   UNK     0      -1.334   6.930   0.000  0.00  0.00           O+0
HETATM   10  O   UNK     0      -0.000   4.620   0.000  0.00  0.00           O+0
HETATM   11  C   UNK     0       2.667   4.620   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       4.001   3.850   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       5.335   4.620   0.000  0.00  0.00           C+0
HETATM   14  S   UNK     0       5.335   6.160   0.000  0.00  0.00           S+0
HETATM   15  N   UNK     0       6.668   3.850   0.000  0.00  0.00           N+0
HETATM   16  C   UNK     0       8.002   4.620   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       9.336   3.850   0.000  0.00  0.00           C+0
HETATM   18  O   UNK     0       9.336   2.310   0.000  0.00  0.00           O+0
HETATM   19  O   UNK     0      10.669   4.620   0.000  0.00  0.00           O+0
HETATM   20  N   UNK     0       4.001   2.310   0.000  0.00  0.00           N+0
CONECT    1    2    7                                                       
CONECT    2    1    3                                                       
CONECT    3    2    4    5                                                  
CONECT    4    3                                                            
CONECT    5    3    6                                                       
CONECT    6    5    7   11                                                  
CONECT    7    6    1    8                                                  
CONECT    8    7    9   10                                                  
CONECT    9    8                                                            
CONECT   10    8                                                            
CONECT   11    6   12                                                       
CONECT   12   11   13   20                                                  
CONECT   13   12   14   15                                                  
CONECT   14   13                                                            
CONECT   15   13   16                                                       
CONECT   16   15   17                                                       
CONECT   17   16   18   19                                                  
CONECT   18   17                                                            
CONECT   19   17                                                            
CONECT   20   12                                                            
MASTER        0    0    0    0    0    0    0    0   20    0   40    0
END

View in JSmol

Synonyms

Value	Source
(2S)-1-[(2R)-2-Amino-2-[(carboxymethyl)thio(carbonoimidyl)]ethyl]-5-oxopiperidine-2-carboxylate	Generator

Chemical Formula

C₁₁H₁₇N₃O₅S

Average Mass

303.3300 Da

Monoisotopic Mass

303.08889 Da

IUPAC Name

(2S)-1-[(2R)-2-amino-2-[(carboxymethyl)carbamothioyl]ethyl]-5-oxopiperidine-2-carboxylic acid

Traditional Name

(2S)-1-[(2R)-2-amino-2-(carboxymethylcarbamothioyl)ethyl]-5-oxopiperidine-2-carboxylic acid

CAS Registry Number

Not Available

SMILES

N[C@H](CN1CC(=O)CC[C@H]1C(O)=O)C(=S)NCC(O)=O

InChI Identifier

InChI=1S/C11H17N3O5S/c12-7(10(20)13-3-9(16)17)5-14-4-6(15)1-2-8(14)11(18)19/h7-8H,1-5,12H2,(H,13,20)(H,16,17)(H,18,19)/t7-,8+/m1/s1

InChI Key

AWUZUPCVMWGRIB-SFYZADRCSA-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, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 252 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 50 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 75 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 101 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 126 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 151 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 176 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 201 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 226 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, 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
Cycas revoluta	Plant	KNApSAcK

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as l-alpha-amino acids. These are alpha amino acids which have the L-configuration of the alpha-carbon atom.

Kingdom

Organic compounds

Super Class

Organic acids and derivatives

Class

Carboxylic acids and derivatives

Sub Class

Amino acids, peptides, and analogues

Direct Parent

L-alpha-amino acids

Alternative Parents

Substituents

L-alpha-amino acid
Piperidinecarboxylic acid
Piperidinone
Piperidine
Dicarboxylic acid or derivatives
Amino acid
Cyclic ketone
Tertiary aliphatic amine
Tertiary amine
Ketone
Azacycle
Organoheterocyclic compound
Organic 1,3-dipolar compound
Propargyl-type 1,3-dipolar organic compound
Imidothioic acid or derivatives
Carboxylic acid
Alkylthiol
Organic nitrogen compound
Organic oxygen compound
Organopnictogen compound
Organic oxide
Hydrocarbon derivative
Primary amine
Organosulfur compound
Organooxygen compound
Organonitrogen compound
Primary aliphatic amine
Carbonyl group
Amine
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
logP	-2.1	ALOGPS
logP	-3.9	ChemAxon
logS	-2.5	ALOGPS
pKa (Strongest Acidic)	3.35	ChemAxon
pKa (Strongest Basic)	8.67	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	7	ChemAxon
Hydrogen Donor Count	4	ChemAxon
Polar Surface Area	132.96 Å²	ChemAxon
Rotatable Bond Count	6	ChemAxon
Refractivity	72.92 m³·mol⁻¹	ChemAxon
Polarizability	29.27 Å³	ChemAxon
Number of Rings	1	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	No	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

154496411

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Not Available

Showing NP-Card for Cycasthioamide (NP0069759)

MOL for NP0069759 (Cycasthioamide)

3D MOL for NP0069759 (Cycasthioamide)

3D SDF for NP0069759 (Cycasthioamide)

3D-SDF for NP0069759 (Cycasthioamide)

PDB for NP0069759 (Cycasthioamide)

3D PDB for NP0069759 (Cycasthioamide)

SMILES for NP0069759 (Cycasthioamide)

INCHI for NP0069759 (Cycasthioamide)

Structure for NP0069759 (Cycasthioamide)

3D Structure for NP0069759 (Cycasthioamide)