NP-MRD: Showing NP-Card for Palythine (NP0081668)

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Record Information

Version

2.0

Created at

2022-04-29 02:43:10 UTC

Updated at

2022-04-29 02:43:11 UTC

NP-MRD ID

NP0081668

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Palythine

Description

Palythine is found in Axinella polypoides.

Structure

MOL 3D MOL SDF PDB SMILES InChI

     RDKit          3D

 33 33  0  0  0  0  0  0  0  0999 V2000
   -1.8711    3.0506   -1.9048 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9591    2.5985   -1.6880 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9838    1.4806   -1.0488 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2346    0.8502   -0.6324 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0061   -0.4406    0.0694 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.8657   -0.1985    1.4333 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2337   -1.3484   -0.0826 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9362   -2.5098    0.6475 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8315   -1.2364   -0.4422 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4135   -0.4247   -0.4564 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6486   -1.0584   -0.1602 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.5420   -0.6060    0.8788 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7291   -1.4860    0.9222 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.8488   -2.4628    0.1265 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.7616   -1.2889    1.8276 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.2907    0.8525   -0.7480 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4532    1.6203   -0.7631 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.5184    2.8599   -0.0617 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9703    0.7529   -1.4823 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7815    1.5215    0.0950 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7544    0.1418    1.7394 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0887   -0.7987    0.3687 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3909   -1.5789   -1.1468 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7846   -3.2705    0.0263 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9980   -1.6403   -1.4447 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6741   -2.0899    0.2481 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8894   -1.8904   -0.7438 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.9242    0.4353    0.6708 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0521   -0.6190    1.8600 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.6027   -0.7756    1.5364 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5257    3.2912   -0.2119 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3665    2.6669    1.0084 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7978    3.6019   -0.4407 H   0  0  0  0  0  0  0  0  0  0  0  0
 18 17  1  0
 17 16  1  0
 16 10  2  0
 10  9  1  0
  9  5  1  0
  5  6  1  1
  5  7  1  0
  7  8  1  0
  5  4  1  0
  4  3  1  0
  3  2  2  0
 10 11  1  0
 11 12  1  0
 12 13  1  0
 13 15  1  0
 13 14  2  0
  3 16  1  0
 18 31  1  0
 18 32  1  0
 18 33  1  0
  9 25  1  0
  9 26  1  0
  6 21  1  0
  7 22  1  0
  7 23  1  0
  8 24  1  0
  4 19  1  0
  4 20  1  0
  2  1  1  0
 11 27  1  0
 12 28  1  0
 12 29  1  0
 15 30  1  0
M  END


  Mrv1652304292204432D          

 17 17  0  0  1  0            999 V2000
    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
   -0.0000    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
    0.0000    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  2  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
    0.3272    1.9659    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7643    2.6656    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.1018    1.9659    0.0000 O   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
    2.1434   -0.4125    0.0000 N   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
    3.5724   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2868   -0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724   -1.2375    0.0000 O   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  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
  6  8  1  1  0  0  0
  8  9  1  0  0  0  0
  6 10  1  6  0  0  0
  2 11  1  0  0  0  0
 11 12  1  0  0  0  0
  1 13  1  0  0  0  0
 13 14  1  0  0  0  0
 14 15  1  0  0  0  0
 15 16  2  0  0  0  0
 15 17  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0081668

> <DATABASE_NAME>
NP-MRD

> <SMILES>
COC1=C(C[C@](O)(CO)CC1=N)NCC(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C10H16N2O5/c1-17-9-6(11)2-10(16,5-13)3-7(9)12-4-8(14)15/h11-13,16H,2-5H2,1H3,(H,14,15)/t10-/m0/s1

> <INCHI_KEY>
AJGGWXHQTXRTPE-JTQLQIEISA-N

> <FORMULA>
C10H16N2O5

> <MOLECULAR_WEIGHT>
244.247

> <EXACT_MASS>
244.105921623

> <JCHEM_ACCEPTOR_COUNT>
7

> <JCHEM_ATOM_COUNT>
33

> <JCHEM_AVERAGE_POLARIZABILITY>
23.962103148114455

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
5

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
2-{[(5R)-5-hydroxy-5-(hydroxymethyl)-3-imino-2-methoxycyclohex-1-en-1-yl]amino}acetic acid

> <ALOGPS_LOGP>
-1.57

> <JCHEM_LOGP>
-5.176036647766625

> <ALOGPS_LOGS>
-2.29

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
13.661481464560918

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.915678730757344

> <JCHEM_PKA_STRONGEST_BASIC>
9.704403738120305

> <JCHEM_POLAR_SURFACE_AREA>
122.87000000000002

> <JCHEM_REFRACTIVITY>
70.7481

> <JCHEM_ROTATABLE_BOND_COUNT>
5

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.25e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
{[(5R)-5-hydroxy-5-(hydroxymethyl)-3-imino-2-methoxycyclohex-1-en-1-yl]amino}acetic acid

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 29-APR-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   29-APR-22         0                                  
HETATM    1  C   UNK     0       2.667   0.000   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -0.000   0.000   0.000  0.00  0.00           C+0
HETATM    4  N   UNK     0      -1.334  -0.770   0.000  0.00  0.00           N+0
HETATM    5  C   UNK     0       0.000   1.540   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       1.334   2.310   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       2.667   1.540   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       0.611   3.670   0.000  0.00  0.00           C+0
HETATM    9  O   UNK     0       1.427   4.976   0.000  0.00  0.00           O+0
HETATM   10  O   UNK     0       2.057   3.670   0.000  0.00  0.00           O+0
HETATM   11  O   UNK     0       1.334  -2.310   0.000  0.00  0.00           O+0
HETATM   12  C   UNK     0      -0.000  -3.080   0.000  0.00  0.00           C+0
HETATM   13  N   UNK     0       4.001  -0.770   0.000  0.00  0.00           N+0
HETATM   14  C   UNK     0       5.335   0.000   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       6.668  -0.770   0.000  0.00  0.00           C+0
HETATM   16  O   UNK     0       8.002  -0.000   0.000  0.00  0.00           O+0
HETATM   17  O   UNK     0       6.668  -2.310   0.000  0.00  0.00           O+0
CONECT    1    2    7   13                                                  
CONECT    2    1    3   11                                                  
CONECT    3    2    4    5                                                  
CONECT    4    3                                                            
CONECT    5    3    6                                                       
CONECT    6    5    7    8   10                                             
CONECT    7    6    1                                                       
CONECT    8    6    9                                                       
CONECT    9    8                                                            
CONECT   10    6                                                            
CONECT   11    2   12                                                       
CONECT   12   11                                                            
CONECT   13    1   14                                                       
CONECT   14   13   15                                                       
CONECT   15   14   16   17                                                  
CONECT   16   15                                                            
CONECT   17   15                                                            
MASTER        0    0    0    0    0    0    0    0   17    0   34    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₁₀H₁₆N₂O₅

Average Mass

244.2470 Da

Monoisotopic Mass

244.10592 Da

IUPAC Name

2-{[(5R)-5-hydroxy-5-(hydroxymethyl)-3-imino-2-methoxycyclohex-1-en-1-yl]amino}acetic acid

Traditional Name

{[(5R)-5-hydroxy-5-(hydroxymethyl)-3-imino-2-methoxycyclohex-1-en-1-yl]amino}acetic acid

CAS Registry Number

Not Available

SMILES

COC1=C(C[C@](O)(CO)CC1=N)NCC(O)=O

InChI Identifier

InChI=1S/C10H16N2O5/c1-17-9-6(11)2-10(16,5-13)3-7(9)12-4-8(14)15/h11-13,16H,2-5H2,1H3,(H,14,15)/t10-/m0/s1

InChI Key

AJGGWXHQTXRTPE-JTQLQIEISA-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
Axinella polypoides	Animalia	KNApSAcK

Chemical Taxonomy

Classification

Not classified

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	-1.6	ALOGPS
logP	-5.2	ChemAxon
logS	-2.3	ALOGPS
pKa (Strongest Acidic)	3.92	ChemAxon
pKa (Strongest Basic)	9.7	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	7	ChemAxon
Hydrogen Donor Count	5	ChemAxon
Polar Surface Area	122.87 Å²	ChemAxon
Rotatable Bond Count	5	ChemAxon
Refractivity	70.75 m³·mol⁻¹	ChemAxon
Polarizability	23.96 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

Not Available

References

General References

Not Available

Showing NP-Card for Palythine (NP0081668)

MOL for NP0081668 (Palythine)

3D MOL for NP0081668 (Palythine)

3D SDF for NP0081668 (Palythine)

3D-SDF for NP0081668 (Palythine)

PDB for NP0081668 (Palythine)

3D PDB for NP0081668 (Palythine)

SMILES for NP0081668 (Palythine)

INCHI for NP0081668 (Palythine)

Structure for NP0081668 (Palythine)

3D Structure for NP0081668 (Palythine)