NP-MRD: Showing NP-Card for n-[2-hydroxy-1-(5-hydroxy-6-methyloxan-2-yl)pyrimidin-4-ylidene]-3-(methylsulfanyl)prop-2-enamide (NP0330302)

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Record Information

Version

1.0

Created at

2022-09-12 15:31:00 UTC

Updated at

2022-09-12 15:31:00 UTC

NP-MRD ID

NP0330302

Secondary Accession Numbers

None

Natural Product Identification

Common Name

n-[2-hydroxy-1-(5-hydroxy-6-methyloxan-2-yl)pyrimidin-4-ylidene]-3-(methylsulfanyl)prop-2-enamide

Description

Based on a literature review very few articles have been published on N-[2-hydroxy-1-(5-hydroxy-6-methyloxan-2-yl)-1,4-dihydropyrimidin-4-ylidene]-3-(methylsulfanyl)prop-2-enamide.

Structure

MOL 3D MOL SDF PDB SMILES InChI

     RDKit          3D

 41 42  0  0  0  0  0  0  0  0999 V2000
    7.7094    0.0703    2.0578 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.0840    0.6974    1.6233 S   0  0  0  0  0  0  0  0  0  0  0  0
    6.0020    1.1164   -0.1068 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.1132    0.5565   -0.8882 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.1912   -0.4137   -0.3272 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2351   -0.7280    0.9101 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.2258   -1.0158   -1.1895 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.9809   -0.8114   -0.9972 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4910   -0.0198    0.0240 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1374    0.1730    0.1944 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7473   -0.4033   -0.6278 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1792   -0.2322   -0.4917 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.5755    1.1177   -1.0532 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0911    1.0985   -1.1091 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5885    0.9026    0.2962 C   0  0  1  0  0  0  0  0  0  0  0  0
   -5.9731    0.7480    0.2548 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9140   -0.1619    1.0539 C   0  0  1  0  0  0  0  0  0  0  0  0
   -4.7043   -1.4621    0.8246 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6243   -0.4324    0.7890 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2654   -1.1850   -1.6366 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1055   -1.8175   -2.5310 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.0696   -1.3746   -1.8040 N   0  0  0  0  0  0  0  0  0  0  0  0
    7.5876   -0.5555    2.9873 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.4054    0.8942    2.3204 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.0808   -0.5647    1.2323 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.6928    1.8460   -0.5366 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.0614    0.8069   -1.9313 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2286    0.4422    0.6846 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2129    0.7903    0.9927 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6611   -0.9935   -1.1364 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1265    1.1981   -2.0560 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2656    1.9083   -0.3577 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5060    1.9859   -1.5909 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3734    0.1871   -1.6923 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4151    1.8827    0.8284 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.3255    0.7468   -0.6548 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0132    0.0189    2.1651 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.7868   -1.2388    0.7207 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3859   -1.9011   -0.1464 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5755   -2.1574    1.6752 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8808   -1.7191   -3.5247 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  2  0
  4  5  1  0
  5  6  2  0
  5  7  1  0
  7  8  2  0
  8  9  1  0
  9 10  2  0
 10 11  1  0
 11 12  1  0
 12 13  1  0
 13 14  1  0
 14 15  1  0
 15 16  1  0
 15 17  1  0
 17 18  1  0
 17 19  1  0
 11 20  1  0
 20 21  1  0
 20 22  2  0
 22  8  1  0
 19 12  1  0
  1 23  1  0
  1 24  1  0
  1 25  1  0
  3 26  1  0
  4 27  1  0
  9 28  1  0
 10 29  1  0
 12 30  1  6
 13 31  1  0
 13 32  1  0
 14 33  1  0
 14 34  1  0
 15 35  1  1
 16 36  1  0
 17 37  1  1
 18 38  1  0
 18 39  1  0
 18 40  1  0
 21 41  1  0
M  END


  Mrv1652309122217312D          

 22 23  0  0  0  0            999 V2000
    1.4289    2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    2.0625    0.0000 S   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
    0.0000    0.8250    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 O   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 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -2.8875    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -3.7125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -4.1250    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
    0.7145   -5.3625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -6.1875    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0000   -4.9500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145   -5.3625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000   -4.1250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000   -2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145   -2.8875    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000   -1.6500    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  3  2  1  4  0  0  0
  3  4  2  0  0  0  0
  4  5  1  0  0  0  0
  5  6  2  0  0  0  0
  7  5  1  4  0  0  0
  7  8  2  0  0  0  0
  8  9  1  0  0  0  0
  9 10  2  0  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  1  0  0  0  0
 14 15  1  0  0  0  0
 15 16  1  0  0  0  0
 15 17  1  0  0  0  0
 17 18  1  0  0  0  0
 17 19  1  0  0  0  0
 12 19  1  0  0  0  0
 11 20  1  0  0  0  0
 20 21  1  0  0  0  0
 20 22  2  0  0  0  0
  8 22  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0330302

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CSC=CC(=O)N=C1C=CN(C2CCC(O)C(C)O2)C(O)=N1

> <INCHI_IDENTIFIER>
InChI=1S/C14H19N3O4S/c1-9-10(18)3-4-13(21-9)17-7-5-11(16-14(17)20)15-12(19)6-8-22-2/h5-10,13,18H,3-4H2,1-2H3,(H,15,16,19,20)

> <INCHI_KEY>
XNWCNBFBQSQVCP-UHFFFAOYSA-N

> <FORMULA>
C14H19N3O4S

> <MOLECULAR_WEIGHT>
325.38

> <EXACT_MASS>
325.109627278

> <JCHEM_ACCEPTOR_COUNT>
7

> <JCHEM_ATOM_COUNT>
41

> <JCHEM_AVERAGE_POLARIZABILITY>
33.9550794370621

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
N-[2-hydroxy-1-(5-hydroxy-6-methyloxan-2-yl)-1,4-dihydropyrimidin-4-ylidene]-3-(methylsulfanyl)prop-2-enamide

> <JCHEM_LOGP>
0.7326901476666672

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
14.1989871436455

> <JCHEM_PKA_STRONGEST_ACIDIC>
6.038808650735305

> <JCHEM_PKA_STRONGEST_BASIC>
0.36488484735516946

> <JCHEM_POLAR_SURFACE_AREA>
94.72000000000001

> <JCHEM_REFRACTIVITY>
84.51930000000003

> <JCHEM_ROTATABLE_BOND_COUNT>
3

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
N-[2-hydroxy-1-(5-hydroxy-6-methyloxan-2-yl)pyrimidin-4-ylidene]-3-(methylsulfanyl)prop-2-enamide

> <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       2.667   4.620   0.000  0.00  0.00           C+0
HETATM    2  S   UNK     0       1.334   3.850   0.000  0.00  0.00           S+0
HETATM    3  C   UNK     0       1.334   2.310   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       0.000   1.540   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0      -1.334  -0.770   0.000  0.00  0.00           O+0
HETATM    7  N   UNK     0       1.334  -0.770   0.000  0.00  0.00           N+0
HETATM    8  C   UNK     0       1.334  -2.310   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       2.667  -3.080   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       2.667  -4.620   0.000  0.00  0.00           C+0
HETATM   11  N   UNK     0       1.334  -5.390   0.000  0.00  0.00           N+0
HETATM   12  C   UNK     0       1.334  -6.930   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       2.667  -7.700   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       2.667  -9.240   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       1.334 -10.010   0.000  0.00  0.00           C+0
HETATM   16  O   UNK     0       1.334 -11.550   0.000  0.00  0.00           O+0
HETATM   17  C   UNK     0      -0.000  -9.240   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0      -1.334 -10.010   0.000  0.00  0.00           C+0
HETATM   19  O   UNK     0       0.000  -7.700   0.000  0.00  0.00           O+0
HETATM   20  C   UNK     0       0.000  -4.620   0.000  0.00  0.00           C+0
HETATM   21  O   UNK     0      -1.334  -5.390   0.000  0.00  0.00           O+0
HETATM   22  N   UNK     0       0.000  -3.080   0.000  0.00  0.00           N+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4    6    7                                                  
CONECT    6    5                                                            
CONECT    7    5    8                                                       
CONECT    8    7    9   22                                                  
CONECT    9    8   10                                                       
CONECT   10    9   11                                                       
CONECT   11   10   12   20                                                  
CONECT   12   11   13   19                                                  
CONECT   13   12   14                                                       
CONECT   14   13   15                                                       
CONECT   15   14   16   17                                                  
CONECT   16   15                                                            
CONECT   17   15   18   19                                                  
CONECT   18   17                                                            
CONECT   19   17   12                                                       
CONECT   20   11   21   22                                                  
CONECT   21   20                                                            
CONECT   22   20    8                                                       
MASTER        0    0    0    0    0    0    0    0   22    0   46    0
END

View in JSmol

Synonyms

Value	Source
N-[2-Hydroxy-1-(5-hydroxy-6-methyloxan-2-yl)-1,4-dihydropyrimidin-4-ylidene]-3-(methylsulphanyl)prop-2-enamide	Generator

Chemical Formula

C₁₄H₁₉N₃O₄S

Average Mass

325.3800 Da

Monoisotopic Mass

325.10963 Da

IUPAC Name

N-[2-hydroxy-1-(5-hydroxy-6-methyloxan-2-yl)-1,4-dihydropyrimidin-4-ylidene]-3-(methylsulfanyl)prop-2-enamide

Traditional Name

N-[2-hydroxy-1-(5-hydroxy-6-methyloxan-2-yl)pyrimidin-4-ylidene]-3-(methylsulfanyl)prop-2-enamide

CAS Registry Number

Not Available

SMILES

CSC=CC(=O)N=C1C=CN(C2CCC(O)C(C)O2)C(O)=N1

InChI Identifier

InChI=1S/C14H19N3O4S/c1-9-10(18)3-4-13(21-9)17-7-5-11(16-14(17)20)15-12(19)6-8-22-2/h5-10,13,18H,3-4H2,1-2H3,(H,15,16,19,20)

InChI Key

XNWCNBFBQSQVCP-UHFFFAOYSA-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

Not Available

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	0.73	ChemAxon
pKa (Strongest Acidic)	6.04	ChemAxon
pKa (Strongest Basic)	0.36	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	7	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	94.72 Å²	ChemAxon
Rotatable Bond Count	3	ChemAxon
Refractivity	84.52 m³·mol⁻¹	ChemAxon
Polarizability	33.96 Å³	ChemAxon
Number of Rings	2	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	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

162901934

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

LOTUS database [Link]

Showing NP-Card for n-[2-hydroxy-1-(5-hydroxy-6-methyloxan-2-yl)pyrimidin-4-ylidene]-3-(methylsulfanyl)prop-2-enamide (NP0330302)

MOL for NP0330302 (n-[2-hydroxy-1-(5-hydroxy-6-methyloxan-2-yl)pyrimidin-4-ylidene]-3-(methylsulfanyl)prop-2-enamide)

3D MOL for NP0330302 (n-[2-hydroxy-1-(5-hydroxy-6-methyloxan-2-yl)pyrimidin-4-ylidene]-3-(methylsulfanyl)prop-2-enamide)

3D SDF for NP0330302 (n-[2-hydroxy-1-(5-hydroxy-6-methyloxan-2-yl)pyrimidin-4-ylidene]-3-(methylsulfanyl)prop-2-enamide)

3D-SDF for NP0330302 (n-[2-hydroxy-1-(5-hydroxy-6-methyloxan-2-yl)pyrimidin-4-ylidene]-3-(methylsulfanyl)prop-2-enamide)

PDB for NP0330302 (n-[2-hydroxy-1-(5-hydroxy-6-methyloxan-2-yl)pyrimidin-4-ylidene]-3-(methylsulfanyl)prop-2-enamide)

3D PDB for NP0330302 (n-[2-hydroxy-1-(5-hydroxy-6-methyloxan-2-yl)pyrimidin-4-ylidene]-3-(methylsulfanyl)prop-2-enamide)

SMILES for NP0330302 (n-[2-hydroxy-1-(5-hydroxy-6-methyloxan-2-yl)pyrimidin-4-ylidene]-3-(methylsulfanyl)prop-2-enamide)

INCHI for NP0330302 (n-[2-hydroxy-1-(5-hydroxy-6-methyloxan-2-yl)pyrimidin-4-ylidene]-3-(methylsulfanyl)prop-2-enamide)

Structure for NP0330302 (n-[2-hydroxy-1-(5-hydroxy-6-methyloxan-2-yl)pyrimidin-4-ylidene]-3-(methylsulfanyl)prop-2-enamide)

3D Structure for NP0330302 (n-[2-hydroxy-1-(5-hydroxy-6-methyloxan-2-yl)pyrimidin-4-ylidene]-3-(methylsulfanyl)prop-2-enamide)