NP-MRD: Showing NP-Card for 4-amino-n-{1-[(2r,4r,5s,6r)-5-{[(1s,2r,3s,4r,5s)-4-(dimethylamino)-2,3,5-trihydroxycyclohexyl]oxy}-4-hydroxy-6-methyloxan-2-yl]-2-hydroxypyrimidin-4-ylidene}benzamide (NP0193710)

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Record Information

Version

2.0

Created at

2022-09-04 11:14:44 UTC

Updated at

2022-09-04 11:14:45 UTC

NP-MRD ID

NP0193710

Secondary Accession Numbers

None

Natural Product Identification

Common Name

4-amino-n-{1-[(2r,4r,5s,6r)-5-{[(1s,2r,3s,4r,5s)-4-(dimethylamino)-2,3,5-trihydroxycyclohexyl]oxy}-4-hydroxy-6-methyloxan-2-yl]-2-hydroxypyrimidin-4-ylidene}benzamide

Description

Oxyplicacetin belongs to the class of organic compounds known as aminobenzoic acids and derivatives. These are benzoic acids (or derivative thereof) containing an amine group attached to the benzene moiety. 4-amino-n-{1-[(2r,4r,5s,6r)-5-{[(1s,2r,3s,4r,5s)-4-(dimethylamino)-2,3,5-trihydroxycyclohexyl]oxy}-4-hydroxy-6-methyloxan-2-yl]-2-hydroxypyrimidin-4-ylidene}benzamide is found in Streptomyces amakusaensis. Based on a literature review very few articles have been published on Oxyplicacetin.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652309042213142D          

 38 41  0  0  1  0            999 V2000
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M  END

     RDKit          3D

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M  END


  Mrv1652309042213142D          

 38 41  0  0  1  0            999 V2000
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    2.1434    1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -0.0000    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.1434   -0.4125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  6  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  1  6  0  0  0
  5  6  1  0  0  0  0
  6  7  2  0  0  0  0
  7  8  1  0  0  0  0
  8  9  2  0  0  0  0
  9 10  1  4  0  0  0
 10 11  2  0  0  0  0
 10 12  1  0  0  0  0
 12 13  2  0  0  0  0
 13 14  1  0  0  0  0
 14 15  2  0  0  0  0
 15 16  1  0  0  0  0
 15 17  1  0  0  0  0
 17 18  2  0  0  0  0
 12 18  1  0  0  0  0
  8 19  1  0  0  0  0
 19 20  2  0  0  0  0
  5 20  1  0  0  0  0
 20 21  1  0  0  0  0
  4 22  1  0  0  0  0
 22 23  1  0  0  0  0
 23 24  1  6  0  0  0
 23 25  1  0  0  0  0
  2 25  1  0  0  0  0
 25 26  1  1  0  0  0
 27 26  1  1  0  0  0
 27 28  1  0  0  0  0
 28 29  1  0  0  0  0
 29 30  1  6  0  0  0
 29 31  1  0  0  0  0
 31 32  1  1  0  0  0
 32 33  1  0  0  0  0
 32 34  1  0  0  0  0
 31 35  1  0  0  0  0
 35 36  1  6  0  0  0
 35 37  1  0  0  0  0
 27 37  1  0  0  0  0
 37 38  1  1  0  0  0
M  END
> <DATABASE_ID>
NP0193710

> <DATABASE_NAME>
NP-MRD

> <SMILES>
C[C@H]1O[C@H](C[C@@H](O)[C@@H]1O[C@H]1C[C@H](O)[C@H]([C@H](O)[C@H]1O)N(C)C)N1C=CC(=NC(=O)C2=CC=C(N)C=C2)N=C1O

> <INCHI_IDENTIFIER>
InChI=1S/C25H35N5O8/c1-12-23(38-17-10-15(31)20(29(2)3)22(34)21(17)33)16(32)11-19(37-12)30-9-8-18(28-25(30)36)27-24(35)13-4-6-14(26)7-5-13/h4-9,12,15-17,19-23,31-34H,10-11,26H2,1-3H3,(H,27,28,35,36)/t12-,15+,16-,17+,19-,20-,21+,22+,23-/m1/s1

> <INCHI_KEY>
NJRKCURACRGUML-IIYKVCNPSA-N

> <FORMULA>
C25H35N5O8

> <MOLECULAR_WEIGHT>
533.582

> <EXACT_MASS>
533.248563107

> <JCHEM_ACCEPTOR_COUNT>
13

> <JCHEM_ATOM_COUNT>
73

> <JCHEM_AVERAGE_POLARIZABILITY>
56.33680846321193

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
6

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
4-amino-N-{1-[(2R,4R,5S,6R)-5-{[(1S,2R,3S,4R,5S)-4-(dimethylamino)-2,3,5-trihydroxycyclohexyl]oxy}-4-hydroxy-6-methyloxan-2-yl]-2-hydroxy-1,4-dihydropyrimidin-4-ylidene}benzamide

> <JCHEM_LOGP>
-3.6936485976288473

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
4

> <JCHEM_PHYSIOLOGICAL_CHARGE>
1

> <JCHEM_PKA>
12.93068640845896

> <JCHEM_PKA_STRONGEST_ACIDIC>
5.743850802960696

> <JCHEM_PKA_STRONGEST_BASIC>
8.633529893066788

> <JCHEM_POLAR_SURFACE_AREA>
193.89999999999998

> <JCHEM_REFRACTIVITY>
136.08190000000002

> <JCHEM_ROTATABLE_BOND_COUNT>
5

> <JCHEM_RULE_OF_FIVE>
0

> <JCHEM_TRADITIONAL_IUPAC>
4-amino-N-{1-[(2R,4R,5S,6R)-5-{[(1S,2R,3S,4R,5S)-4-(dimethylamino)-2,3,5-trihydroxycyclohexyl]oxy}-4-hydroxy-6-methyloxan-2-yl]-2-hydroxypyrimidin-4-ylidene}benzamide

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 04-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   04-SEP-22         0                                  
HETATM    1  C   UNK     0      -1.334  -0.770   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -1.334  -2.310   0.000  0.00  0.00           C+0
HETATM    3  O   UNK     0      -2.667  -3.080   0.000  0.00  0.00           O+0
HETATM    4  C   UNK     0      -2.667  -4.620   0.000  0.00  0.00           C+0
HETATM    5  N   UNK     0      -4.001  -5.390   0.000  0.00  0.00           N+0
HETATM    6  C   UNK     0      -4.001  -6.930   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      -5.335  -7.700   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      -6.668  -6.930   0.000  0.00  0.00           C+0
HETATM    9  N   UNK     0      -8.002  -7.700   0.000  0.00  0.00           N+0
HETATM   10  C   UNK     0      -8.002  -9.240   0.000  0.00  0.00           C+0
HETATM   11  O   UNK     0      -6.668 -10.010   0.000  0.00  0.00           O+0
HETATM   12  C   UNK     0      -9.336 -10.010   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      -9.336 -11.550   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0     -10.669 -12.320   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0     -12.003 -11.550   0.000  0.00  0.00           C+0
HETATM   16  N   UNK     0     -13.337 -12.320   0.000  0.00  0.00           N+0
HETATM   17  C   UNK     0     -12.003 -10.010   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0     -10.669  -9.240   0.000  0.00  0.00           C+0
HETATM   19  N   UNK     0      -6.668  -5.390   0.000  0.00  0.00           N+0
HETATM   20  C   UNK     0      -5.335  -4.620   0.000  0.00  0.00           C+0
HETATM   21  O   UNK     0      -5.335  -3.080   0.000  0.00  0.00           O+0
HETATM   22  C   UNK     0      -1.334  -5.390   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0       0.000  -4.620   0.000  0.00  0.00           C+0
HETATM   24  O   UNK     0       1.334  -5.390   0.000  0.00  0.00           O+0
HETATM   25  C   UNK     0       0.000  -3.080   0.000  0.00  0.00           C+0
HETATM   26  O   UNK     0       1.334  -2.310   0.000  0.00  0.00           O+0
HETATM   27  C   UNK     0       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0       0.000  -0.000   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0       0.000   1.540   0.000  0.00  0.00           C+0
HETATM   30  O   UNK     0      -1.334   2.310   0.000  0.00  0.00           O+0
HETATM   31  C   UNK     0       1.334   2.310   0.000  0.00  0.00           C+0
HETATM   32  N   UNK     0       1.334   3.850   0.000  0.00  0.00           N+0
HETATM   33  C   UNK     0       0.000   4.620   0.000  0.00  0.00           C+0
HETATM   34  C   UNK     0       2.667   4.620   0.000  0.00  0.00           C+0
HETATM   35  C   UNK     0       2.667   1.540   0.000  0.00  0.00           C+0
HETATM   36  O   UNK     0       4.001   2.310   0.000  0.00  0.00           O+0
HETATM   37  C   UNK     0       2.667  -0.000   0.000  0.00  0.00           C+0
HETATM   38  O   UNK     0       4.001  -0.770   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3   25                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5   22                                                  
CONECT    5    4    6   20                                                  
CONECT    6    5    7                                                       
CONECT    7    6    8                                                       
CONECT    8    7    9   19                                                  
CONECT    9    8   10                                                       
CONECT   10    9   11   12                                                  
CONECT   11   10                                                            
CONECT   12   10   13   18                                                  
CONECT   13   12   14                                                       
CONECT   14   13   15                                                       
CONECT   15   14   16   17                                                  
CONECT   16   15                                                            
CONECT   17   15   18                                                       
CONECT   18   17   12                                                       
CONECT   19    8   20                                                       
CONECT   20   19    5   21                                                  
CONECT   21   20                                                            
CONECT   22    4   23                                                       
CONECT   23   22   24   25                                                  
CONECT   24   23                                                            
CONECT   25   23    2   26                                                  
CONECT   26   25   27                                                       
CONECT   27   26   28   37                                                  
CONECT   28   27   29                                                       
CONECT   29   28   30   31                                                  
CONECT   30   29                                                            
CONECT   31   29   32   35                                                  
CONECT   32   31   33   34                                                  
CONECT   33   32                                                            
CONECT   34   32                                                            
CONECT   35   31   36   37                                                  
CONECT   36   35                                                            
CONECT   37   35   27   38                                                  
CONECT   38   37                                                            
MASTER        0    0    0    0    0    0    0    0   38    0   82    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₂₅H₃₅N₅O₈

Average Mass

533.5820 Da

Monoisotopic Mass

533.24856 Da

IUPAC Name

4-amino-N-{1-[(2R,4R,5S,6R)-5-{[(1S,2R,3S,4R,5S)-4-(dimethylamino)-2,3,5-trihydroxycyclohexyl]oxy}-4-hydroxy-6-methyloxan-2-yl]-2-hydroxy-1,4-dihydropyrimidin-4-ylidene}benzamide

Traditional Name

4-amino-N-{1-[(2R,4R,5S,6R)-5-{[(1S,2R,3S,4R,5S)-4-(dimethylamino)-2,3,5-trihydroxycyclohexyl]oxy}-4-hydroxy-6-methyloxan-2-yl]-2-hydroxypyrimidin-4-ylidene}benzamide

CAS Registry Number

Not Available

SMILES

C[C@H]1O[C@H](C[C@@H](O)[C@@H]1O[C@H]1C[C@H](O)[C@H]([C@H](O)[C@H]1O)N(C)C)N1C=CC(=NC(=O)C2=CC=C(N)C=C2)N=C1O

InChI Identifier

InChI=1S/C25H35N5O8/c1-12-23(38-17-10-15(31)20(29(2)3)22(34)21(17)33)16(32)11-19(37-12)30-9-8-18(28-25(30)36)27-24(35)13-4-6-14(26)7-5-13/h4-9,12,15-17,19-23,31-34H,10-11,26H2,1-3H3,(H,27,28,35,36)/t12-,15+,16-,17+,19-,20-,21+,22+,23-/m1/s1

InChI Key

NJRKCURACRGUML-IIYKVCNPSA-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
Streptomyces aMAKUSAENSIS	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as aminobenzoic acids and derivatives. These are benzoic acids (or derivative thereof) containing an amine group attached to the benzene moiety.

Kingdom

Organic compounds

Super Class

Benzenoids

Class

Benzene and substituted derivatives

Sub Class

Benzoic acids and derivatives

Direct Parent

Aminobenzoic acids and derivatives

Alternative Parents

Substituents

Aminobenzoic acid or derivatives
Aminocyclitol
Aniline or substituted anilines
Benzoyl
Aminocyclitol or derivatives
Hydroxypyrimidine
Cyclohexylamine
Cyclohexanol
Pyrimidine
Oxane
Hydropyrimidine
Cyclitol or derivatives
Heteroaromatic compound
Cyclic alcohol
Tertiary aliphatic amine
Tertiary amine
Secondary alcohol
Amino acid or derivatives
1,2-aminoalcohol
Oxacycle
Azacycle
Organoheterocyclic compound
Polyol
Ether
Dialkyl ether
Carboxylic acid derivative
Organic nitrogen compound
Organic oxygen compound
Organopnictogen compound
Organic oxide
Hydrocarbon derivative
Primary amine
Organooxygen compound
Organonitrogen compound
Amine
Alcohol
Aromatic heteromonocyclic compound

Molecular Framework

Aromatic 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	-3.7	ChemAxon
pKa (Strongest Acidic)	5.74	ChemAxon
pKa (Strongest Basic)	8.63	ChemAxon
Physiological Charge	1	ChemAxon
Hydrogen Acceptor Count	13	ChemAxon
Hydrogen Donor Count	6	ChemAxon
Polar Surface Area	193.9 Å²	ChemAxon
Rotatable Bond Count	5	ChemAxon
Refractivity	136.08 m³·mol⁻¹	ChemAxon
Polarizability	56.34 Å³	ChemAxon
Number of Rings	4	ChemAxon
Bioavailability	No	ChemAxon
Rule of Five	No	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

113110

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

127483

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

LOTUS database [Link]

Showing NP-Card for 4-amino-n-{1-[(2r,4r,5s,6r)-5-{[(1s,2r,3s,4r,5s)-4-(dimethylamino)-2,3,5-trihydroxycyclohexyl]oxy}-4-hydroxy-6-methyloxan-2-yl]-2-hydroxypyrimidin-4-ylidene}benzamide (NP0193710)

MOL for NP0193710 (4-amino-n-{1-[(2r,4r,5s,6r)-5-{[(1s,2r,3s,4r,5s)-4-(dimethylamino)-2,3,5-trihydroxycyclohexyl]oxy}-4-hydroxy-6-methyloxan-2-yl]-2-hydroxypyrimidin-4-ylidene}benzamide)

3D MOL for NP0193710 (4-amino-n-{1-[(2r,4r,5s,6r)-5-{[(1s,2r,3s,4r,5s)-4-(dimethylamino)-2,3,5-trihydroxycyclohexyl]oxy}-4-hydroxy-6-methyloxan-2-yl]-2-hydroxypyrimidin-4-ylidene}benzamide)

3D SDF for NP0193710 (4-amino-n-{1-[(2r,4r,5s,6r)-5-{[(1s,2r,3s,4r,5s)-4-(dimethylamino)-2,3,5-trihydroxycyclohexyl]oxy}-4-hydroxy-6-methyloxan-2-yl]-2-hydroxypyrimidin-4-ylidene}benzamide)

3D-SDF for NP0193710 (4-amino-n-{1-[(2r,4r,5s,6r)-5-{[(1s,2r,3s,4r,5s)-4-(dimethylamino)-2,3,5-trihydroxycyclohexyl]oxy}-4-hydroxy-6-methyloxan-2-yl]-2-hydroxypyrimidin-4-ylidene}benzamide)

PDB for NP0193710 (4-amino-n-{1-[(2r,4r,5s,6r)-5-{[(1s,2r,3s,4r,5s)-4-(dimethylamino)-2,3,5-trihydroxycyclohexyl]oxy}-4-hydroxy-6-methyloxan-2-yl]-2-hydroxypyrimidin-4-ylidene}benzamide)

3D PDB for NP0193710 (4-amino-n-{1-[(2r,4r,5s,6r)-5-{[(1s,2r,3s,4r,5s)-4-(dimethylamino)-2,3,5-trihydroxycyclohexyl]oxy}-4-hydroxy-6-methyloxan-2-yl]-2-hydroxypyrimidin-4-ylidene}benzamide)

SMILES for NP0193710 (4-amino-n-{1-[(2r,4r,5s,6r)-5-{[(1s,2r,3s,4r,5s)-4-(dimethylamino)-2,3,5-trihydroxycyclohexyl]oxy}-4-hydroxy-6-methyloxan-2-yl]-2-hydroxypyrimidin-4-ylidene}benzamide)

INCHI for NP0193710 (4-amino-n-{1-[(2r,4r,5s,6r)-5-{[(1s,2r,3s,4r,5s)-4-(dimethylamino)-2,3,5-trihydroxycyclohexyl]oxy}-4-hydroxy-6-methyloxan-2-yl]-2-hydroxypyrimidin-4-ylidene}benzamide)

Structure for NP0193710 (4-amino-n-{1-[(2r,4r,5s,6r)-5-{[(1s,2r,3s,4r,5s)-4-(dimethylamino)-2,3,5-trihydroxycyclohexyl]oxy}-4-hydroxy-6-methyloxan-2-yl]-2-hydroxypyrimidin-4-ylidene}benzamide)

3D Structure for NP0193710 (4-amino-n-{1-[(2r,4r,5s,6r)-5-{[(1s,2r,3s,4r,5s)-4-(dimethylamino)-2,3,5-trihydroxycyclohexyl]oxy}-4-hydroxy-6-methyloxan-2-yl]-2-hydroxypyrimidin-4-ylidene}benzamide)