NP-MRD: Showing NP-Card for Cytospotone C (NP0332163)

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Record Information

Version

1.0

Created at

2023-11-29 08:06:14 UTC

Updated at

2024-04-19 10:01:40 UTC

NP-MRD ID

NP0332163

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Cytospotone C

Description

Not Available

Structure

MOL SDF PDB SMILES InChI


  Mrv2104 11292308062D          

 18 18  0  0  1  0            999 V2000
    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 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
    2.1434   -2.8875    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.1434   -3.7125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579   -2.4750    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.8579   -1.6500    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724   -2.8875    0.0000 C   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
    4.2868   -1.6500    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
    5.0013   -2.8875    0.0000 C   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
    5.7158   -1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0013   -3.7125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2868   -4.1250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2868   -4.9500    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724   -3.7125    0.0000 O   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
  4  3  1  0  0  0  0
  4  5  1  6  0  0  0
  4  6  1  0  0  0  0
  6  7  1  1  0  0  0
  6  8  1  0  0  0  0
  8  9  2  0  0  0  0
  9 10  1  0  0  0  0
 10 11  1  0  0  0  0
  9 12  1  0  0  0  0
 12 13  1  0  0  0  0
 13 14  1  0  0  0  0
 12 15  2  0  0  0  0
 15 16  1  0  0  0  0
 16 17  2  0  0  0  0
 16 18  1  0  0  0  0
  8 18  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0332163

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CCC[C@@H](O)[C@@H](O)C1=C(CO)C(OC)=CC(=O)O1

> <INCHI_IDENTIFIER>
InChI=1S/C12H18O6/c1-3-4-8(14)11(16)12-7(6-13)9(17-2)5-10(15)18-12/h5,8,11,13-14,16H,3-4,6H2,1-2H3/t8-,11-/m1/s1

> <INCHI_KEY>
YCOXTKWBRHCFKY-LDYMZIIASA-N

> <FORMULA>
C12H18O6

> <MOLECULAR_WEIGHT>
258.27

> <EXACT_MASS>
258.1103383

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_ATOM_COUNT>
36

> <JCHEM_AVERAGE_POLARIZABILITY>
25.593937215741754

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
6-[(1R,2R)-1,2-dihydroxypentyl]-5-(hydroxymethyl)-4-methoxy-2H-pyran-2-one

> <JCHEM_LOGP>
-0.6690796699999996

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
14.629974881321754

> <JCHEM_PKA_STRONGEST_ACIDIC>
12.827753614010003

> <JCHEM_PKA_STRONGEST_BASIC>
-2.8363643377999423

> <JCHEM_POLAR_SURFACE_AREA>
96.22000000000001

> <JCHEM_REFRACTIVITY>
65.66480000000001

> <JCHEM_ROTATABLE_BOND_COUNT>
6

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
6-[(1R,2R)-1,2-dihydroxypentyl]-5-(hydroxymethyl)-4-methoxypyran-2-one

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 29-NOV-23   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   29-NOV-23         0                                  
HETATM    1  C   UNK     0       0.000  -4.620   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       1.334  -5.390   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       2.667  -4.620   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       4.001  -5.390   0.000  0.00  0.00           C+0
HETATM    5  O   UNK     0       4.001  -6.930   0.000  0.00  0.00           O+0
HETATM    6  C   UNK     0       5.335  -4.620   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0       5.335  -3.080   0.000  0.00  0.00           O+0
HETATM    8  C   UNK     0       6.668  -5.390   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       8.002  -4.620   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       8.002  -3.080   0.000  0.00  0.00           C+0
HETATM   11  O   UNK     0       9.336  -2.310   0.000  0.00  0.00           O+0
HETATM   12  C   UNK     0       9.336  -5.390   0.000  0.00  0.00           C+0
HETATM   13  O   UNK     0      10.669  -4.620   0.000  0.00  0.00           O+0
HETATM   14  C   UNK     0      10.669  -3.080   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       9.336  -6.930   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       8.002  -7.700   0.000  0.00  0.00           C+0
HETATM   17  O   UNK     0       8.002  -9.240   0.000  0.00  0.00           O+0
HETATM   18  O   UNK     0       6.668  -6.930   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4                                                       
CONECT    4    3    5    6                                                  
CONECT    5    4                                                            
CONECT    6    4    7    8                                                  
CONECT    7    6                                                            
CONECT    8    6    9   18                                                  
CONECT    9    8   10   12                                                  
CONECT   10    9   11                                                       
CONECT   11   10                                                            
CONECT   12    9   13   15                                                  
CONECT   13   12   14                                                       
CONECT   14   13                                                            
CONECT   15   12   16                                                       
CONECT   16   15   17   18                                                  
CONECT   17   16                                                            
CONECT   18   16    8                                                       
MASTER        0    0    0    0    0    0    0    0   18    0   36    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₁₂H₁₈O₆

Average Mass

258.2700 Da

Monoisotopic Mass

258.11034 Da

IUPAC Name

6-[(1R,2R)-1,2-dihydroxypentyl]-5-(hydroxymethyl)-4-methoxy-2H-pyran-2-one

Traditional Name

6-[(1R,2R)-1,2-dihydroxypentyl]-5-(hydroxymethyl)-4-methoxypyran-2-one

CAS Registry Number

Not Available

SMILES

CCC[C@@H](O)[C@@H](O)C1=C(CO)C(OC)=CC(=O)O1

InChI Identifier

InChI=1S/C12H18O6/c1-3-4-8(14)11(16)12-7(6-13)9(17-2)5-10(15)18-12/h5,8,11,13-14,16H,3-4,6H2,1-2H3/t8-,11-/m1/s1

InChI Key

YCOXTKWBRHCFKY-LDYMZIIASA-N

Experimental Spectra

Spectrum Type	Description	Depositor Email	Depositor Organization	Depositor	Deposition Date	View
HSQC NMR	[¹H, ¹³C] NMR Spectrum (2D, 500 MHz, CD3OD, experimental)	mawp1998@163.com	School of Pharmacy, Guangdong Pharmaceutical University	Weipeng Ma	2023-11-29	View Spectrum
NOESY NMR	[¹H, ¹H] NMR Spectrum (2D, 500 MHz, CD3OD, experimental)	mawp1998@163.com	School of Pharmacy, Guangdong Pharmaceutical University	Weipeng Ma	2023-11-29	View Spectrum
1D NMR	[¹H, ] NMR Spectrum (2D, 500 MHz, CD3OD, experimental)	mawp1998@163.com	School of Pharmacy, Guangdong Pharmaceutical University	Weipeng Ma	2023-11-29	View Spectrum
COSY NMR	[¹H, ¹H] NMR Spectrum (2D, 500 MHz, CD3OD, experimental)	mawp1998@163.com	School of Pharmacy, Guangdong Pharmaceutical University	Weipeng Ma	2023-11-29	View Spectrum
1D NMR	[¹³C, ] NMR Spectrum (2D, 126 MHz, CD3OD, experimental)	mawp1998@163.com	School of Pharmacy, Guangdong Pharmaceutical University	Weipeng Ma	2023-11-29	View Spectrum
HMBC NMR	[¹H, ¹³C] NMR Spectrum (2D, 500 MHz, CD3OD, experimental)	mawp1998@163.com	School of Pharmacy, Guangdong Pharmaceutical University	Weipeng Ma	2023-11-29	View Spectrum

Predicted Spectra

Not Available

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	-0.67	ChemAxon
pKa (Strongest Acidic)	12.83	ChemAxon
pKa (Strongest Basic)	-2.8	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	5	ChemAxon
Hydrogen Donor Count	3	ChemAxon
Polar Surface Area	96.22 Å²	ChemAxon
Rotatable Bond Count	6	ChemAxon
Refractivity	65.66 m³·mol⁻¹	ChemAxon
Polarizability	25.59 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 Cytospotone C (NP0332163)

MOL for NP0332163 (Cytospotone C)

3D MOL for NP0332163 (Cytospotone C)

3D SDF for NP0332163 (Cytospotone C)

3D-SDF for NP0332163 (Cytospotone C)

PDB for NP0332163 (Cytospotone C)

3D PDB for NP0332163 (Cytospotone C)

SMILES for NP0332163 (Cytospotone C)

INCHI for NP0332163 (Cytospotone C)

Structure for NP0332163 (Cytospotone C)

3D Structure for NP0332163 (Cytospotone C)