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Showing NP-Card for Cytospotone D (NP0332160)

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Record Information
Version2.0
Created at2023-11-29 08:00:41 UTC
Updated at2026-02-27 12:03:46 UTC
NP-MRD IDNP0332160
Natural Product DOIhttps://doi.org/10.57994/1317
Secondary Accession NumbersNone
Natural Product Identification
Common NameCytospotone D
DescriptionCytospotone D belongs to the class of organic compounds known as cyclohexenones. Cyclohexenones are compounds containing a cylohexenone moiety, which is a six-membered aliphatic ring that carries a ketone and has one endocyclic double bond. Cytospotone D was first documented in 2024 (PMID: 37977303). Based on a literature review very few articles have been published on Cytospotone D.
Structure
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MOLSDFPDBSMILESInChI

MOL for NP0332160 (Cytospotone D)


  Mrv2104 11292308002D          

 12 12  0  0  1  0            999 V2000
   -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
    0.0000    0.8250    0.0000 C   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
    0.7145    1.2375    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.1842    1.8695    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2448    1.8695    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.8250    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    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  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
    0.7145   -1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  2  0  0  0  0
  3  4  1  0  0  0  0
  5  3  1  0  0  0  0
  5  6  1  1  0  0  0
  5  7  1  6  0  0  0
  5  8  1  0  0  0  0
  8  9  1  1  0  0  0
  8 10  1  0  0  0  0
 10 11  1  0  0  0  0
  2 11  1  0  0  0  0
 11 12  2  0  0  0  0
M  END
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3D MOL for NP0332160 (Cytospotone D)

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3D SDF for NP0332160 (Cytospotone D)

  Mrv2104 11292308002D          

 12 12  0  0  1  0            999 V2000
   -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
    0.0000    0.8250    0.0000 C   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
    0.7145    1.2375    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.1842    1.8695    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2448    1.8695    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.8250    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    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  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
    0.7145   -1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  2  0  0  0  0
  3  4  1  0  0  0  0
  5  3  1  0  0  0  0
  5  6  1  1  0  0  0
  5  7  1  6  0  0  0
  5  8  1  0  0  0  0
  8  9  1  1  0  0  0
  8 10  1  0  0  0  0
 10 11  1  0  0  0  0
  2 11  1  0  0  0  0
 11 12  2  0  0  0  0
M  END
> <DATABASE_ID>
NP0332160

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CC1=C(O)[C@](C)(O)[C@@H](O)CC1=O

> <INCHI_IDENTIFIER>
InChI=1S/C8H12O4/c1-4-5(9)3-6(10)8(2,12)7(4)11/h6,10-12H,3H2,1-2H3/t6-,8+/m0/s1

> <INCHI_KEY>
LQQBVYVGDUNGRS-POYBYMJQSA-N

> <FORMULA>
C8H12O4

> <MOLECULAR_WEIGHT>
172.18

> <EXACT_MASS>
172.073558866

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_ATOM_COUNT>
24

> <JCHEM_AVERAGE_POLARIZABILITY>
16.850546214401703

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(4R,5S)-3,4,5-trihydroxy-2,4-dimethylcyclohex-2-en-1-one

> <JCHEM_LOGP>
-0.6585092009999997

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
13.2630537039772

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.254003738573109

> <JCHEM_PKA_STRONGEST_BASIC>
-3.3783453939970527

> <JCHEM_POLAR_SURFACE_AREA>
77.75999999999999

> <JCHEM_REFRACTIVITY>
42.9513

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
(4R,5S)-3,4,5-trihydroxy-2,4-dimethylcyclohex-2-en-1-one

> <JCHEM_VEBER_RULE>
0

$$$$

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3D-SDF for NP0332160 (Cytospotone D)
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PDB for NP0332160 (Cytospotone D)
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      -1.334  -0.770   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       0.000  -0.000   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       0.000   1.540   0.000  0.00  0.00           C+0
HETATM    4  O   UNK     0      -1.334   2.310   0.000  0.00  0.00           O+0
HETATM    5  C   UNK     0       1.334   2.310   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       0.344   3.490   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0       2.324   3.490   0.000  0.00  0.00           O+0
HETATM    8  C   UNK     0       2.667   1.540   0.000  0.00  0.00           C+0
HETATM    9  O   UNK     0       4.001   2.310   0.000  0.00  0.00           O+0
HETATM   10  C   UNK     0       2.667   0.000   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM   12  O   UNK     0       1.334  -2.310   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3   11                                                  
CONECT    3    2    4    5                                                  
CONECT    4    3                                                            
CONECT    5    3    6    7    8                                             
CONECT    6    5                                                            
CONECT    7    5                                                            
CONECT    8    5    9   10                                                  
CONECT    9    8                                                            
CONECT   10    8   11                                                       
CONECT   11   10    2   12                                                  
CONECT   12   11                                                            
MASTER        0    0    0    0    0    0    0    0   12    0   24    0
END

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3D PDB for NP0332160 (Cytospotone D)
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SMILES for NP0332160 (Cytospotone D)
CC1=C(O)[C@](C)(O)[C@@H](O)CC1=O
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INCHI for NP0332160 (Cytospotone D)
InChI=1S/C8H12O4/c1-4-5(9)3-6(10)8(2,12)7(4)11/h6,10-12H,3H2,1-2H3/t6-,8+/m0/s1
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View in JSmol
SynonymsNot Available
Chemical FormulaC8H12O4
Average Mass172.1800 Da
Monoisotopic Mass172.07356 Da
IUPAC Name(4R,5S)-3,4,5-trihydroxy-2,4-dimethylcyclohex-2-en-1-one
Traditional Name(4R,5S)-3,4,5-trihydroxy-2,4-dimethylcyclohex-2-en-1-one
CAS Registry NumberNot Available
SMILES
CC1=C(O)[C@](C)(O)[C@@H](O)CC1=O
InChI Identifier
InChI=1S/C8H12O4/c1-4-5(9)3-6(10)8(2,12)7(4)11/h6,10-12H,3H2,1-2H3/t6-,8+/m0/s1
InChI KeyLQQBVYVGDUNGRS-POYBYMJQSA-N
Experimental Spectra
Spectrum TypeDescriptionDepositor EmailDepositor OrganizationDepositorDeposition DateView
HSQC NMR[1H, 13C] NMR Spectrum (2D, 500 MHz, CD3OD, experimental)mawp1998@163.comSchool of Pharmacy, Guangdong Pharmaceutical UniversityWeipeng Ma2023-11-29View Spectrum
NOESY NMR[1H, 1H] NMR Spectrum (2D, 500 MHz, CD3OD, experimental)mawp1998@163.comSchool of Pharmacy, Guangdong Pharmaceutical UniversityWeipeng Ma2023-11-29View Spectrum
COSY NMR[1H, 1H] NMR Spectrum (2D, 500 MHz, CD3OD, experimental)mawp1998@163.comSchool of Pharmacy, Guangdong Pharmaceutical UniversityWeipeng Ma2023-11-29View Spectrum
1D NMR1H NMR Spectrum (1D, 500 MHz, CD3OD, experimental)mawp1998@163.comSchool of Pharmacy, Guangdong Pharmaceutical UniversityWeipeng Ma2023-11-29View Spectrum
HMBC NMR[1H, 13C] NMR Spectrum (2D, 500 MHz, CD3OD, experimental)mawp1998@163.comSchool of Pharmacy, Guangdong Pharmaceutical UniversityWeipeng Ma2023-11-29View Spectrum
1D NMR13C NMR Spectrum (1D, 126 MHz, CD3OD, experimental)mawp1998@163.comSchool of Pharmacy, Guangdong Pharmaceutical UniversityWeipeng Ma2023-11-29View Spectrum
Predicted Spectra
Spectrum TypeDescriptionDepositor IDDepositor OrganizationDepositorDeposition DateView
Chemical Shift Submissions
Spectrum TypeDescriptionDepositor EmailDepositor OrganizationDepositorDeposition DateView
1D NMR1H NMR Spectrum (1D, 500.0, Methanol-d4, simulated)epoynton@sfu.caNot AvailableNot Available2026-02-27View Spectrum
1D NMR13C NMR Spectrum (1D, 125.0, Methanol-d4, simulated)epoynton@sfu.caNot AvailableNot Available2026-02-27View Spectrum
Species
Species of Origin
Species NameSourceReference
Cytospora sp. A879
      Not Available
Chemical Taxonomy
DescriptionThis compound belongs to the class of organic compounds known as cyclohexenones. These are compounds containing a cylohexenone moiety, which is a six-membered aliphatic ring that carries a ketone and has one endocyclic double bond.
KingdomOrganic compounds  
Super ClassOrganic oxygen compounds  
ClassOrganooxygen compounds  
Sub ClassCarbonyl compounds  
Direct ParentCyclohexenones  
Alternative Parents
Substituents
  • Cyclohexenone
    • 

  • B'-hydroxy-alpha,beta-unsaturated-ketone
    • 

  • Alpha-branched alpha,beta-unsaturated-ketone
    • 

  • Beta-hydroxy ketone
    • 

  • Vinylogous acid
    • 

  • Alpha,beta-unsaturated ketone
    • 

  • Tertiary alcohol
    • 

  • Enone
    • 

  • Acryloyl-group
    • 

  • Secondary alcohol
    • 

  • Organic oxide
    • 

  • Hydrocarbon derivative
    • 

  • Alcohol
    • 

  • Aliphatic homomonocyclic compound
Molecular FrameworkAliphatic homomonocyclic compounds
External DescriptorsNot Available
Physical Properties
StateNot Available
Experimental Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Predicted Properties
PropertyValueSource
logP-0.66ChemAxon
pKa (Strongest Acidic)3.25ChemAxon
pKa (Strongest Basic)-3.4ChemAxon
Physiological Charge-1ChemAxon
Hydrogen Acceptor Count4ChemAxon
Hydrogen Donor Count3ChemAxon
Polar Surface Area77.76 ŲChemAxon
Rotatable Bond Count0ChemAxon
Refractivity42.95 m³·mol⁻¹ChemAxon
Polarizability16.85 ųChemAxon
Number of Rings1ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
HMDB IDNot Available
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FoodDB IDNot Available
KNApSAcK IDNot Available
Chemspider IDNot Available
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem CompoundNot Available
PDB IDNot Available
ChEBI IDNot Available
Good Scents IDNot Available
References
General References
  1. Ma W, Shao Z, Chen Y, Li S, Liu H, Zhang W, Gao X: Cytospotones A-D, four new polyketones from the endophytic fungus Cytospora sp. A879. Fitoterapia. 2024 Mar;173:105751. doi: 10.1016/j.fitote.2023.105751. Epub 2023  Nov 17. [PubMed:37977303  ] 
  2. DOI: 10.1016/j.fitote.2023.105751