NP-MRD: Showing NP-Card for epiketide C (NP0350836)

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Record Information

Version

2.0

Created at

2025-03-14 03:50:50 UTC

Updated at

2025-03-16 00:03:40 UTC

NP-MRD ID

NP0350836

Natural Product DOI

https://doi.org/10.57994/3821

Secondary Accession Numbers

None

Natural Product Identification

Common Name

epiketide C

Description

epiketide C was first documented in 2025 (PMID: 40062959). Based on a literature review very few articles have been published on epiketide C.

Structure

MOL SDF PDB SMILES InChI


  Mrv2104 06112303572D          

 14 14  0  0  1  0            999 V2000
   -1.4289   -1.6500    0.0000 C   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
   -0.7145   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4289   -0.0000    0.0000 O   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   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.0000    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
    0.7145    1.2375    0.0000 C   0  0  1  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
    0.3272    1.9659    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434    1.2375    0.0000 C   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
  3  4  1  0  0  0  0
  3  5  2  0  0  0  0
  5  6  1  0  0  0  0
  6  7  2  0  0  0  0
  5  8  1  0  0  0  0
  8  9  1  0  0  0  0
 10  9  1  0  0  0  0
 10 11  1  0  0  0  0
 11  6  1  0  0  0  0
 11 12  1  6  0  0  0
 11 13  1  1  0  0  0
 10 14  1  1  0  0  0
M  END
> <DATABASE_ID>
NP0350836

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CC\C(O)=C1/CO[C@H](C)[C@@](C)(O)C1=O

> <INCHI_IDENTIFIER>
InChI=1S/C10H16O4/c1-4-8(11)7-5-14-6(2)10(3,13)9(7)12/h6,11,13H,4-5H2,1-3H3/b8-7-/t6-,10-/m1/s1

> <INCHI_KEY>
QFEGZSCPNHWEHO-ZRPKAMAHSA-N

> <FORMULA>
C10H16O4

> <MOLECULAR_WEIGHT>
200.234

> <EXACT_MASS>
200.104858995

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_ATOM_COUNT>
30

> <JCHEM_AVERAGE_POLARIZABILITY>
20.57311277080308

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
(2R,3R,5Z)-3-hydroxy-5-(1-hydroxypropylidene)-2,3-dimethyloxan-4-one

> <JCHEM_LOGP>
0.6974521613333337

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
12.913203385847813

> <JCHEM_PKA_STRONGEST_ACIDIC>
9.239223127215809

> <JCHEM_PKA_STRONGEST_BASIC>
-3.9796440659301164

> <JCHEM_POLAR_SURFACE_AREA>
66.76

> <JCHEM_REFRACTIVITY>
52.6569

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
(2R,3R,5Z)-3-hydroxy-5-(1-hydroxypropylidene)-2,3-dimethyloxan-4-one

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 11-JUN-23   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   11-JUN-23         0                                  
HETATM    1  C   UNK     0      -2.667  -3.080   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  C   UNK     0      -1.334  -0.770   0.000  0.00  0.00           C+0
HETATM    4  O   UNK     0      -2.667  -0.000   0.000  0.00  0.00           O+0
HETATM    5  C   UNK     0       0.000  -0.000   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       0.000   1.540   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0      -1.334   2.310   0.000  0.00  0.00           O+0
HETATM    8  C   UNK     0       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM    9  O   UNK     0       2.667   0.000   0.000  0.00  0.00           O+0
HETATM   10  C   UNK     0       2.667   1.540   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       1.334   2.310   0.000  0.00  0.00           C+0
HETATM   12  O   UNK     0       2.057   3.670   0.000  0.00  0.00           O+0
HETATM   13  C   UNK     0       0.611   3.670   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       4.001   2.310   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4    5                                                  
CONECT    4    3                                                            
CONECT    5    3    6    8                                                  
CONECT    6    5    7   11                                                  
CONECT    7    6                                                            
CONECT    8    5    9                                                       
CONECT    9    8   10                                                       
CONECT   10    9   11   14                                                  
CONECT   11   10    6   12   13                                             
CONECT   12   11                                                            
CONECT   13   11                                                            
CONECT   14   10                                                            
MASTER        0    0    0    0    0    0    0    0   14    0   28    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₁₀H₁₆O₄

Average Mass

200.2340 Da

Monoisotopic Mass

200.10486 Da

IUPAC Name

(2R,3R,5Z)-3-hydroxy-5-(1-hydroxypropylidene)-2,3-dimethyloxan-4-one

Traditional Name

(2R,3R,5Z)-3-hydroxy-5-(1-hydroxypropylidene)-2,3-dimethyloxan-4-one

CAS Registry Number

Not Available

SMILES

CC\C(O)=C1/CO[C@H](C)[C@@](C)(O)C1=O

InChI Identifier

InChI=1S/C10H16O4/c1-4-8(11)7-5-14-6(2)10(3,13)9(7)12/h6,11,13H,4-5H2,1-3H3/b8-7-/t6-,10-/m1/s1

InChI Key

QFEGZSCPNHWEHO-ZRPKAMAHSA-N

Experimental Spectra

Spectrum Type	Description	Depositor Email	Depositor Organization	Depositor	Deposition Date	View
ROESY NMR	[¹H, ¹H] NMR Spectrum (2D, 500 MHz, CD3OD, experimental)	zhanganxin19950802@163.com	chinese academy of science	Zhang Anxin	2025-03-14	View Spectrum
HMBC NMR	[¹H, ¹³C] NMR Spectrum (2D, 500 MHz, CD3OD, experimental)	zhanganxin19950802@163.com	chinese academy of science	Zhang Anxin	2025-03-14	View Spectrum
HSQC NMR	[¹H, ¹³C] NMR Spectrum (2D, 500 MHz, CD3OD, experimental)	zhanganxin19950802@163.com	chinese academy of science	Zhang Anxin	2025-03-14	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, CD3OD, experimental)	zhanganxin19950802@163.com	chinese academy of science	Zhang Anxin	2025-03-14	View Spectrum
COSY NMR	[¹H, ¹H] NMR Spectrum (2D, 500 MHz, CD3OD, experimental)	zhanganxin19950802@163.com	chinese academy of science	Zhang Anxin	2025-03-14	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 126 MHz, CD3OD, experimental)	zhanganxin19950802@163.com	chinese academy of science	Zhang Anxin	2025-03-14	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 125.751504144 MHz, CD₃OD, experimental)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum

Predicted Spectra

Spectrum Type	Description	Depositor ID	Depositor Organization	Depositor	Deposition Date	View

Chemical Shift Submissions

Spectrum Type	Description	Depositor Email	Depositor Organization	Depositor	Deposition Date	View
1D NMR	¹³C NMR Spectrum (1D, 125.751504144, CD₃OD, simulated)	zhanganxin19950802@163.com	chinese academy of science	Zhang Anxin	2025-03-14	View Spectrum

Species

Species of Origin

Species Name	Source	Reference
Epicoccum dendrobii		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	0.7	ChemAxon
pKa (Strongest Acidic)	9.24	ChemAxon
pKa (Strongest Basic)	-4	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	4	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	66.76 Å²	ChemAxon
Rotatable Bond Count	1	ChemAxon
Refractivity	52.66 m³·mol⁻¹	ChemAxon
Polarizability	20.57 Å³	ChemAxon
Number of Rings	1	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

Not Available

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Zhang A, Xu X, Yin WB: Genome Mining of Epicoccum dendrobii Reveals Diverse Antimicrobial Natural Products. J Agric Food Chem. 2025 Mar 10. doi: 10.1021/acs.jafc.4c11808. [PubMed:40062959 ]
DOI: 10.1021/acs.jafc.4c11808
PMID: 40062959

Showing NP-Card for epiketide C (NP0350836)

MOL for NP0350836 (epiketide C)

3D MOL for NP0350836 (epiketide C)

3D SDF for NP0350836 (epiketide C)

3D-SDF for NP0350836 (epiketide C)

PDB for NP0350836 (epiketide C)

3D PDB for NP0350836 (epiketide C)

SMILES for NP0350836 (epiketide C)

INCHI for NP0350836 (epiketide C)

Structure for NP0350836 (epiketide C)

3D Structure for NP0350836 (epiketide C)