NP-MRD: Showing NP-Card for epiketide D (NP0350837)

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Record Information

Version

2.0

Created at

2025-03-14 03:53:50 UTC

Updated at

2025-03-16 00:03:42 UTC

NP-MRD ID

NP0350837

Natural Product DOI

https://doi.org/10.57994/3822

Secondary Accession Numbers

None

Natural Product Identification

Common Name

epiketide D

Description

Epiketide D belongs to the class of organic compounds known as pyranones and derivatives. Pyranones and derivatives are compounds containing a pyran ring which bears a ketone. epiketide D was first documented in 2025 (PMID: 40062959). Based on a literature review very few articles have been published on epiketide D.

Structure

MOL SDF PDB SMILES InChI


  Mrv2104 06112304002D          

 16 17  0  0  1  0            999 V2000
    0.5303    0.6320    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000   -0.0000    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.7145   -0.4125    0.0000 C   0  0  2  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
    0.0000   -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
    2.1434   -0.4125    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
    2.8579   -1.6500    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 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579   -0.0000    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
   -0.5303    0.6320    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  1  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  2  0  0  0  0
  2  7  1  0  0  0  0
  7  8  1  0  0  0  0
  8  9  1  0  0  0  0
  9 10  1  0  0  0  0
 10 11  1  0  0  0  0
 10 12  2  0  0  0  0
  6 12  1  0  0  0  0
 12 13  1  0  0  0  0
  9 14  2  0  0  0  0
  3 15  1  6  0  0  0
  2 16  1  6  0  0  0
M  END
> <DATABASE_ID>
NP0350837

> <DATABASE_NAME>
NP-MRD

> <SMILES>
C[C@H]1OCC2=C(OC(=O)C(C)=C2O)[C@]1(C)O

> <INCHI_IDENTIFIER>
InChI=1S/C11H14O5/c1-5-8(12)7-4-15-6(2)11(3,14)9(7)16-10(5)13/h6,12,14H,4H2,1-3H3/t6-,11-/m1/s1

> <INCHI_KEY>
LORTWVPBXJUYJM-KSBSHMNSSA-N

> <FORMULA>
C11H14O5

> <MOLECULAR_WEIGHT>
226.228

> <EXACT_MASS>
226.084123551

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_ATOM_COUNT>
30

> <JCHEM_AVERAGE_POLARIZABILITY>
22.190924684854373

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
(7R,8R)-4,8-dihydroxy-3,7,8-trimethyl-2H,5H,7H,8H-pyrano[3,2-c]pyran-2-one

> <JCHEM_LOGP>
0.08883261066666714

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
12.967304636745418

> <JCHEM_PKA_STRONGEST_ACIDIC>
6.781246762353256

> <JCHEM_PKA_STRONGEST_BASIC>
-3.7843317938746996

> <JCHEM_POLAR_SURFACE_AREA>
75.99000000000001

> <JCHEM_REFRACTIVITY>
57.2738

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
(7R,8R)-4,8-dihydroxy-3,7,8-trimethyl-5H,7H-pyrano[3,2-c]pyran-2-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  O   UNK     0       0.990   1.180   0.000  0.00  0.00           O+0
HETATM    2  C   UNK     0       0.000  -0.000   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      -1.334  -2.310   0.000  0.00  0.00           O+0
HETATM    5  C   UNK     0       0.000  -3.080   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       1.334  -2.310   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0       2.667  -0.000   0.000  0.00  0.00           O+0
HETATM    9  C   UNK     0       4.001  -0.770   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       4.001  -2.310   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       5.335  -3.080   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       2.667  -3.080   0.000  0.00  0.00           C+0
HETATM   13  O   UNK     0       2.667  -4.620   0.000  0.00  0.00           O+0
HETATM   14  O   UNK     0       5.335  -0.000   0.000  0.00  0.00           O+0
HETATM   15  C   UNK     0      -2.667  -0.000   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0      -0.990   1.180   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3    7   16                                             
CONECT    3    2    4   15                                                  
CONECT    4    3    5                                                       
CONECT    5    4    6                                                       
CONECT    6    5    7   12                                                  
CONECT    7    6    2    8                                                  
CONECT    8    7    9                                                       
CONECT    9    8   10   14                                                  
CONECT   10    9   11   12                                                  
CONECT   11   10                                                            
CONECT   12   10    6   13                                                  
CONECT   13   12                                                            
CONECT   14    9                                                            
CONECT   15    3                                                            
CONECT   16    2                                                            
MASTER        0    0    0    0    0    0    0    0   16    0   34    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₁₁H₁₄O₅

Average Mass

226.2280 Da

Monoisotopic Mass

226.08412 Da

IUPAC Name

(7R,8R)-4,8-dihydroxy-3,7,8-trimethyl-2H,5H,7H,8H-pyrano[3,2-c]pyran-2-one

Traditional Name

(7R,8R)-4,8-dihydroxy-3,7,8-trimethyl-5H,7H-pyrano[3,2-c]pyran-2-one

CAS Registry Number

Not Available

SMILES

C[C@H]1OCC2=C(OC(=O)C(C)=C2O)[C@]1(C)O

InChI Identifier

InChI=1S/C11H14O5/c1-5-8(12)7-4-15-6(2)11(3,14)9(7)16-10(5)13/h6,12,14H,4H2,1-3H3/t6-,11-/m1/s1

InChI Key

LORTWVPBXJUYJM-KSBSHMNSSA-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
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
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
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

Description

This compound belongs to the class of organic compounds known as pyranones and derivatives. These are compounds containing a pyran ring which bears a ketone.

Kingdom

Organic compounds

Super Class

Organoheterocyclic compounds

Class

Pyrans

Sub Class

Pyranones and derivatives

Direct Parent

Pyranones and derivatives

Alternative Parents

Substituents

Pyranone
Fatty acid ester
Fatty acyl
Heteroaromatic compound
Vinylogous acid
Alpha,beta-unsaturated carboxylic ester
Enoate ester
Tertiary alcohol
Enol ester
Lactone
Carboxylic acid ester
Oxacycle
Ether
Dialkyl ether
Carboxylic acid derivative
Organic oxygen compound
Organic oxide
Hydrocarbon derivative
Organooxygen compound
Alcohol
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic heteropolycyclic 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	0.089	ChemAxon
pKa (Strongest Acidic)	6.78	ChemAxon
pKa (Strongest Basic)	-3.8	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	4	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	75.99 Å²	ChemAxon
Rotatable Bond Count	0	ChemAxon
Refractivity	57.27 m³·mol⁻¹	ChemAxon
Polarizability	22.19 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

54749910

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 D (NP0350837)

MOL for NP0350837 (epiketide D)

3D MOL for NP0350837 (epiketide D)

3D SDF for NP0350837 (epiketide D)

3D-SDF for NP0350837 (epiketide D)

PDB for NP0350837 (epiketide D)

3D PDB for NP0350837 (epiketide D)

SMILES for NP0350837 (epiketide D)

INCHI for NP0350837 (epiketide D)

Structure for NP0350837 (epiketide D)

3D Structure for NP0350837 (epiketide D)