NP-MRD: Showing NP-Card for Agglopyranone B (NP0350673)

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Record Information

Version

2.0

Created at

2025-01-28 06:49:15 UTC

Updated at

2025-07-30 22:23:14 UTC

NP-MRD ID

NP0350673

Natural Product DOI

https://doi.org/10.57994/3652

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Agglopyranone B

Description

Based on a literature review very few articles have been published on dichlorpyranonemycin B.

Structure

MOL SDF PDB SMILES InChI


  Mrv2104 04272306572D          

 19 19  0  0  1  0            999 V2000
    0.7145    2.0625    0.0000 O   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
    1.4289    0.8250    0.0000 C   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
    2.1434   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579   -0.0000    0.0000 Cl  0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -1.2375    0.0000 Cl  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
    0.0000    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  2  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
   -0.7145   -1.2375    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
   -2.1434   -1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4289   -2.4750    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.7145   -2.8875    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1434   -2.8875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1434   -3.7125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.8250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0  0  0  0
  2  3  1  0  0  0  0
  3  4  2  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  5  7  1  0  0  0  0
  4  8  1  0  0  0  0
  8  9  2  0  0  0  0
 10  9  1  0  0  0  0
 10 11  1  1  0  0  0
 10 12  1  0  0  0  0
 12 13  2  0  0  0  0
 13 14  1  0  0  0  0
 15 13  1  0  0  0  0
 15 16  1  1  0  0  0
 15 17  1  0  0  0  0
 17 18  1  0  0  0  0
  9 19  1  0  0  0  0
  2 19  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0350673

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CC[C@H](O)C(\C)=C\[C@@H](O)C1=CC(=CC(=O)O1)C(Cl)Cl

> <INCHI_IDENTIFIER>
InChI=1S/C13H16Cl2O4/c1-3-9(16)7(2)4-10(17)11-5-8(13(14)15)6-12(18)19-11/h4-6,9-10,13,16-17H,3H2,1-2H3/b7-4+/t9-,10+/m0/s1

> <INCHI_KEY>
OMROSWUGSFEYFE-JDWDQXLLSA-N

> <FORMULA>
C13H16Cl2O4

> <MOLECULAR_WEIGHT>
307.17

> <EXACT_MASS>
306.0425644

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_ATOM_COUNT>
35

> <JCHEM_AVERAGE_POLARIZABILITY>
29.502816634587422

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
4-(dichloromethyl)-6-[(1R,2E,4S)-1,4-dihydroxy-3-methylhex-2-en-1-yl]-2H-pyran-2-one

> <JCHEM_LOGP>
1.9664069053333337

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
14.664484607115332

> <JCHEM_PKA_STRONGEST_ACIDIC>
13.448267107332695

> <JCHEM_PKA_STRONGEST_BASIC>
-2.964521564266718

> <JCHEM_POLAR_SURFACE_AREA>
66.76

> <JCHEM_REFRACTIVITY>
77.12599999999999

> <JCHEM_ROTATABLE_BOND_COUNT>
5

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
4-(dichloromethyl)-6-[(1R,2E,4S)-1,4-dihydroxy-3-methylhex-2-en-1-yl]pyran-2-one

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 27-APR-23   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   27-APR-23         0                                  
HETATM    1  O   UNK     0       1.334   3.850   0.000  0.00  0.00           O+0
HETATM    2  C   UNK     0       1.334   2.310   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       2.667   1.540   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       2.667  -0.000   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       4.001  -0.770   0.000  0.00  0.00           C+0
HETATM    6 Cl   UNK     0       5.335  -0.000   0.000  0.00  0.00          Cl+0
HETATM    7 Cl   UNK     0       4.001  -2.310   0.000  0.00  0.00          Cl+0
HETATM    8  C   UNK     0       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      -1.334  -0.770   0.000  0.00  0.00           C+0
HETATM   11  O   UNK     0      -2.667   0.000   0.000  0.00  0.00           O+0
HETATM   12  C   UNK     0      -1.334  -2.310   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      -2.667  -3.080   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
HETATM   15  C   UNK     0      -2.667  -4.620   0.000  0.00  0.00           C+0
HETATM   16  O   UNK     0      -1.334  -5.390   0.000  0.00  0.00           O+0
HETATM   17  C   UNK     0      -4.001  -5.390   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0      -4.001  -6.930   0.000  0.00  0.00           C+0
HETATM   19  O   UNK     0       0.000   1.540   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3   19                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5    8                                                  
CONECT    5    4    6    7                                                  
CONECT    6    5                                                            
CONECT    7    5                                                            
CONECT    8    4    9                                                       
CONECT    9    8   10   19                                                  
CONECT   10    9   11   12                                                  
CONECT   11   10                                                            
CONECT   12   10   13                                                       
CONECT   13   12   14   15                                                  
CONECT   14   13                                                            
CONECT   15   13   16   17                                                  
CONECT   16   15                                                            
CONECT   17   15   18                                                       
CONECT   18   17                                                            
CONECT   19    9    2                                                       
MASTER        0    0    0    0    0    0    0    0   19    0   38    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₁₃H₁₆Cl₂O₄

Average Mass

307.1700 Da

Monoisotopic Mass

306.04256 Da

IUPAC Name

4-(dichloromethyl)-6-[(1R,2E,4S)-1,4-dihydroxy-3-methylhex-2-en-1-yl]-2H-pyran-2-one

Traditional Name

4-(dichloromethyl)-6-[(1R,2E,4S)-1,4-dihydroxy-3-methylhex-2-en-1-yl]pyran-2-one

CAS Registry Number

Not Available

SMILES

CC[C@H](O)C(\C)=C\[C@@H](O)C1=CC(=CC(=O)O1)C(Cl)Cl

InChI Identifier

InChI=1S/C13H16Cl2O4/c1-3-9(16)7(2)4-10(17)11-5-8(13(14)15)6-12(18)19-11/h4-6,9-10,13,16-17H,3H2,1-2H3/b7-4+/t9-,10+/m0/s1

InChI Key

OMROSWUGSFEYFE-JDWDQXLLSA-N

Experimental Spectra

Spectrum Type	Description	Depositor Email	Depositor Organization	Depositor	Deposition Date	View
NOESY NMR	[¹H, ¹H] NMR Spectrum (2D, 600 MHz, CDCl3, experimental)	doudou_dong@sjtu.edu.cn	Shanghai Jiao Tong University	Doudou_Dong	2025-01-28	View Spectrum
COSY NMR	[¹H, ¹H] NMR Spectrum (2D, 600 MHz, CDCl3, experimental)	doudou_dong@sjtu.edu.cn	Shanghai Jiao Tong University	Doudou_Dong	2025-01-28	View Spectrum
HSQC NMR	[¹H, ¹³C] NMR Spectrum (2D, 600 MHz, CDCl3, experimental)	doudou_dong@sjtu.edu.cn	Shanghai Jiao Tong University	Doudou_Dong	2025-01-28	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, CDCl3, experimental)	doudou_dong@sjtu.edu.cn	Shanghai Jiao Tong University	Doudou_Dong	2025-01-28	View Spectrum
HMBC NMR	[¹H, ¹³C] NMR Spectrum (2D, 600 MHz, CDCl3, experimental)	doudou_dong@sjtu.edu.cn	Shanghai Jiao Tong University	Doudou_Dong	2025-01-28	View Spectrum
1D_DEPT NMR	¹³C NMR Spectrum (1D, 151 MHz, CDCl3, experimental)	doudou_dong@sjtu.edu.cn	Shanghai Jiao Tong University	Doudou_Dong	2025-01-28	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 151 MHz, CDCl3, experimental)	doudou_dong@sjtu.edu.cn	Shanghai Jiao Tong University	Doudou_Dong	2025-01-28	View Spectrum

Predicted Spectra

Spectrum Type	Description	Depositor ID	Depositor Organization	Depositor	Deposition Date	View

Chemical Shift Submissions

Not Available

Species

Species of Origin

Species Name	Source	Reference
Streptomyces sp. agglomeratus 5-2-6		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	1.97	ChemAxon
pKa (Strongest Acidic)	13.45	ChemAxon
pKa (Strongest Basic)	-3	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	3	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	66.76 Å²	ChemAxon
Rotatable Bond Count	5	ChemAxon
Refractivity	77.13 m³·mol⁻¹	ChemAxon
Polarizability	29.5 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

Showing NP-Card for Agglopyranone B (NP0350673)

MOL for NP0350673 (Agglopyranone B)

3D MOL for NP0350673 (Agglopyranone B)

3D SDF for NP0350673 (Agglopyranone B)

3D-SDF for NP0350673 (Agglopyranone B)

PDB for NP0350673 (Agglopyranone B)

3D PDB for NP0350673 (Agglopyranone B)

SMILES for NP0350673 (Agglopyranone B)

INCHI for NP0350673 (Agglopyranone B)

Structure for NP0350673 (Agglopyranone B)

3D Structure for NP0350673 (Agglopyranone B)