NP-MRD: Showing NP-Card for amphicordin B (NP0332014)

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Record Information

Version

2.0

Created at

2023-10-23 12:02:11 UTC

Updated at

2024-09-03 04:17:43 UTC

NP-MRD ID

NP0332014

Natural Product DOI

https://doi.org/10.57994/1142

Secondary Accession Numbers

None

Natural Product Identification

Common Name

amphicordin B

Description

amphicordin B was first documented in 2023 (PMID: 37967166).

Structure

MOL SDF PDB SMILES InChI


  Mrv2104 10232312022D          

 24 26  0  0  1  0            999 V2000
   -1.7111   -3.2502    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
   -1.4289   -1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2414   -2.3317    0.0000 C   0  0  0  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
    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
    0.7145   -3.7125    0.0000 O   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
    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 O   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
    3.1401   -0.8748    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6704   -1.7933    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579   -2.4750    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    3.5724   -2.8875    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724   -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
    2.8579   -4.1250    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
    0.7145   -1.2375    0.0000 C   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 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
  2  4  1  0  0  0  0
  2  5  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  2  0  0  0  0
  7  8  1  0  0  0  0
  7  9  1  0  0  0  0
  9 10  2  0  0  0  0
 10 11  1  0  0  0  0
 11 12  1  0  0  0  0
 12 13  1  0  0  0  0
 12 14  1  0  0  0  0
 15 12  1  0  0  0  0
 15 16  1  6  0  0  0
 16 17  1  0  0  0  0
 17 18  1  0  0  0  0
 17 19  2  0  0  0  0
 15 20  1  0  0  0  0
  9 20  1  0  0  0  0
 10 21  1  0  0  0  0
 21 22  2  0  0  0  0
  6 22  1  0  0  0  0
 22 23  1  0  0  0  0
  3 23  1  0  0  0  0
 23 24  2  0  0  0  0
M  END
> <DATABASE_ID>
NP0332014

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CC(=O)O[C@@H]1CC2=C(OC1(C)C)C=C1C(=O)CC(C)(C)OC1=C2O

> <INCHI_IDENTIFIER>
InChI=1S/C18H22O6/c1-9(19)22-14-7-11-13(23-18(14,4)5)6-10-12(20)8-17(2,3)24-16(10)15(11)21/h6,14,21H,7-8H2,1-5H3/t14-/m1/s1

> <INCHI_KEY>
PGGBXLDXDPDZMW-CQSZACIVSA-N

> <FORMULA>
C18H22O6

> <MOLECULAR_WEIGHT>
334.368

> <EXACT_MASS>
334.141638428

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_ATOM_COUNT>
46

> <JCHEM_AVERAGE_POLARIZABILITY>
35.53115617634147

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
(6R)-9-hydroxy-5,5,12,12-tetramethyl-14-oxo-4,11-dioxatricyclo[8.4.0.0^{3,8}]tetradeca-1,3(8),9-trien-6-yl acetate

> <JCHEM_LOGP>
2.0953096013333323

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
15.731421836236454

> <JCHEM_PKA_STRONGEST_ACIDIC>
9.14381508433281

> <JCHEM_PKA_STRONGEST_BASIC>
-4.629403038562286

> <JCHEM_POLAR_SURFACE_AREA>
82.06

> <JCHEM_REFRACTIVITY>
86.04599999999998

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
(6R)-9-hydroxy-5,5,12,12-tetramethyl-14-oxo-4,11-dioxatricyclo[8.4.0.0^{3,8}]tetradeca-1,3(8),9-trien-6-yl acetate

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 23-OCT-23   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   23-OCT-23         0                                  
HETATM    1  C   UNK     0      -3.194  -6.067   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -2.667  -4.620   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -2.667  -3.080   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -4.184  -4.353   0.000  0.00  0.00           C+0
HETATM    5  O   UNK     0      -1.334  -5.390   0.000  0.00  0.00           O+0
HETATM    6  C   UNK     0       0.000  -4.620   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       1.334  -5.390   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0       1.334  -6.930   0.000  0.00  0.00           O+0
HETATM    9  C   UNK     0       2.667  -4.620   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       2.667  -3.080   0.000  0.00  0.00           C+0
HETATM   11  O   UNK     0       4.001  -2.310   0.000  0.00  0.00           O+0
HETATM   12  C   UNK     0       5.335  -3.080   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       5.861  -1.633   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       6.851  -3.347   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       5.335  -4.620   0.000  0.00  0.00           C+0
HETATM   16  O   UNK     0       6.668  -5.390   0.000  0.00  0.00           O+0
HETATM   17  C   UNK     0       6.668  -6.930   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       8.002  -7.700   0.000  0.00  0.00           C+0
HETATM   19  O   UNK     0       5.335  -7.700   0.000  0.00  0.00           O+0
HETATM   20  C   UNK     0       4.001  -5.390   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0       1.334  -2.310   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0       0.000  -3.080   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0      -1.334  -2.310   0.000  0.00  0.00           C+0
HETATM   24  O   UNK     0      -1.334  -0.770   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3    4    5                                             
CONECT    3    2   23                                                       
CONECT    4    2                                                            
CONECT    5    2    6                                                       
CONECT    6    5    7   22                                                  
CONECT    7    6    8    9                                                  
CONECT    8    7                                                            
CONECT    9    7   10   20                                                  
CONECT   10    9   11   21                                                  
CONECT   11   10   12                                                       
CONECT   12   11   13   14   15                                             
CONECT   13   12                                                            
CONECT   14   12                                                            
CONECT   15   12   16   20                                                  
CONECT   16   15   17                                                       
CONECT   17   16   18   19                                                  
CONECT   18   17                                                            
CONECT   19   17                                                            
CONECT   20   15    9                                                       
CONECT   21   10   22                                                       
CONECT   22   21    6   23                                                  
CONECT   23   22    3   24                                                  
CONECT   24   23                                                            
MASTER        0    0    0    0    0    0    0    0   24    0   52    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₁₈H₂₂O₆

Average Mass

334.3680 Da

Monoisotopic Mass

334.14164 Da

IUPAC Name

(6R)-9-hydroxy-5,5,12,12-tetramethyl-14-oxo-4,11-dioxatricyclo[8.4.0.0^{3,8}]tetradeca-1,3(8),9-trien-6-yl acetate

Traditional Name

(6R)-9-hydroxy-5,5,12,12-tetramethyl-14-oxo-4,11-dioxatricyclo[8.4.0.0^{3,8}]tetradeca-1,3(8),9-trien-6-yl acetate

CAS Registry Number

Not Available

SMILES

CC(=O)O[C@@H]1CC2=C(OC1(C)C)C=C1C(=O)CC(C)(C)OC1=C2O

InChI Identifier

InChI=1S/C18H22O6/c1-9(19)22-14-7-11-13(23-18(14,4)5)6-10-12(20)8-17(2,3)24-16(10)15(11)21/h6,14,21H,7-8H2,1-5H3/t14-/m1/s1

InChI Key

PGGBXLDXDPDZMW-CQSZACIVSA-N

Experimental Spectra

Spectrum Type	Description	Depositor Email	Depositor Organization	Depositor	Deposition Date	View
NOESY NMR	[¹H, ¹H] NMR Spectrum (2D, 400 MHz, CDCl3, experimental)	617572349@qq.com	Not Available	Not Available	2024-05-04	View Spectrum
HSQC NMR	[¹H, ¹³C] NMR Spectrum (2D, 400 MHz, CDCl3, experimental)	617572349@qq.com	Not Available	Not Available	2024-05-04	View Spectrum
HMBC NMR	[¹H, ¹³C] NMR Spectrum (2D, 400 MHz, CDCl3, experimental)	617572349@qq.com	Not Available	Not Available	2024-05-04	View Spectrum
COSY NMR	[¹H, ¹H] NMR Spectrum (2D, 400 MHz, CDCl3, experimental)	617572349@qq.com	Not Available	Not Available	2024-05-04	View Spectrum
1D_DEPT NMR	¹³C NMR Spectrum (1D, 101 MHz, CDCl3, experimental)	617572349@qq.com	Not Available	Not Available	2024-05-04	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, CDCl3, experimental)	617572349@qq.com	Not Available	Not Available	2024-05-04	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 101 MHz, CDCl3, experimental)	617572349@qq.com	Not Available	Not Available	2024-05-04	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	¹H NMR Spectrum (1D, 400, CDCl₃, simulated)	617572349@qq.com	SYSU	jiangmh	2024-05-04	View Spectrum

Species

Species of Origin

Species Name	Source	Reference
felina		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	2.1	ChemAxon
pKa (Strongest Acidic)	9.14	ChemAxon
pKa (Strongest Basic)	-4.6	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	5	ChemAxon
Hydrogen Donor Count	1	ChemAxon
Polar Surface Area	82.06 Å²	ChemAxon
Rotatable Bond Count	2	ChemAxon
Refractivity	86.05 m³·mol⁻¹	ChemAxon
Polarizability	35.53 Å³	ChemAxon
Number of Rings	3	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

Not Available

References

General References

Not Available

Showing NP-Card for amphicordin B (NP0332014)

MOL for NP0332014 (amphicordin B)

3D MOL for NP0332014 (amphicordin B)

3D SDF for NP0332014 (amphicordin B)

3D-SDF for NP0332014 (amphicordin B)

PDB for NP0332014 (amphicordin B)

3D PDB for NP0332014 (amphicordin B)

SMILES for NP0332014 (amphicordin B)

INCHI for NP0332014 (amphicordin B)

Structure for NP0332014 (amphicordin B)

3D Structure for NP0332014 (amphicordin B)