NP-MRD: Showing NP-Card for Acidonemycin B (NP0331895)

Jump To Section:

Identification Spectra BioTaxonomy ChemoTaxonomy Physical properties Links References XML

Record Information

Version

2.0

Created at

2023-09-27 04:14:21 UTC

Updated at

2024-09-03 04:17:20 UTC

NP-MRD ID

NP0331895

Natural Product DOI

https://doi.org/10.57994/1001

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Acidonemycin B

Description

Not Available

Structure

MOL SDF PDB SMILES InChI


  Mrv2104 09272304142D          

 36 40  0  0  1  0            999 V2000
    5.0352   -0.2111    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.3052    0.5684    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.7651    1.1921    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9550    1.0361    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6850    0.2566    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2251   -0.3671    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8748    0.1007    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6048   -0.6789    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.3347    0.7243    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6048    1.5039    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4149    1.6598    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6850    2.4393    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.0647    2.1275    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2546    1.9716    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9845    1.1921    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5246    0.5684    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2546   -0.2111    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7946   -0.8348    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.4444   -0.3671    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0957    0.2566    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.1744    1.0361    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9058    0.1007    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0352    1.9716    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.8453    2.1275    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    6.1154    2.9071    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.9255    3.0630    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.4656    2.4393    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    7.1955    1.6598    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    6.3854    1.5039    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    6.1154    0.7243    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.7356    1.0361    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    8.2757    2.5952    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.1955    3.8425    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.6555    4.4662    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    8.0057    3.9984    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    8.2757    4.7780    0.0000 C   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  2  0  0  0  0
  1  6  1  0  0  0  0
  5  7  1  0  0  0  0
  7  8  2  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
  4 11  1  0  0  0  0
 11 12  2  0  0  0  0
 10 13  1  0  0  0  0
 13 14  2  0  0  0  0
 14 15  1  0  0  0  0
 15 16  2  0  0  0  0
  9 16  1  0  0  0  0
 16 17  1  0  0  0  0
 17 18  2  0  0  0  0
 17 19  1  0  0  0  0
 20 19  1  0  0  0  0
 20 21  1  0  0  0  0
 15 21  1  0  0  0  0
 20 22  1  1  0  0  0
  3 23  1  0  0  0  0
 24 23  1  6  0  0  0
 24 25  1  0  0  0  0
 25 26  1  0  0  0  0
 27 26  1  0  0  0  0
 28 27  1  0  0  0  0
 28 29  1  0  0  0  0
 29 24  1  0  0  0  0
 29 30  1  1  0  0  0
 28 31  1  6  0  0  0
 27 32  1  1  0  0  0
 26 33  1  0  0  0  0
 33 34  2  0  0  0  0
 33 35  1  0  0  0  0
 35 36  1  0  0  0  0
M  END


  Mrv2104 09272304142D          

 36 40  0  0  1  0            999 V2000
    5.0352   -0.2111    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.3052    0.5684    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.7651    1.1921    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9550    1.0361    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6850    0.2566    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2251   -0.3671    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8748    0.1007    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6048   -0.6789    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.3347    0.7243    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6048    1.5039    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4149    1.6598    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6850    2.4393    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.0647    2.1275    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2546    1.9716    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9845    1.1921    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5246    0.5684    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2546   -0.2111    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7946   -0.8348    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.4444   -0.3671    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0957    0.2566    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.1744    1.0361    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9058    0.1007    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0352    1.9716    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.8453    2.1275    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    6.1154    2.9071    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.9255    3.0630    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.4656    2.4393    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    7.1955    1.6598    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    6.3854    1.5039    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    6.1154    0.7243    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.7356    1.0361    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    8.2757    2.5952    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.1955    3.8425    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.6555    4.4662    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    8.0057    3.9984    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    8.2757    4.7780    0.0000 C   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  2  0  0  0  0
  1  6  1  0  0  0  0
  5  7  1  0  0  0  0
  7  8  2  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
  4 11  1  0  0  0  0
 11 12  2  0  0  0  0
 10 13  1  0  0  0  0
 13 14  2  0  0  0  0
 14 15  1  0  0  0  0
 15 16  2  0  0  0  0
  9 16  1  0  0  0  0
 16 17  1  0  0  0  0
 17 18  2  0  0  0  0
 17 19  1  0  0  0  0
 20 19  1  0  0  0  0
 20 21  1  0  0  0  0
 15 21  1  0  0  0  0
 20 22  1  1  0  0  0
  3 23  1  0  0  0  0
 24 23  1  6  0  0  0
 24 25  1  0  0  0  0
 25 26  1  0  0  0  0
 27 26  1  0  0  0  0
 28 27  1  0  0  0  0
 28 29  1  0  0  0  0
 29 24  1  0  0  0  0
 29 30  1  1  0  0  0
 28 31  1  6  0  0  0
 27 32  1  1  0  0  0
 26 33  1  0  0  0  0
 33 34  2  0  0  0  0
 33 35  1  0  0  0  0
 35 36  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0331895

> <DATABASE_NAME>
NP-MRD

> <SMILES>
COC(=O)C1O[C@@H](OC2=C3C(=O)C4=C(C(=O)C3=CC=C2)C2=C(C[C@H](C)CC2=O)C=C4)[C@H](O)[C@@H](O)[C@@H]1O

> <INCHI_IDENTIFIER>
InChI=1S/C26H24O10/c1-10-8-11-6-7-13-18(16(11)14(27)9-10)20(29)12-4-3-5-15(17(12)19(13)28)35-26-23(32)21(30)22(31)24(36-26)25(33)34-2/h3-7,10,21-24,26,30-32H,8-9H2,1-2H3/t10-,21-,22-,23+,24?,26+/m0/s1

> <INCHI_KEY>
NFVIUMJBNNNWMP-BHZZFQASSA-N

> <FORMULA>
C26H24O10

> <MOLECULAR_WEIGHT>
496.468

> <EXACT_MASS>
496.136946973

> <JCHEM_ACCEPTOR_COUNT>
9

> <JCHEM_ATOM_COUNT>
60

> <JCHEM_AVERAGE_POLARIZABILITY>
49.948541370755336

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
methyl (3S,4S,5R,6S)-3,4,5-trihydroxy-6-{[(3S)-3-methyl-1,7,12-trioxo-1,2,3,4,7,12-hexahydrotetraphen-8-yl]oxy}oxane-2-carboxylate

> <JCHEM_LOGP>
1.408139202333333

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
5

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
13.079869661356321

> <JCHEM_PKA_STRONGEST_ACIDIC>
12.165659498715781

> <JCHEM_PKA_STRONGEST_BASIC>
-3.686831478570142

> <JCHEM_POLAR_SURFACE_AREA>
156.66

> <JCHEM_REFRACTIVITY>
122.7301

> <JCHEM_ROTATABLE_BOND_COUNT>
4

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
methyl (3S,4S,5R,6S)-3,4,5-trihydroxy-6-{[(3S)-3-methyl-1,7,12-trioxo-3,4-dihydro-2H-tetraphen-8-yl]oxy}oxane-2-carboxylate

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 27-SEP-23   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   27-SEP-23         0                                  
HETATM    1  C   UNK     0       9.399  -0.394   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       9.903   1.061   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       8.895   2.225   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       7.383   1.934   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       6.879   0.479   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       7.887  -0.685   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       5.366   0.188   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0       4.862  -1.267   0.000  0.00  0.00           O+0
HETATM    9  C   UNK     0       4.358   1.352   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       4.862   2.807   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       6.375   3.098   0.000  0.00  0.00           C+0
HETATM   12  O   UNK     0       6.879   4.553   0.000  0.00  0.00           O+0
HETATM   13  C   UNK     0       3.854   3.971   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       2.342   3.680   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       1.838   2.225   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       2.846   1.061   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       2.342  -0.394   0.000  0.00  0.00           C+0
HETATM   18  O   UNK     0       3.350  -1.558   0.000  0.00  0.00           O+0
HETATM   19  C   UNK     0       0.830  -0.685   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0      -0.179   0.479   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0       0.326   1.934   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0      -1.691   0.188   0.000  0.00  0.00           C+0
HETATM   23  O   UNK     0       9.399   3.680   0.000  0.00  0.00           O+0
HETATM   24  C   UNK     0      10.911   3.971   0.000  0.00  0.00           C+0
HETATM   25  O   UNK     0      11.415   5.427   0.000  0.00  0.00           O+0
HETATM   26  C   UNK     0      12.928   5.718   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0      13.936   4.553   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0      13.432   3.098   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0      11.919   2.807   0.000  0.00  0.00           C+0
HETATM   30  O   UNK     0      11.415   1.352   0.000  0.00  0.00           O+0
HETATM   31  O   UNK     0      14.440   1.934   0.000  0.00  0.00           O+0
HETATM   32  O   UNK     0      15.448   4.844   0.000  0.00  0.00           O+0
HETATM   33  C   UNK     0      13.432   7.173   0.000  0.00  0.00           C+0
HETATM   34  O   UNK     0      12.424   8.337   0.000  0.00  0.00           O+0
HETATM   35  O   UNK     0      14.944   7.464   0.000  0.00  0.00           O+0
HETATM   36  C   UNK     0      15.448   8.919   0.000  0.00  0.00           C+0
CONECT    1    2    6                                                       
CONECT    2    1    3                                                       
CONECT    3    2    4   23                                                  
CONECT    4    3    5   11                                                  
CONECT    5    4    6    7                                                  
CONECT    6    5    1                                                       
CONECT    7    5    8    9                                                  
CONECT    8    7                                                            
CONECT    9    7   10   16                                                  
CONECT   10    9   11   13                                                  
CONECT   11   10    4   12                                                  
CONECT   12   11                                                            
CONECT   13   10   14                                                       
CONECT   14   13   15                                                       
CONECT   15   14   16   21                                                  
CONECT   16   15    9   17                                                  
CONECT   17   16   18   19                                                  
CONECT   18   17                                                            
CONECT   19   17   20                                                       
CONECT   20   19   21   22                                                  
CONECT   21   20   15                                                       
CONECT   22   20                                                            
CONECT   23    3   24                                                       
CONECT   24   23   25   29                                                  
CONECT   25   24   26                                                       
CONECT   26   25   27   33                                                  
CONECT   27   26   28   32                                                  
CONECT   28   27   29   31                                                  
CONECT   29   28   24   30                                                  
CONECT   30   29                                                            
CONECT   31   28                                                            
CONECT   32   27                                                            
CONECT   33   26   34   35                                                  
CONECT   34   33                                                            
CONECT   35   33   36                                                       
CONECT   36   35                                                            
MASTER        0    0    0    0    0    0    0    0   36    0   80    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₂₆H₂₄O₁₀

Average Mass

496.4680 Da

Monoisotopic Mass

496.13695 Da

IUPAC Name

methyl (3S,4S,5R,6S)-3,4,5-trihydroxy-6-{[(3S)-3-methyl-1,7,12-trioxo-1,2,3,4,7,12-hexahydrotetraphen-8-yl]oxy}oxane-2-carboxylate

Traditional Name

methyl (3S,4S,5R,6S)-3,4,5-trihydroxy-6-{[(3S)-3-methyl-1,7,12-trioxo-3,4-dihydro-2H-tetraphen-8-yl]oxy}oxane-2-carboxylate

CAS Registry Number

Not Available

SMILES

COC(=O)C1O[C@@H](OC2=C3C(=O)C4=C(C(=O)C3=CC=C2)C2=C(C[C@H](C)CC2=O)C=C4)[C@H](O)[C@@H](O)[C@@H]1O

InChI Identifier

InChI=1S/C26H24O10/c1-10-8-11-6-7-13-18(16(11)14(27)9-10)20(29)12-4-3-5-15(17(12)19(13)28)35-26-23(32)21(30)22(31)24(36-26)25(33)34-2/h3-7,10,21-24,26,30-32H,8-9H2,1-2H3/t10-,21-,22-,23+,24?,26+/m0/s1

InChI Key

NFVIUMJBNNNWMP-BHZZFQASSA-N

Experimental Spectra

Spectrum Type	Description	Depositor Email	Depositor Organization	Depositor	Deposition Date	View
HMBC NMR	[¹H, ¹³C] NMR Spectrum (2D, 600 MHz, C2D6OS, experimental)	hkang@konkuk.ac.kr	Not Available	Not Available	2023-09-27	View Spectrum
COSY NMR	[¹H, ¹H] NMR Spectrum (2D, 600 MHz, C2D6OS, experimental)	hkang@konkuk.ac.kr	Not Available	Not Available	2023-09-27	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 151 MHz, C2D6OS, experimental)	hkang@konkuk.ac.kr	Not Available	Not Available	2023-09-27	View Spectrum
HSQC NMR	[¹H, ¹³C] NMR Spectrum (2D, 600 MHz, C2D6OS, experimental)	hkang@konkuk.ac.kr	Not Available	Not Available	2023-09-27	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, C2D6OS, experimental)	hkang@konkuk.ac.kr	Not Available	Not Available	2023-09-27	View Spectrum

Predicted Spectra

Spectrum Type	Description	Depositor ID	Depositor Organization	Depositor	Deposition Date	View

Chemical Shift Submissions

Not Available

Species

Species of Origin

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	1.41	ChemAxon
pKa (Strongest Acidic)	12.17	ChemAxon
pKa (Strongest Basic)	-3.7	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	9	ChemAxon
Hydrogen Donor Count	3	ChemAxon
Polar Surface Area	156.66 Å²	ChemAxon
Rotatable Bond Count	4	ChemAxon
Refractivity	122.73 m³·mol⁻¹	ChemAxon
Polarizability	49.95 Å³	ChemAxon
Number of Rings	5	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

External Links

Not Available

References

General References

Not Available

Showing NP-Card for Acidonemycin B (NP0331895)

MOL for NP0331895 (Acidonemycin B)

3D MOL for NP0331895 (Acidonemycin B)

3D SDF for NP0331895 (Acidonemycin B)

3D-SDF for NP0331895 (Acidonemycin B)

PDB for NP0331895 (Acidonemycin B)

3D PDB for NP0331895 (Acidonemycin B)

SMILES for NP0331895 (Acidonemycin B)

INCHI for NP0331895 (Acidonemycin B)

Structure for NP0331895 (Acidonemycin B)

3D Structure for NP0331895 (Acidonemycin B)