NP-MRD: Showing NP-Card for Allamcidin B (NP0057626)

Jump To Section:

Identification Spectra BioTaxonomy ChemoTaxonomy Physical properties Links References XML

Record Information

Version

2.0

Created at

2022-04-28 03:01:57 UTC

Updated at

2022-04-28 03:01:57 UTC

NP-MRD ID

NP0057626

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Allamcidin B

Description

Methyl (1R,4R,4aR,7R,7aS)-1-hydroxy-4'-[(1R)-1-hydroxyethyl]-5'-oxo-3,4,4a,7a-tetrahydro-1H,5'H-spiro[cyclopenta[c]pyran-7,2'-furan]-4-carboxylate belongs to the class of organic compounds known as terpene lactones. These are prenol lipids containing a lactone ring. Allamcidin B is found in Allamanda neriifolia. Based on a literature review very few articles have been published on methyl (1R,4R,4aR,7R,7aS)-1-hydroxy-4'-[(1R)-1-hydroxyethyl]-5'-oxo-3,4,4a,7a-tetrahydro-1H,5'H-spiro[cyclopenta[c]pyran-7,2'-furan]-4-carboxylate.

Structure

MOL 3D MOL SDF PDB SMILES InChI

     RDKit          3D

 40 42  0  0  0  0  0  0  0  0999 V2000
   -5.4364    0.9932   -0.7160 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6006    0.1773    0.0864 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2565    0.4843    0.2413 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8244    1.4926   -0.3468 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3943   -0.3803    1.0851 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.4377   -1.7840    0.4605 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1956   -2.4025    0.5369 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3207   -1.8485   -0.4061 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.6909   -2.3724   -1.6468 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5149   -0.3868   -0.4253 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.9838    0.0783    0.9651 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.8070    1.5298    0.8028 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1691    1.7793   -0.0658 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7137    0.4477   -0.5447 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.7756    0.1030    0.3888 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9032   -0.0165   -0.2727 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2631   -0.3600    0.2665 C   0  0  1  0  0  0  0  0  0  0  0  0
    5.2272    0.7857   -0.0380 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.1900   -0.5868    1.6289 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.6149    0.2482   -1.6731 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4856    0.2192   -2.6080 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.2677    0.5279   -1.8008 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9812    1.1296   -1.7044 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.4223    0.5134   -0.7604 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.5490    2.0124   -0.2747 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7679   -0.4042    2.1301 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7677   -1.7221   -0.5991 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1915   -2.3604    1.0092 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7105   -2.1865   -0.2134 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3696   -1.8461   -2.1064 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2593   -0.0466   -1.1400 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3421   -0.3619    1.7482 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4122    2.2739    1.3391 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5056    2.7687   -0.3689 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6515   -0.0335    1.4647 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.6799   -1.2567   -0.2273 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.6977    1.7613    0.1357 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.0979    0.7707    0.6164 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.4596    0.7206   -1.1079 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.1128   -0.4611    2.0149 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  2  0
  3  5  1  0
  5  6  1  0
  6  7  1  0
  7  8  1  0
  8  9  1  0
  8 10  1  0
 10 11  1  0
 11 12  1  0
 12 13  2  0
 13 14  1  0
 14 22  1  6
 22 20  1  0
 20 21  2  0
 20 16  1  0
 16 15  2  0
 16 17  1  0
 17 18  1  0
 17 19  1  0
 11  5  1  0
 15 14  1  0
 14 10  1  0
  1 23  1  0
  1 24  1  0
  1 25  1  0
  5 26  1  1
  6 27  1  0
  6 28  1  0
  8 29  1  1
  9 30  1  0
 10 31  1  6
 11 32  1  1
 12 33  1  0
 13 34  1  0
 15 35  1  0
 17 36  1  6
 18 37  1  0
 18 38  1  0
 18 39  1  0
 19 40  1  0
M  END


  Mrv1652304282205012D          

 22 24  0  0  1  0            999 V2000
    0.5638   -1.1704    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.0573   -0.5192    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.7186   -0.7998    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.6915   -1.6243    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1011   -1.8534    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4944   -1.0803    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0010   -0.4291    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8255   -0.4562    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5382    0.2538    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7456    0.0248    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8187    1.0297    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.6309    1.1746    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2871    1.6606    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3679    0.2450    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.1851    0.3582    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.6917   -0.2930    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3810   -1.0573    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.8876   -1.7085    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7048   -1.5954    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.5770   -2.4727    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.0835   -3.1239    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1386    0.8962    0.0000 O   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  2  0  0  0  0
  1  5  1  6  0  0  0
  3  6  1  6  0  0  0
  6  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
  3 10  1  0  0  0  0
  9 11  1  0  0  0  0
 11 12  1  6  0  0  0
 11 13  1  0  0  0  0
  2 14  1  0  0  0  0
 14 15  1  0  0  0  0
 15 16  1  0  0  0  0
 16 17  1  0  0  0  0
  1 17  1  0  0  0  0
 17 18  1  6  0  0  0
 18 19  2  0  0  0  0
 18 20  1  0  0  0  0
 20 21  1  0  0  0  0
 14 22  1  6  0  0  0
M  END
> <DATABASE_ID>
NP0057626

> <DATABASE_NAME>
NP-MRD

> <SMILES>
COC(=O)[C@H]1CO[C@@H](O)[C@H]2[C@H]1C=C[C@]21OC(=O)C(=C1)[C@@H](C)O

> <INCHI_IDENTIFIER>
InChI=1S/C15H18O7/c1-7(16)9-5-15(22-13(9)18)4-3-8-10(12(17)20-2)6-21-14(19)11(8)15/h3-5,7-8,10-11,14,16,19H,6H2,1-2H3/t7-,8+,10+,11-,14-,15-/m1/s1

> <INCHI_KEY>
MWYGUUCBPMDIGE-SOJOIFAWSA-N

> <FORMULA>
C15H18O7

> <MOLECULAR_WEIGHT>
310.302

> <EXACT_MASS>
310.10525292

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_ATOM_COUNT>
40

> <JCHEM_AVERAGE_POLARIZABILITY>
30.178138950873763

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
methyl (1R,4R,4aR,7R,7aS)-1-hydroxy-4'-[(1R)-1-hydroxyethyl]-5'-oxo-3,4,4a,7a-tetrahydro-1H,5'H-spiro[cyclopenta[c]pyran-7,2'-furan]-4-carboxylate

> <ALOGPS_LOGP>
-0.61

> <JCHEM_LOGP>
-0.1676162380000006

> <ALOGPS_LOGS>
-1.43

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
14.64396799884019

> <JCHEM_PKA_STRONGEST_ACIDIC>
12.05438175711782

> <JCHEM_PKA_STRONGEST_BASIC>
-2.9550424174607812

> <JCHEM_POLAR_SURFACE_AREA>
102.29000000000002

> <JCHEM_REFRACTIVITY>
74.61120000000001

> <JCHEM_ROTATABLE_BOND_COUNT>
3

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.16e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
methyl (1R,4R,4aR,7R,7aS)-1-hydroxy-4'-[(1R)-1-hydroxyethyl]-5'-oxo-3,4,4a,7a-tetrahydro-1H-spiro[cyclopenta[c]pyran-7,2'-furan]-4-carboxylate

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 28-APR-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   28-APR-22         0                                  
HETATM    1  C   UNK     0       1.052  -2.185   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       0.107  -0.969   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -1.341  -1.493   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -1.291  -3.032   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       0.189  -3.460   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0      -2.790  -2.017   0.000  0.00  0.00           O+0
HETATM    7  C   UNK     0      -3.735  -0.801   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0      -5.274  -0.852   0.000  0.00  0.00           O+0
HETATM    9  C   UNK     0      -2.871   0.474   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      -1.392   0.046   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      -3.395   1.922   0.000  0.00  0.00           C+0
HETATM   12  O   UNK     0      -4.911   2.193   0.000  0.00  0.00           O+0
HETATM   13  C   UNK     0      -2.403   3.100   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       0.687   0.457   0.000  0.00  0.00           C+0
HETATM   15  O   UNK     0       2.212   0.669   0.000  0.00  0.00           O+0
HETATM   16  C   UNK     0       3.158  -0.547   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       2.578  -1.974   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       3.524  -3.189   0.000  0.00  0.00           C+0
HETATM   19  O   UNK     0       5.049  -2.978   0.000  0.00  0.00           O+0
HETATM   20  O   UNK     0       2.944  -4.616   0.000  0.00  0.00           O+0
HETATM   21  C   UNK     0       3.889  -5.831   0.000  0.00  0.00           C+0
HETATM   22  O   UNK     0      -0.259   1.673   0.000  0.00  0.00           O+0
CONECT    1    2    5   17                                                  
CONECT    2    1    3   14                                                  
CONECT    3    2    4    6   10                                             
CONECT    4    3    5                                                       
CONECT    5    4    1                                                       
CONECT    6    3    7                                                       
CONECT    7    6    8    9                                                  
CONECT    8    7                                                            
CONECT    9    7   10   11                                                  
CONECT   10    9    3                                                       
CONECT   11    9   12   13                                                  
CONECT   12   11                                                            
CONECT   13   11                                                            
CONECT   14    2   15   22                                                  
CONECT   15   14   16                                                       
CONECT   16   15   17                                                       
CONECT   17   16    1   18                                                  
CONECT   18   17   19   20                                                  
CONECT   19   18                                                            
CONECT   20   18   21                                                       
CONECT   21   20                                                            
CONECT   22   14                                                            
MASTER        0    0    0    0    0    0    0    0   22    0   48    0
END

View in JSmol

Synonyms

Value	Source
Methyl (1R,4R,4ar,7R,7as)-1-hydroxy-4'-[(1R)-1-hydroxyethyl]-5'-oxo-3,4,4a,7a-tetrahydro-1H,5'H-spiro[cyclopenta[c]pyran-7,2'-furan]-4-carboxylic acid	Generator

Chemical Formula

C₁₅H₁₈O₇

Average Mass

310.3020 Da

Monoisotopic Mass

310.10525 Da

IUPAC Name

methyl (1R,4R,4aR,7R,7aS)-1-hydroxy-4'-[(1R)-1-hydroxyethyl]-5'-oxo-3,4,4a,7a-tetrahydro-1H,5'H-spiro[cyclopenta[c]pyran-7,2'-furan]-4-carboxylate

Traditional Name

methyl (1R,4R,4aR,7R,7aS)-1-hydroxy-4'-[(1R)-1-hydroxyethyl]-5'-oxo-3,4,4a,7a-tetrahydro-1H-spiro[cyclopenta[c]pyran-7,2'-furan]-4-carboxylate

CAS Registry Number

Not Available

SMILES

COC(=O)[C@H]1CO[C@@H](O)[C@H]2[C@H]1C=C[C@]21OC(=O)C(=C1)[C@@H](C)O

InChI Identifier

InChI=1S/C15H18O7/c1-7(16)9-5-15(22-13(9)18)4-3-8-10(12(17)20-2)6-21-14(19)11(8)15/h3-5,7-8,10-11,14,16,19H,6H2,1-2H3/t7-,8+,10+,11-,14-,15-/m1/s1

InChI Key

MWYGUUCBPMDIGE-SOJOIFAWSA-N

Experimental Spectra

Not Available

Predicted Spectra

Spectrum Type	Description	Depositor ID	Depositor Organization	Depositor	Deposition Date	View
1D NMR	¹³C NMR Spectrum (1D, 25 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 252 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 50 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 75 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 101 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 126 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 151 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 176 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 201 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 226 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum

Chemical Shift Submissions

Not Available

Species

Species of Origin

Species Name	Source	Reference
Allamanda neriifolia	Plant	KNApSAcK

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as terpene lactones. These are prenol lipids containing a lactone ring.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Prenol lipids

Sub Class

Terpene lactones

Direct Parent

Terpene lactones

Alternative Parents

Substituents

Terpene lactone
Iridoid-skeleton
Monoterpenoid
Bicyclic monoterpenoid
Oxane
Dicarboxylic acid or derivatives
2-furanone
Alpha,beta-unsaturated carboxylic ester
Enoate ester
Methyl ester
Dihydrofuran
Secondary alcohol
Lactone
Hemiacetal
Carboxylic acid ester
Oxacycle
Organoheterocyclic compound
Carboxylic acid derivative
Organic oxygen compound
Organic oxide
Hydrocarbon derivative
Organooxygen compound
Carbonyl group
Alcohol
Aliphatic heteropolycyclic compound

Molecular Framework

Aliphatic 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	-0.61	ALOGPS
logP	-0.17	ChemAxon
logS	-1.4	ALOGPS
pKa (Strongest Acidic)	12.05	ChemAxon
pKa (Strongest Basic)	-3	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	5	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	102.29 Å²	ChemAxon
Rotatable Bond Count	3	ChemAxon
Refractivity	74.61 m³·mol⁻¹	ChemAxon
Polarizability	30.18 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

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

162905762

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Not Available

Showing NP-Card for Allamcidin B (NP0057626)

MOL for NP0057626 (Allamcidin B)

3D MOL for NP0057626 (Allamcidin B)

3D SDF for NP0057626 (Allamcidin B)

3D-SDF for NP0057626 (Allamcidin B)

PDB for NP0057626 (Allamcidin B)

3D PDB for NP0057626 (Allamcidin B)

SMILES for NP0057626 (Allamcidin B)

INCHI for NP0057626 (Allamcidin B)

Structure for NP0057626 (Allamcidin B)

3D Structure for NP0057626 (Allamcidin B)