NP-MRD: Showing NP-Card for (+)-Mycalamide D (NP0081269)

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Record Information

Version

2.0

Created at

2022-04-29 02:13:37 UTC

Updated at

2022-04-29 02:13:37 UTC

NP-MRD ID

NP0081269

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(+)-Mycalamide D

Description

Mycalamide D belongs to the class of organic compounds known as pyranodioxins. These are polycyclic compounds containing a pyranodioxin moiety, which consists of a pyran ring fused to a dioxin ring. (+)-Mycalamide D is found in Mycale sp. and Stylinos n.sp.. (+)-Mycalamide D was first documented in 2000 (PMID: 10843597). Based on a literature review very few articles have been published on Mycalamide D.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652304292204132D          

 34 36  0  0  1  0            999 V2000
    0.0000    0.8250    0.0000 N   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 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145    2.0625    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.4289    2.4750    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.2414    2.6183    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5236    3.3935    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.9933    4.0255    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.1808    3.8822    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6505    4.5142    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8986    3.1070    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2754    4.8007    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3360    3.5368    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7111    1.6998    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5236    1.5565    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    2.4750    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000   -0.0000    0.0000 C   0  0  1  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
   -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 O   0  0  0  0  0  0  0  0  0  0  0  0
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    1.4289   -1.6500    0.0000 C   0  0  2  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
    2.9679   -1.2663    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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    2.8579   -0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579    0.8250    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    3.5724    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2868    0.8250    0.0000 O   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
  1  2  1  0  0  0  0
  2  3  2  0  0  0  0
  2  4  1  0  0  0  0
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  8  9  1  0  0  0  0
  9 10  2  0  0  0  0
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  5 11  1  0  0  0  0
  8 12  1  6  0  0  0
  7 13  1  6  0  0  0
  5 14  1  1  0  0  0
 14 15  1  0  0  0  0
  4 16  1  6  0  0  0
 17  1  1  6  0  0  0
 17 18  1  0  0  0  0
 18 19  1  0  0  0  0
 19 20  1  0  0  0  0
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 21 22  1  0  0  0  0
 17 22  1  0  0  0  0
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 24 30  1  6  0  0  0
 30 31  1  0  0  0  0
 31 32  1  0  0  0  0
 32 33  1  0  0  0  0
 31 34  1  6  0  0  0
M  END

     RDKit          3D

 73 75  0  0  0  0  0  0  0  0999 V2000
    2.1666    2.3243    1.2316 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8644    1.2327    1.0294 C   0  0  0  0  0  0  0  0  0  0  0  0
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   -2.9146   -1.7913   -3.3174 O   0  0  0  0  0  0  0  0  0  0  0  0
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   -5.1769   -0.0815   -2.6470 O   0  0  0  0  0  0  0  0  0  0  0  0
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   -4.6608    1.9035   -0.5896 C   0  0  0  0  0  0  0  0  0  0  0  0
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  6  5  1  0
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M  END


  Mrv1652304292204132D          

 34 36  0  0  1  0            999 V2000
    0.0000    0.8250    0.0000 N   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
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 32 33  1  0  0  0  0
 31 34  1  6  0  0  0
M  END
> <DATABASE_ID>
NP0081269

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CO[C@@]1(CC(=C)[C@@H](C)[C@@H](C)O1)[C@H](O)C(=O)N[C@H]1OCO[C@@H]2[C@@H](O)C(C)(C)[C@@H](C[C@H](O)CO)O[C@@H]12

> <INCHI_IDENTIFIER>
InChI=1S/C23H39NO10/c1-11-8-23(30-6,34-13(3)12(11)2)19(28)20(29)24-21-17-16(31-10-32-21)18(27)22(4,5)15(33-17)7-14(26)9-25/h12-19,21,25-28H,1,7-10H2,2-6H3,(H,24,29)/t12-,13-,14+,15-,16+,17-,18-,19-,21+,23-/m1/s1

> <INCHI_KEY>
MPSRCJWTLGCJFM-GBFCGSDTSA-N

> <FORMULA>
C23H39NO10

> <MOLECULAR_WEIGHT>
489.562

> <EXACT_MASS>
489.25739646

> <JCHEM_ACCEPTOR_COUNT>
10

> <JCHEM_ATOM_COUNT>
73

> <JCHEM_AVERAGE_POLARIZABILITY>
50.55976747207385

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
5

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2S)-N-[(4S,4aR,6R,8S,8aR)-6-[(2S)-2,3-dihydroxypropyl]-8-hydroxy-7,7-dimethyl-hexahydro-2H-pyrano[3,2-d][1,3]dioxin-4-yl]-2-hydroxy-2-[(2R,5R,6R)-2-methoxy-5,6-dimethyl-4-methylideneoxan-2-yl]acetamide

> <ALOGPS_LOGP>
-0.37

> <JCHEM_LOGP>
-0.3309576596666665

> <ALOGPS_LOGS>
-1.86

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
12.00306471734453

> <JCHEM_PKA_STRONGEST_ACIDIC>
11.083625235118786

> <JCHEM_PKA_STRONGEST_BASIC>
-2.9377126835561347

> <JCHEM_POLAR_SURFACE_AREA>
156.17000000000002

> <JCHEM_REFRACTIVITY>
117.66879999999998

> <JCHEM_ROTATABLE_BOND_COUNT>
7

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
6.79e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(2S)-N-[(4S,4aR,6R,8S,8aR)-6-[(2S)-2,3-dihydroxypropyl]-8-hydroxy-7,7-dimethyl-hexahydropyrano[3,2-d][1,3]dioxin-4-yl]-2-hydroxy-2-[(2R,5R,6R)-2-methoxy-5,6-dimethyl-4-methylideneoxan-2-yl]acetamide

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 29-APR-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   29-APR-22         0                                  
HETATM    1  N   UNK     0       0.000   1.540   0.000  0.00  0.00           N+0
HETATM    2  C   UNK     0      -1.334   2.310   0.000  0.00  0.00           C+0
HETATM    3  O   UNK     0      -2.667   1.540   0.000  0.00  0.00           O+0
HETATM    4  C   UNK     0      -1.334   3.850   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      -2.667   4.620   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0      -4.184   4.887   0.000  0.00  0.00           O+0
HETATM    7  C   UNK     0      -4.711   6.335   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      -3.721   7.514   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      -2.204   7.247   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      -1.214   8.427   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      -1.677   5.800   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      -4.247   8.961   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      -6.227   6.602   0.000  0.00  0.00           C+0
HETATM   14  O   UNK     0      -3.194   3.173   0.000  0.00  0.00           O+0
HETATM   15  C   UNK     0      -4.711   2.905   0.000  0.00  0.00           C+0
HETATM   16  O   UNK     0       0.000   4.620   0.000  0.00  0.00           O+0
HETATM   17  C   UNK     0       0.000  -0.000   0.000  0.00  0.00           C+0
HETATM   18  O   UNK     0      -1.334  -0.770   0.000  0.00  0.00           O+0
HETATM   19  C   UNK     0      -1.334  -2.310   0.000  0.00  0.00           C+0
HETATM   20  O   UNK     0       0.000  -3.080   0.000  0.00  0.00           O+0
HETATM   21  C   UNK     0       1.334  -2.310   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM   23  O   UNK     0       2.667  -0.000   0.000  0.00  0.00           O+0
HETATM   24  C   UNK     0       4.001  -0.770   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0       4.001  -2.310   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0       2.667  -3.080   0.000  0.00  0.00           C+0
HETATM   27  O   UNK     0       2.667  -4.620   0.000  0.00  0.00           O+0
HETATM   28  C   UNK     0       5.540  -2.364   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0       4.817  -3.616   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0       5.335  -0.000   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0       5.335   1.540   0.000  0.00  0.00           C+0
HETATM   32  C   UNK     0       6.668   2.310   0.000  0.00  0.00           C+0
HETATM   33  O   UNK     0       8.002   1.540   0.000  0.00  0.00           O+0
HETATM   34  O   UNK     0       4.001   2.310   0.000  0.00  0.00           O+0
CONECT    1    2   17                                                       
CONECT    2    1    3    4                                                  
CONECT    3    2                                                            
CONECT    4    2    5   16                                                  
CONECT    5    4    6   11   14                                             
CONECT    6    5    7                                                       
CONECT    7    6    8   13                                                  
CONECT    8    7    9   12                                                  
CONECT    9    8   10   11                                                  
CONECT   10    9                                                            
CONECT   11    9    5                                                       
CONECT   12    8                                                            
CONECT   13    7                                                            
CONECT   14    5   15                                                       
CONECT   15   14                                                            
CONECT   16    4                                                            
CONECT   17    1   18   22                                                  
CONECT   18   17   19                                                       
CONECT   19   18   20                                                       
CONECT   20   19   21                                                       
CONECT   21   20   22   26                                                  
CONECT   22   21   17   23                                                  
CONECT   23   22   24                                                       
CONECT   24   23   25   30                                                  
CONECT   25   24   26   28   29                                             
CONECT   26   25   21   27                                                  
CONECT   27   26                                                            
CONECT   28   25                                                            
CONECT   29   25                                                            
CONECT   30   24   31                                                       
CONECT   31   30   32   34                                                  
CONECT   32   31   33                                                       
CONECT   33   32                                                            
CONECT   34   31                                                            
MASTER        0    0    0    0    0    0    0    0   34    0   72    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₂₃H₃₉NO₁₀

Average Mass

489.5620 Da

Monoisotopic Mass

489.25740 Da

IUPAC Name

(2S)-N-[(4S,4aR,6R,8S,8aR)-6-[(2S)-2,3-dihydroxypropyl]-8-hydroxy-7,7-dimethyl-hexahydro-2H-pyrano[3,2-d][1,3]dioxin-4-yl]-2-hydroxy-2-[(2R,5R,6R)-2-methoxy-5,6-dimethyl-4-methylideneoxan-2-yl]acetamide

Traditional Name

(2S)-N-[(4S,4aR,6R,8S,8aR)-6-[(2S)-2,3-dihydroxypropyl]-8-hydroxy-7,7-dimethyl-hexahydropyrano[3,2-d][1,3]dioxin-4-yl]-2-hydroxy-2-[(2R,5R,6R)-2-methoxy-5,6-dimethyl-4-methylideneoxan-2-yl]acetamide

CAS Registry Number

Not Available

SMILES

CO[C@@]1(CC(=C)[C@@H](C)[C@@H](C)O1)[C@H](O)C(=O)N[C@H]1OCO[C@@H]2[C@@H](O)C(C)(C)[C@@H](C[C@H](O)CO)O[C@@H]12

InChI Identifier

InChI=1S/C23H39NO10/c1-11-8-23(30-6,34-13(3)12(11)2)19(28)20(29)24-21-17-16(31-10-32-21)18(27)22(4,5)15(33-17)7-14(26)9-25/h12-19,21,25-28H,1,7-10H2,2-6H3,(H,24,29)/t12-,13-,14+,15-,16+,17-,18-,19-,21+,23-/m1/s1

InChI Key

MPSRCJWTLGCJFM-GBFCGSDTSA-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
Mycale sp.	-	KNApSAcK
Stylinos n.sp.	-	KNApSAcK

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as pyranodioxins. These are polycyclic compounds containing a pyranodioxin moiety, which consists of a pyran ring fused to a dioxin ring.

Kingdom

Organic compounds

Super Class

Organoheterocyclic compounds

Class

Pyranodioxins

Sub Class

Not Available

Direct Parent

Pyranodioxins

Alternative Parents

Substituents

Pyranodioxin
Ketal
Oxane
Monosaccharide
Meta-dioxane
Secondary alcohol
Oxacycle
Organic 1,3-dipolar compound
Propargyl-type 1,3-dipolar organic compound
Ether
Dialkyl ether
Carboximidic acid derivative
Carboximidic acid
Acetal
Organic nitrogen compound
Organic oxygen compound
Organopnictogen compound
Hydrocarbon derivative
Primary alcohol
Organooxygen compound
Organonitrogen compound
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	-0.37	ALOGPS
logP	-0.33	ChemAxon
logS	-1.9	ALOGPS
pKa (Strongest Acidic)	11.08	ChemAxon
pKa (Strongest Basic)	-2.9	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	10	ChemAxon
Hydrogen Donor Count	5	ChemAxon
Polar Surface Area	156.17 Å²	ChemAxon
Rotatable Bond Count	7	ChemAxon
Refractivity	117.67 m³·mol⁻¹	ChemAxon
Polarizability	50.56 Å³	ChemAxon
Number of Rings	3	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	Yes	ChemAxon

External Links

HMDB ID

Not Available

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

Not Available

KNApSAcK ID

C00047067

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

138319335

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

West LM, Northcote PT, Hood KA, Miller JH, Page MJ: Mycalamide D, a new cytotoxic amide from the New Zealand marine sponge Mycale species. J Nat Prod. 2000 May;63(5):707-9. doi: 10.1021/np9904511. [PubMed:10843597 ]

Showing NP-Card for (+)-Mycalamide D (NP0081269)

MOL for NP0081269 ((+)-Mycalamide D)

3D MOL for NP0081269 ((+)-Mycalamide D)

3D SDF for NP0081269 ((+)-Mycalamide D)

3D-SDF for NP0081269 ((+)-Mycalamide D)

PDB for NP0081269 ((+)-Mycalamide D)

3D PDB for NP0081269 ((+)-Mycalamide D)

SMILES for NP0081269 ((+)-Mycalamide D)

INCHI for NP0081269 ((+)-Mycalamide D)

Structure for NP0081269 ((+)-Mycalamide D)

3D Structure for NP0081269 ((+)-Mycalamide D)