NP-MRD: Showing NP-Card for (+)-Dymacrin H (NP0076478)

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Record Information

Version

2.0

Created at

2022-04-28 21:39:13 UTC

Updated at

2022-04-28 21:39:13 UTC

NP-MRD ID

NP0076478

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(+)-Dymacrin H

Description

Dymacrin H belongs to the class of organic compounds known as triterpenoids. These are terpene molecules containing six isoprene units. (+)-Dymacrin H is found in Dysoxylum macranthum. Based on a literature review very few articles have been published on Dymacrin H.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652304282223392D          

 35 39  0  0  1  0            999 V2000
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M  END

     RDKit          3D

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M  END


  Mrv1652304282223392D          

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  6  9  1  0  0  0  0
  9 10  1  6  0  0  0
 10 11  2  0  0  0  0
 11 12  1  0  0  0  0
  5 12  1  6  0  0  0
 10 13  1  0  0  0  0
 13 14  1  0  0  0  0
 14 15  1  0  0  0  0
 15 16  1  0  0  0  0
  9 16  1  0  0  0  0
 14 17  1  0  0  0  0
 17 18  1  0  0  0  0
 18 19  1  0  0  0  0
 13 19  1  0  0  0  0
 17 20  1  1  0  0  0
 20 21  1  0  0  0  0
 21 22  1  0  0  0  0
 22 23  2  0  0  0  0
 24 22  1  1  0  0  0
 24 25  1  0  0  0  0
 25 26  1  0  0  0  0
 25 27  1  0  0  0  0
 25 28  1  0  0  0  0
 24 28  1  0  0  0  0
 20 29  1  1  0  0  0
 14 30  1  1  0  0  0
 13 31  1  6  0  0  0
  6 32  1  6  0  0  0
  4 33  1  6  0  0  0
 33 34  1  0  0  0  0
  4 35  1  1  0  0  0
M  END
> <DATABASE_ID>
NP0076478

> <DATABASE_NAME>
NP-MRD

> <SMILES>
C[C@@H](CC(=O)[C@@H]1OC1(C)C)[C@@H]1CC[C@]2(C)C3=CC[C@H]4[C@@](C)(CO)C(=O)C[C@@H](O)[C@]4(C)[C@H]3CC[C@@]12C

> <INCHI_IDENTIFIER>
InChI=1S/C30H46O5/c1-17(14-21(32)25-26(2,3)35-25)18-10-12-29(6)19-8-9-22-27(4,16-31)23(33)15-24(34)30(22,7)20(19)11-13-28(18,29)5/h8,17-18,20,22,24-25,31,34H,9-16H2,1-7H3/t17-,18-,20-,22-,24+,25-,27+,28-,29+,30+/m0/s1

> <INCHI_KEY>
BSHJLQQNFATZFT-UHUHJXBZSA-N

> <FORMULA>
C30H46O5

> <MOLECULAR_WEIGHT>
486.693

> <EXACT_MASS>
486.334524581

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_ATOM_COUNT>
81

> <JCHEM_AVERAGE_POLARIZABILITY>
56.91317142858799

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(1S,2R,3R,6S,7R,11S,14S,15S)-14-[(2S)-4-[(2R)-3,3-dimethyloxiran-2-yl]-4-oxobutan-2-yl]-3-hydroxy-6-(hydroxymethyl)-2,6,11,15-tetramethyltetracyclo[8.7.0.0^{2,7}.0^{11,15}]heptadec-9-en-5-one

> <ALOGPS_LOGP>
5.17

> <JCHEM_LOGP>
4.315882930333333

> <ALOGPS_LOGS>
-5.01

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
5

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
15.084967975962979

> <JCHEM_PKA_STRONGEST_ACIDIC>
14.328328215178502

> <JCHEM_PKA_STRONGEST_BASIC>
-2.8188372038743026

> <JCHEM_POLAR_SURFACE_AREA>
87.13

> <JCHEM_REFRACTIVITY>
136.42680000000001

> <JCHEM_ROTATABLE_BOND_COUNT>
5

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
4.77e-03 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(1S,2R,3R,6S,7R,11S,14S,15S)-14-[(2S)-4-[(2R)-3,3-dimethyloxiran-2-yl]-4-oxobutan-2-yl]-3-hydroxy-6-(hydroxymethyl)-2,6,11,15-tetramethyltetracyclo[8.7.0.0^{2,7}.0^{11,15}]heptadec-9-en-5-one

> <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       7.929   4.020   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       8.452   2.572   0.000  0.00  0.00           C+0
HETATM    3  O   UNK     0       9.968   2.301   0.000  0.00  0.00           O+0
HETATM    4  C   UNK     0       7.459   1.394   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       5.943   1.666   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       5.420   3.114   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       6.413   4.291   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0       5.889   5.740   0.000  0.00  0.00           O+0
HETATM    9  C   UNK     0       3.904   3.385   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       2.911   2.208   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       3.434   0.759   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       4.950   0.488   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       1.395   2.479   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       0.872   3.927   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       1.865   5.104   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       3.381   4.833   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0      -0.667   3.877   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0      -1.095   2.398   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       0.179   1.534   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0      -1.612   5.093   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0      -1.032   6.519   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0      -1.977   7.735   0.000  0.00  0.00           C+0
HETATM   23  O   UNK     0      -3.503   7.525   0.000  0.00  0.00           O+0
HETATM   24  C   UNK     0      -1.397   9.162   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0      -1.607  10.687   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0      -3.146  10.745   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0      -1.284  12.193   0.000  0.00  0.00           C+0
HETATM   28  O   UNK     0      -0.181  10.107   0.000  0.00  0.00           O+0
HETATM   29  C   UNK     0      -3.138   4.882   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0       0.200   5.313   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0       1.764   0.984   0.000  0.00  0.00           C+0
HETATM   32  C   UNK     0       4.897   4.562   0.000  0.00  0.00           C+0
HETATM   33  C   UNK     0       8.601   0.361   0.000  0.00  0.00           C+0
HETATM   34  O   UNK     0       8.277  -1.144   0.000  0.00  0.00           O+0
HETATM   35  C   UNK     0       7.241  -0.130   0.000  0.00  0.00           C+0
CONECT    1    2    7                                                       
CONECT    2    1    3    4                                                  
CONECT    3    2                                                            
CONECT    4    2    5   33   35                                             
CONECT    5    4    6   12                                                  
CONECT    6    5    7    9   32                                             
CONECT    7    6    1    8                                                  
CONECT    8    7                                                            
CONECT    9    6   10   16                                                  
CONECT   10    9   11   13                                                  
CONECT   11   10   12                                                       
CONECT   12   11    5                                                       
CONECT   13   10   14   19   31                                             
CONECT   14   13   15   17   30                                             
CONECT   15   14   16                                                       
CONECT   16   15    9                                                       
CONECT   17   14   18   20                                                  
CONECT   18   17   19                                                       
CONECT   19   18   13                                                       
CONECT   20   17   21   29                                                  
CONECT   21   20   22                                                       
CONECT   22   21   23   24                                                  
CONECT   23   22                                                            
CONECT   24   22   25   28                                                  
CONECT   25   24   26   27   28                                             
CONECT   26   25                                                            
CONECT   27   25                                                            
CONECT   28   25   24                                                       
CONECT   29   20                                                            
CONECT   30   14                                                            
CONECT   31   13                                                            
CONECT   32    6                                                            
CONECT   33    4   34                                                       
CONECT   34   33                                                            
CONECT   35    4                                                            
MASTER        0    0    0    0    0    0    0    0   35    0   78    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₃₀H₄₆O₅

Average Mass

486.6930 Da

Monoisotopic Mass

486.33452 Da

IUPAC Name

(1S,2R,3R,6S,7R,11S,14S,15S)-14-[(2S)-4-[(2R)-3,3-dimethyloxiran-2-yl]-4-oxobutan-2-yl]-3-hydroxy-6-(hydroxymethyl)-2,6,11,15-tetramethyltetracyclo[8.7.0.0^{2,7}.0^{11,15}]heptadec-9-en-5-one

Traditional Name

(1S,2R,3R,6S,7R,11S,14S,15S)-14-[(2S)-4-[(2R)-3,3-dimethyloxiran-2-yl]-4-oxobutan-2-yl]-3-hydroxy-6-(hydroxymethyl)-2,6,11,15-tetramethyltetracyclo[8.7.0.0^{2,7}.0^{11,15}]heptadec-9-en-5-one

CAS Registry Number

Not Available

SMILES

C[C@@H](CC(=O)[C@@H]1OC1(C)C)[C@@H]1CC[C@]2(C)C3=CC[C@H]4[C@@](C)(CO)C(=O)C[C@@H](O)[C@]4(C)[C@H]3CC[C@@]12C

InChI Identifier

InChI=1S/C30H46O5/c1-17(14-21(32)25-26(2,3)35-25)18-10-12-29(6)19-8-9-22-27(4,16-31)23(33)15-24(34)30(22,7)20(19)11-13-28(18,29)5/h8,17-18,20,22,24-25,31,34H,9-16H2,1-7H3/t17-,18-,20-,22-,24+,25-,27+,28-,29+,30+/m0/s1

InChI Key

BSHJLQQNFATZFT-UHUHJXBZSA-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
Dysoxylum macranthum	Plant	KNApSAcK

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as triterpenoids. These are terpene molecules containing six isoprene units.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Prenol lipids

Sub Class

Triterpenoids

Direct Parent

Triterpenoids

Alternative Parents

Substituents

Triterpenoid
Cholesterol-skeleton
Cholestane-skeleton
Dihydroxy bile acid, alcohol, or derivatives
Hydroxy bile acid, alcohol, or derivatives
23-oxosteroid
Bile acid, alcohol, or derivatives
3-oxo-delta-7-steroid
3-oxosteroid
1-hydroxysteroid
Hydroxysteroid
Oxosteroid
11-alpha-hydroxysteroid
11-hydroxysteroid
3-oxo-5-alpha-steroid
Steroid
Delta-7-steroid
Cyclic alcohol
Cyclic ketone
Ketone
Secondary alcohol
Oxacycle
Organoheterocyclic compound
Dialkyl ether
Oxirane
Ether
Primary alcohol
Organooxygen compound
Hydrocarbon derivative
Organic oxide
Alcohol
Carbonyl group
Organic oxygen compound
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	5.17	ALOGPS
logP	4.32	ChemAxon
logS	-5	ALOGPS
pKa (Strongest Acidic)	14.33	ChemAxon
pKa (Strongest Basic)	-2.8	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	5	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	87.13 Å²	ChemAxon
Rotatable Bond Count	5	ChemAxon
Refractivity	136.43 m³·mol⁻¹	ChemAxon
Polarizability	56.91 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

HMDB ID

Not Available

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

Not Available

KNApSAcK ID

C00039065

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

15894667

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Not Available

Showing NP-Card for (+)-Dymacrin H (NP0076478)

MOL for NP0076478 ((+)-Dymacrin H)

3D MOL for NP0076478 ((+)-Dymacrin H)

3D SDF for NP0076478 ((+)-Dymacrin H)

3D-SDF for NP0076478 ((+)-Dymacrin H)

PDB for NP0076478 ((+)-Dymacrin H)

3D PDB for NP0076478 ((+)-Dymacrin H)

SMILES for NP0076478 ((+)-Dymacrin H)

INCHI for NP0076478 ((+)-Dymacrin H)

Structure for NP0076478 ((+)-Dymacrin H)

3D Structure for NP0076478 ((+)-Dymacrin H)