NP-MRD: Showing NP-Card for (±)-Cleichalmyrcin D2 (NP0333487)

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Record Information

Version

2.0

Created at

2024-06-24 12:52:00 UTC

Updated at

2024-10-07 12:35:15 UTC

NP-MRD ID

NP0333487

Natural Product DOI

https://doi.org/10.57994/2941

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(±)-Cleichalmyrcin D2

Description

(±)-Cleichalmyrcin D2 belongs to the class of organic compounds known as diterpenoids. These are terpene compounds formed by four isoprene units. Based on a literature review very few articles have been published on (±)-Cleichalmyrcin D2.

Structure

MOL SDF PDB SMILES InChI


  Mrv2104 03082315262D          

 33 35  0  0  1  0            999 V2000
    3.5724   -0.4125    0.0000 O   0  0  0  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   -1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0013   -1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2868   -2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0013   -2.8875    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.7158   -2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724   -2.8875    0.0000 C   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  1  0  0  0  0  0  0  0  0  0
    5.0013   -3.7125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.7158   -4.1250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.4302   -3.7125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.4302   -2.8875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.1447   -2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.8592   -2.8875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.8592   -3.7125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.5737   -2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.7158   -4.9500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0013   -5.3625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2868   -4.9500    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    3.5724   -5.3625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724   -6.1875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579   -6.6000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -6.1875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -5.3625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579   -4.9500    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
    2.8579   -2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -2.8875    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
    2.1434   -1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -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  2  0  0  0  0
  3  4  1  0  0  0  0
  3  5  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  1  0  0  0  0
  5  8  2  0  0  0  0
  8  9  1  0  0  0  0
 10  9  1  1  0  0  0
 10 11  1  0  0  0  0
 11 12  1  0  0  0  0
 12 13  1  0  0  0  0
 13 14  1  0  0  0  0
 14 15  1  0  0  0  0
 15 16  2  0  0  0  0
 16 17  1  0  0  0  0
 16 18  1  0  0  0  0
 12 19  2  0  0  0  0
 19 20  1  0  0  0  0
 21 20  1  0  0  0  0
 10 21  1  0  0  0  0
 21 22  1  6  0  0  0
 22 23  2  0  0  0  0
 23 24  1  0  0  0  0
 24 25  2  0  0  0  0
 25 26  1  0  0  0  0
 26 27  2  0  0  0  0
 22 27  1  0  0  0  0
  9 28  2  0  0  0  0
  8 29  1  0  0  0  0
 29 30  1  0  0  0  0
 29 31  2  0  0  0  0
  2 31  1  0  0  0  0
 31 32  1  0  0  0  0
 32 33  2  0  0  0  0
M  END


  Mrv2104 03082315262D          

 33 35  0  0  1  0            999 V2000
    3.5724   -0.4125    0.0000 O   0  0  0  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   -1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0013   -1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2868   -2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0013   -2.8875    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.7158   -2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724   -2.8875    0.0000 C   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  1  0  0  0  0  0  0  0  0  0
    5.0013   -3.7125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.7158   -4.1250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.4302   -3.7125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.4302   -2.8875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.1447   -2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.8592   -2.8875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.8592   -3.7125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.5737   -2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.7158   -4.9500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0013   -5.3625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2868   -4.9500    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    3.5724   -5.3625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724   -6.1875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579   -6.6000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -6.1875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -5.3625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579   -4.9500    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
    2.8579   -2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -2.8875    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
    2.1434   -1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -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  2  0  0  0  0
  3  4  1  0  0  0  0
  3  5  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  1  0  0  0  0
  5  8  2  0  0  0  0
  8  9  1  0  0  0  0
 10  9  1  1  0  0  0
 10 11  1  0  0  0  0
 11 12  1  0  0  0  0
 12 13  1  0  0  0  0
 13 14  1  0  0  0  0
 14 15  1  0  0  0  0
 15 16  2  0  0  0  0
 16 17  1  0  0  0  0
 16 18  1  0  0  0  0
 12 19  2  0  0  0  0
 19 20  1  0  0  0  0
 21 20  1  0  0  0  0
 10 21  1  0  0  0  0
 21 22  1  6  0  0  0
 22 23  2  0  0  0  0
 23 24  1  0  0  0  0
 24 25  2  0  0  0  0
 25 26  1  0  0  0  0
 26 27  2  0  0  0  0
 22 27  1  0  0  0  0
  9 28  2  0  0  0  0
  8 29  1  0  0  0  0
 29 30  1  0  0  0  0
 29 31  2  0  0  0  0
  2 31  1  0  0  0  0
 31 32  1  0  0  0  0
 32 33  2  0  0  0  0
M  END
> <DATABASE_ID>
NP0333487

> <DATABASE_NAME>
NP-MRD

> <SMILES>
COC1=C(C(=O)[C@H]2CC(CCC=C(C)C)=CC[C@@H]2C2=CC=CC=C2)C(O)=C(C=O)C(O)=C1C

> <INCHI_IDENTIFIER>
InChI=1S/C28H32O5/c1-17(2)9-8-10-19-13-14-21(20-11-6-5-7-12-20)22(15-19)26(31)24-27(32)23(16-29)25(30)18(3)28(24)33-4/h5-7,9,11-13,16,21-22,30,32H,8,10,14-15H2,1-4H3/t21-,22+/m1/s1

> <INCHI_KEY>
XLJIRBMYVUVTKC-YADHBBJMSA-N

> <FORMULA>
C28H32O5

> <MOLECULAR_WEIGHT>
448.559

> <EXACT_MASS>
448.22497413

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_ATOM_COUNT>
65

> <JCHEM_AVERAGE_POLARIZABILITY>
49.992427587800435

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
2,6-dihydroxy-4-methoxy-3-methyl-5-[(1S,6S)-3-(4-methylpent-3-en-1-yl)-6-phenylcyclohex-3-ene-1-carbonyl]benzaldehyde

> <JCHEM_LOGP>
8.017494336333334

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
9.187394007787162

> <JCHEM_PKA_STRONGEST_ACIDIC>
7.277932157293083

> <JCHEM_PKA_STRONGEST_BASIC>
-4.631494322881959

> <JCHEM_POLAR_SURFACE_AREA>
83.83000000000001

> <JCHEM_REFRACTIVITY>
133.558

> <JCHEM_ROTATABLE_BOND_COUNT>
8

> <JCHEM_RULE_OF_FIVE>
0

> <JCHEM_TRADITIONAL_IUPAC>
2,6-dihydroxy-4-methoxy-3-methyl-5-[(1S,6S)-3-(4-methylpent-3-en-1-yl)-6-phenylcyclohex-3-ene-1-carbonyl]benzaldehyde

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 08-MAR-23   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   08-MAR-23         0                                  
HETATM    1  O   UNK     0       6.668  -0.770   0.000  0.00  0.00           O+0
HETATM    2  C   UNK     0       6.668  -2.310   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       8.002  -3.080   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       9.336  -2.310   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       8.002  -4.620   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0       9.336  -5.390   0.000  0.00  0.00           O+0
HETATM    7  C   UNK     0      10.669  -4.620   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       6.668  -5.390   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       6.668  -6.930   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       8.002  -7.700   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       9.336  -6.930   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      10.669  -7.700   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      12.003  -6.930   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      12.003  -5.390   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0      13.337  -4.620   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0      14.670  -5.390   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0      14.670  -6.930   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0      16.004  -4.620   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0      10.669  -9.240   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       9.336 -10.010   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0       8.002  -9.240   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0       6.668 -10.010   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0       6.668 -11.550   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0       5.335 -12.320   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0       4.001 -11.550   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0       4.001 -10.010   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0       5.335  -9.240   0.000  0.00  0.00           C+0
HETATM   28  O   UNK     0       5.335  -7.700   0.000  0.00  0.00           O+0
HETATM   29  C   UNK     0       5.335  -4.620   0.000  0.00  0.00           C+0
HETATM   30  O   UNK     0       4.001  -5.390   0.000  0.00  0.00           O+0
HETATM   31  C   UNK     0       5.335  -3.080   0.000  0.00  0.00           C+0
HETATM   32  C   UNK     0       4.001  -2.310   0.000  0.00  0.00           C+0
HETATM   33  O   UNK     0       4.001  -0.770   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3   31                                                  
CONECT    3    2    4    5                                                  
CONECT    4    3                                                            
CONECT    5    3    6    8                                                  
CONECT    6    5    7                                                       
CONECT    7    6                                                            
CONECT    8    5    9   29                                                  
CONECT    9    8   10   28                                                  
CONECT   10    9   11   21                                                  
CONECT   11   10   12                                                       
CONECT   12   11   13   19                                                  
CONECT   13   12   14                                                       
CONECT   14   13   15                                                       
CONECT   15   14   16                                                       
CONECT   16   15   17   18                                                  
CONECT   17   16                                                            
CONECT   18   16                                                            
CONECT   19   12   20                                                       
CONECT   20   19   21                                                       
CONECT   21   20   10   22                                                  
CONECT   22   21   23   27                                                  
CONECT   23   22   24                                                       
CONECT   24   23   25                                                       
CONECT   25   24   26                                                       
CONECT   26   25   27                                                       
CONECT   27   26   22                                                       
CONECT   28    9                                                            
CONECT   29    8   30   31                                                  
CONECT   30   29                                                            
CONECT   31   29    2   32                                                  
CONECT   32   31   33                                                       
CONECT   33   32                                                            
MASTER        0    0    0    0    0    0    0    0   33    0   70    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₂₈H₃₂O₅

Average Mass

448.5590 Da

Monoisotopic Mass

448.22497 Da

IUPAC Name

2,6-dihydroxy-4-methoxy-3-methyl-5-[(1S,6S)-3-(4-methylpent-3-en-1-yl)-6-phenylcyclohex-3-ene-1-carbonyl]benzaldehyde

Traditional Name

2,6-dihydroxy-4-methoxy-3-methyl-5-[(1S,6S)-3-(4-methylpent-3-en-1-yl)-6-phenylcyclohex-3-ene-1-carbonyl]benzaldehyde

CAS Registry Number

Not Available

SMILES

COC1=C(C(=O)[C@H]2CC(CCC=C(C)C)=CC[C@@H]2C2=CC=CC=C2)C(O)=C(C=O)C(O)=C1C

InChI Identifier

InChI=1S/C28H32O5/c1-17(2)9-8-10-19-13-14-21(20-11-6-5-7-12-20)22(15-19)26(31)24-27(32)23(16-29)25(30)18(3)28(24)33-4/h5-7,9,11-13,16,21-22,30,32H,8,10,14-15H2,1-4H3/t21-,22+/m1/s1

InChI Key

XLJIRBMYVUVTKC-YADHBBJMSA-N

Experimental Spectra

Spectrum Type	Description	Depositor Email	Depositor Organization	Depositor	Deposition Date	View
1D NMR	¹³C NMR Spectrum (1D, 101 MHz, CDCL3, experimental)	maihieu@snu.ac.kr	Seoul National University	Van-Hieu, MAI	2024-06-24	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, CDCL3, experimental)	maihieu@snu.ac.kr	Seoul National University	Van-Hieu, MAI	2024-06-24	View Spectrum

Predicted Spectra

Not Available

Chemical Shift Submissions

Not Available

Species

Species of Origin

Species Name	Source	Reference
Cleistocalyx operculatus		Not Available

Chemical Taxonomy

Description

This compound belongs to the class of organic compounds known as diterpenoids. These are terpene compounds formed by four isoprene units.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Prenol lipids

Sub Class

Diterpenoids

Direct Parent

Diterpenoids

Alternative Parents

Substituents

Diterpenoid
Linear 1,7-diphenylheptane skeleton
Alkyl-phenylketone
Methoxyphenol
Phenylketone
Hydroxybenzaldehyde
Phenoxy compound
Methoxybenzene
Aryl alkyl ketone
Aryl ketone
Phenol ether
P-cresol
O-cresol
Benzoyl
Benzaldehyde
Anisole
Aryl-aldehyde
Phenol
Alkyl aryl ether
Alpha-branched alpha,beta-unsaturated-ketone
Benzenoid
Beta-hydroxy ketone
Monocyclic benzene moiety
Vinylogous acid
Alpha,beta-unsaturated ketone
Enone
Acryloyl-group
Ketone
Ether
Organic oxygen compound
Organic oxide
Hydrocarbon derivative
Organooxygen compound
Carbonyl group
Aldehyde
Aromatic homomonocyclic compound

Molecular Framework

Aromatic homomonocyclic 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	8.02	ChemAxon
pKa (Strongest Acidic)	7.28	ChemAxon
pKa (Strongest Basic)	-4.6	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	5	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	83.83 Å²	ChemAxon
Rotatable Bond Count	8	ChemAxon
Refractivity	133.56 m³·mol⁻¹	ChemAxon
Polarizability	49.99 Å³	ChemAxon
Number of Rings	3	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	No	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

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KNApSAcK ID

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Chemspider ID

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KEGG Compound ID

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BioCyc ID

Not Available

BiGG ID

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Wikipedia Link

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METLIN ID

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PubChem Compound

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PDB ID

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ChEBI ID

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Good Scents ID

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References

General References

Showing NP-Card for (±)-Cleichalmyrcin D2 (NP0333487)

MOL for NP0333487 ((±)-Cleichalmyrcin D2)

3D MOL for NP0333487 ((±)-Cleichalmyrcin D2)

3D SDF for NP0333487 ((±)-Cleichalmyrcin D2)

3D-SDF for NP0333487 ((±)-Cleichalmyrcin D2)

PDB for NP0333487 ((±)-Cleichalmyrcin D2)

3D PDB for NP0333487 ((±)-Cleichalmyrcin D2)

SMILES for NP0333487 ((±)-Cleichalmyrcin D2)

INCHI for NP0333487 ((±)-Cleichalmyrcin D2)

Structure for NP0333487 ((±)-Cleichalmyrcin D2)

3D Structure for NP0333487 ((±)-Cleichalmyrcin D2)