NP-MRD: Showing NP-Card for (±)-Cleichalmyrcin D1 (NP0333486)

Jump To Section:

Identification Spectra BioTaxonomy ChemoTaxonomy Physical properties Links References XML

Record Information

Version

2.0

Created at

2024-06-24 12:51:29 UTC

Updated at

2024-10-07 12:35:14 UTC

NP-MRD ID

NP0333486

Natural Product DOI

https://doi.org/10.57994/2940

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(±)-Cleichalmyrcin D1

Description

(±)-Cleichalmyrcin D1 belongs to the class of organic compounds known as linear diarylheptanoids. These are diarylheptanoids with an open heptane chain. The two aromatic rings are linked only by the heptane chain. Based on a literature review very few articles have been published on (±)-Cleichalmyrcin D1.

Structure

MOL SDF PDB SMILES InChI


  Mrv2104 03082315262D          

 32 34  0  0  1  0            999 V2000
   -2.1434   -0.4125    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
   -1.4289   -1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145   -1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000   -1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4289   -2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145   -2.8875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145   -3.7125    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.0000   -4.1250    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.0000   -4.9500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145   -5.3625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145   -6.1875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4289   -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
   -1.4289   -4.9500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4289   -4.1250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -3.7125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -2.8875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -2.8875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -3.7125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -4.1250    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
   -2.8579   -1.6500    0.0000 C   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
   -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 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1434   -2.8875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1434   -3.7125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5724   -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  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  3  6  2  0  0  0  0
  6  7  1  0  0  0  0
  8  7  1  6  0  0  0
  8  9  1  0  0  0  0
  9 10  1  0  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  2  0  0  0  0
 15 16  1  0  0  0  0
 11 17  2  0  0  0  0
 17 18  1  0  0  0  0
  8 18  1  0  0  0  0
  9 19  1  1  0  0  0
 19 20  2  0  0  0  0
 20 21  1  0  0  0  0
 21 22  2  0  0  0  0
 22 23  1  0  0  0  0
 23 24  2  0  0  0  0
 19 24  1  0  0  0  0
  7 25  2  0  0  0  0
  2 26  2  0  0  0  0
 26 27  1  0  0  0  0
 27 28  1  0  0  0  0
 28 29  2  0  0  0  0
 27 30  2  0  0  0  0
  6 30  1  0  0  0  0
 30 31  1  0  0  0  0
 26 32  1  0  0  0  0
M  END


  Mrv2104 03082315262D          

 32 34  0  0  1  0            999 V2000
   -2.1434   -0.4125    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
   -1.4289   -1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145   -1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000   -1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4289   -2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145   -2.8875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145   -3.7125    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.0000   -4.1250    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.0000   -4.9500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145   -5.3625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145   -6.1875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4289   -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
   -1.4289   -4.9500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4289   -4.1250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -3.7125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -2.8875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -2.8875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -3.7125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -4.1250    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
   -2.8579   -1.6500    0.0000 C   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
   -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 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1434   -2.8875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1434   -3.7125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5724   -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  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  3  6  2  0  0  0  0
  6  7  1  0  0  0  0
  8  7  1  6  0  0  0
  8  9  1  0  0  0  0
  9 10  1  0  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  2  0  0  0  0
 15 16  1  0  0  0  0
 11 17  2  0  0  0  0
 17 18  1  0  0  0  0
  8 18  1  0  0  0  0
  9 19  1  1  0  0  0
 19 20  2  0  0  0  0
 20 21  1  0  0  0  0
 21 22  2  0  0  0  0
 22 23  1  0  0  0  0
 23 24  2  0  0  0  0
 19 24  1  0  0  0  0
  7 25  2  0  0  0  0
  2 26  2  0  0  0  0
 26 27  1  0  0  0  0
 27 28  1  0  0  0  0
 28 29  2  0  0  0  0
 27 30  2  0  0  0  0
  6 30  1  0  0  0  0
 30 31  1  0  0  0  0
 26 32  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0333486

> <DATABASE_NAME>
NP-MRD

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

> <INCHI_IDENTIFIER>
InChI=1S/C27H30O5/c1-4-5-7-10-18-13-14-20(21(15-18)19-11-8-6-9-12-19)25(30)23-26(31)22(16-28)24(29)17(2)27(23)32-3/h4-6,8-9,11-13,16,20-21,29,31H,7,10,14-15H2,1-3H3/b5-4+/t20-,21+/m0/s1

> <INCHI_KEY>
JSIGZZPEMQBJRH-ARMKIQIJSA-N

> <FORMULA>
C27H30O5

> <MOLECULAR_WEIGHT>
434.532

> <EXACT_MASS>
434.209324066

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_ATOM_COUNT>
62

> <JCHEM_AVERAGE_POLARIZABILITY>
48.42243138793398

> <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)-4-[(3E)-pent-3-en-1-yl]-6-phenylcyclohex-3-ene-1-carbonyl]benzaldehyde

> <JCHEM_LOGP>
7.774133064666666

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
9.18742814500676

> <JCHEM_PKA_STRONGEST_ACIDIC>
7.277966542530288

> <JCHEM_PKA_STRONGEST_BASIC>
-4.631489518343438

> <JCHEM_POLAR_SURFACE_AREA>
83.83000000000001

> <JCHEM_REFRACTIVITY>
129.276

> <JCHEM_ROTATABLE_BOND_COUNT>
8

> <JCHEM_RULE_OF_FIVE>
0

> <JCHEM_TRADITIONAL_IUPAC>
2,6-dihydroxy-4-methoxy-3-methyl-5-[(1S,6S)-4-[(3E)-pent-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  C   UNK     0      -4.001  -0.770   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -4.001  -2.310   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -2.667  -3.080   0.000  0.00  0.00           C+0
HETATM    4  O   UNK     0      -1.334  -2.310   0.000  0.00  0.00           O+0
HETATM    5  C   UNK     0       0.000  -3.080   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      -2.667  -4.620   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      -1.334  -5.390   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      -1.334  -6.930   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       0.000  -7.700   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      -0.000  -9.240   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      -1.334 -10.010   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      -1.334 -11.550   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      -2.667 -12.320   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      -4.001 -11.550   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0      -4.001 -10.010   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0      -5.335  -9.240   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0      -2.667  -9.240   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0      -2.667  -7.700   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       1.334  -6.930   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       1.334  -5.390   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0       2.667  -4.620   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0       4.001  -5.390   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0       4.001  -6.930   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0       2.667  -7.700   0.000  0.00  0.00           C+0
HETATM   25  O   UNK     0       0.000  -4.620   0.000  0.00  0.00           O+0
HETATM   26  C   UNK     0      -5.335  -3.080   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0      -5.335  -4.620   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0      -6.668  -5.390   0.000  0.00  0.00           C+0
HETATM   29  O   UNK     0      -6.668  -6.930   0.000  0.00  0.00           O+0
HETATM   30  C   UNK     0      -4.001  -5.390   0.000  0.00  0.00           C+0
HETATM   31  O   UNK     0      -4.001  -6.930   0.000  0.00  0.00           O+0
HETATM   32  O   UNK     0      -6.668  -2.310   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3   26                                                  
CONECT    3    2    4    6                                                  
CONECT    4    3    5                                                       
CONECT    5    4                                                            
CONECT    6    3    7   30                                                  
CONECT    7    6    8   25                                                  
CONECT    8    7    9   18                                                  
CONECT    9    8   10   19                                                  
CONECT   10    9   11                                                       
CONECT   11   10   12   17                                                  
CONECT   12   11   13                                                       
CONECT   13   12   14                                                       
CONECT   14   13   15                                                       
CONECT   15   14   16                                                       
CONECT   16   15                                                            
CONECT   17   11   18                                                       
CONECT   18   17    8                                                       
CONECT   19    9   20   24                                                  
CONECT   20   19   21                                                       
CONECT   21   20   22                                                       
CONECT   22   21   23                                                       
CONECT   23   22   24                                                       
CONECT   24   23   19                                                       
CONECT   25    7                                                            
CONECT   26    2   27   32                                                  
CONECT   27   26   28   30                                                  
CONECT   28   27   29                                                       
CONECT   29   28                                                            
CONECT   30   27    6   31                                                  
CONECT   31   30                                                            
CONECT   32   26                                                            
MASTER        0    0    0    0    0    0    0    0   32    0   68    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₂₇H₃₀O₅

Average Mass

434.5320 Da

Monoisotopic Mass

434.20932 Da

IUPAC Name

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

Traditional Name

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

CAS Registry Number

Not Available

SMILES

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

InChI Identifier

InChI=1S/C27H30O5/c1-4-5-7-10-18-13-14-20(21(15-18)19-11-8-6-9-12-19)25(30)23-26(31)22(16-28)24(29)17(2)27(23)32-3/h4-6,8-9,11-13,16,20-21,29,31H,7,10,14-15H2,1-3H3/b5-4+/t20-,21+/m0/s1

InChI Key

JSIGZZPEMQBJRH-ARMKIQIJSA-N

Experimental Spectra

Spectrum Type	Description	Depositor Email	Depositor Organization	Depositor	Deposition Date	View
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
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

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 linear diarylheptanoids. These are diarylheptanoids with an open heptane chain. The two aromatic rings are linked only by the heptane chain.

Kingdom

Organic compounds

Super Class

Phenylpropanoids and polyketides

Class

Diarylheptanoids

Sub Class

Linear diarylheptanoids

Direct Parent

Linear diarylheptanoids

Alternative Parents

Substituents

Linear 1,7-diphenylheptane skeleton
Sesquiterpenoid
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	7.77	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	129.28 m³·mol⁻¹	ChemAxon
Polarizability	48.42 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

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

Not Available

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Showing NP-Card for (±)-Cleichalmyrcin D1 (NP0333486)

MOL for NP0333486 ((±)-Cleichalmyrcin D1)

3D MOL for NP0333486 ((±)-Cleichalmyrcin D1)

3D SDF for NP0333486 ((±)-Cleichalmyrcin D1)

3D-SDF for NP0333486 ((±)-Cleichalmyrcin D1)

PDB for NP0333486 ((±)-Cleichalmyrcin D1)

3D PDB for NP0333486 ((±)-Cleichalmyrcin D1)

SMILES for NP0333486 ((±)-Cleichalmyrcin D1)

INCHI for NP0333486 ((±)-Cleichalmyrcin D1)

Structure for NP0333486 ((±)-Cleichalmyrcin D1)

3D Structure for NP0333486 ((±)-Cleichalmyrcin D1)