NP-MRD: Showing NP-Card for lamesticumin b (NP0279988)

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Record Information

Version

2.0

Created at

2022-09-09 05:34:24 UTC

Updated at

2022-09-09 05:34:25 UTC

NP-MRD ID

NP0279988

Secondary Accession Numbers

None

Natural Product Identification

Common Name

lamesticumin b

Description

Lamesticumin B belongs to the class of organic compounds known as bicyclic monoterpenoids. These are monoterpenoids containing exactly 2 rings, which are fused to each other. lamesticumin b is found in Lansium domesticum. It was first documented in 2011 (PMID: 21401117). Based on a literature review very few articles have been published on lamesticumin B (PMID: 34136135).

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652309092207342D          

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     RDKit          3D

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M  END


  Mrv1652309092207342D          

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    4.9514   -1.0156    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.9514   -1.8406    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.6659   -2.2531    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.6659   -3.0781    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.3804   -1.8406    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.0948   -2.2531    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  5  4  1  1  0  0  0
  5  6  1  0  0  0  0
  6  7  1  0  0  0  0
  6  8  1  0  0  0  0
  6  9  1  0  0  0  0
  9 10  1  1  0  0  0
  9 11  1  0  0  0  0
 11 12  1  0  0  0  0
 12 13  1  0  0  0  0
  5 13  1  0  0  0  0
 13 14  1  1  0  0  0
 13 15  1  0  0  0  0
  2 15  1  0  0  0  0
 15 16  1  1  0  0  0
 16 17  1  0  0  0  0
 18 17  1  1  0  0  0
 18 19  1  0  0  0  0
 19 20  1  0  0  0  0
 19 21  2  0  0  0  0
 21 22  1  0  0  0  0
 22 23  1  0  0  0  0
 23 24  1  1  0  0  0
 24 25  1  0  0  0  0
 24 26  1  0  0  0  0
 24 27  1  0  0  0  0
 23 28  1  0  0  0  0
 18 28  1  0  0  0  0
 28 29  1  1  0  0  0
 28 30  1  6  0  0  0
 30 31  1  0  0  0  0
 31 32  1  0  0  0  0
 32 33  2  0  0  0  0
 32 34  1  0  0  0  0
 34 35  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0279988

> <DATABASE_NAME>
NP-MRD

> <SMILES>
COC(=O)CC[C@]1(C)[C@@H](CC[C@H]2C(=C)CC[C@H]3C(C)(C)[C@@H](O)CC[C@]23C)C(C)=CC[C@H]1C(C)(C)O

> <INCHI_IDENTIFIER>
InChI=1S/C31H52O4/c1-20-10-14-24-28(3,4)26(32)16-18-30(24,7)22(20)12-13-23-21(2)11-15-25(29(5,6)34)31(23,8)19-17-27(33)35-9/h11,22-26,32,34H,1,10,12-19H2,2-9H3/t22-,23-,24-,25-,26-,30+,31+/m0/s1

> <INCHI_KEY>
KYHATJJXUGJUJJ-LUFVGXTESA-N

> <FORMULA>
C31H52O4

> <MOLECULAR_WEIGHT>
488.753

> <EXACT_MASS>
488.386560154

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_ATOM_COUNT>
87

> <JCHEM_AVERAGE_POLARIZABILITY>
58.99838022012191

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
methyl 3-[(1R,2S,6R)-2-{2-[(1S,4aR,6S,8aR)-6-hydroxy-5,5,8a-trimethyl-2-methylidene-decahydronaphthalen-1-yl]ethyl}-6-(2-hydroxypropan-2-yl)-1,3-dimethylcyclohex-3-en-1-yl]propanoate

> <JCHEM_LOGP>
5.849002799666668

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
19.94091094580536

> <JCHEM_PKA_STRONGEST_ACIDIC>
19.489414018698508

> <JCHEM_PKA_STRONGEST_BASIC>
-0.4242280566675579

> <JCHEM_POLAR_SURFACE_AREA>
66.76

> <JCHEM_REFRACTIVITY>
143.86050000000003

> <JCHEM_ROTATABLE_BOND_COUNT>
8

> <JCHEM_RULE_OF_FIVE>
0

> <JCHEM_TRADITIONAL_IUPAC>
methyl 3-[(1R,2S,6R)-2-{2-[(1S,4aR,6S,8aR)-6-hydroxy-5,5,8a-trimethyl-2-methylidene-hexahydro-1H-naphthalen-1-yl]ethyl}-6-(2-hydroxypropan-2-yl)-1,3-dimethylcyclohex-3-en-1-yl]propanoate

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 09-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   09-SEP-22         0                                  
HETATM    1  C   UNK     0       5.740  -5.205   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       4.201  -5.259   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       3.478  -6.618   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       1.939  -6.672   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       1.123  -5.366   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      -0.416  -5.420   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      -0.096  -6.926   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      -1.844  -5.997   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      -1.232  -4.114   0.000  0.00  0.00           C+0
HETATM   10  O   UNK     0      -2.771  -4.168   0.000  0.00  0.00           O+0
HETATM   11  C   UNK     0      -0.509  -2.754   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       1.030  -2.700   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       1.846  -4.006   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       2.569  -2.647   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       3.385  -3.953   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       4.108  -2.593   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       5.647  -2.539   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       6.370  -1.179   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       5.554   0.127   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       4.015   0.073   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0       6.277   1.486   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0       7.816   1.540   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0       8.632   0.234   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0      10.171   0.288   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0      10.117   1.827   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0      11.710   0.341   0.000  0.00  0.00           C+0
HETATM   27  O   UNK     0      10.225  -1.251   0.000  0.00  0.00           O+0
HETATM   28  C   UNK     0       7.909  -1.126   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0       8.016  -2.662   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0       9.243  -1.896   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0       9.243  -3.436   0.000  0.00  0.00           C+0
HETATM   32  C   UNK     0      10.576  -4.206   0.000  0.00  0.00           C+0
HETATM   33  O   UNK     0      10.576  -5.746   0.000  0.00  0.00           O+0
HETATM   34  O   UNK     0      11.910  -3.436   0.000  0.00  0.00           O+0
HETATM   35  C   UNK     0      13.244  -4.206   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3   15                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4    6   13                                                  
CONECT    6    5    7    8    9                                             
CONECT    7    6                                                            
CONECT    8    6                                                            
CONECT    9    6   10   11                                                  
CONECT   10    9                                                            
CONECT   11    9   12                                                       
CONECT   12   11   13                                                       
CONECT   13   12    5   14   15                                             
CONECT   14   13                                                            
CONECT   15   13    2   16                                                  
CONECT   16   15   17                                                       
CONECT   17   16   18                                                       
CONECT   18   17   19   28                                                  
CONECT   19   18   20   21                                                  
CONECT   20   19                                                            
CONECT   21   19   22                                                       
CONECT   22   21   23                                                       
CONECT   23   22   24   28                                                  
CONECT   24   23   25   26   27                                             
CONECT   25   24                                                            
CONECT   26   24                                                            
CONECT   27   24                                                            
CONECT   28   23   18   29   30                                             
CONECT   29   28                                                            
CONECT   30   28   31                                                       
CONECT   31   30   32                                                       
CONECT   32   31   33   34                                                  
CONECT   33   32                                                            
CONECT   34   32   35                                                       
CONECT   35   34                                                            
MASTER        0    0    0    0    0    0    0    0   35    0   74    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₃₁H₅₂O₄

Average Mass

488.7530 Da

Monoisotopic Mass

488.38656 Da

IUPAC Name

methyl 3-[(1R,2S,6R)-2-{2-[(1S,4aR,6S,8aR)-6-hydroxy-5,5,8a-trimethyl-2-methylidene-decahydronaphthalen-1-yl]ethyl}-6-(2-hydroxypropan-2-yl)-1,3-dimethylcyclohex-3-en-1-yl]propanoate

Traditional Name

methyl 3-[(1R,2S,6R)-2-{2-[(1S,4aR,6S,8aR)-6-hydroxy-5,5,8a-trimethyl-2-methylidene-hexahydro-1H-naphthalen-1-yl]ethyl}-6-(2-hydroxypropan-2-yl)-1,3-dimethylcyclohex-3-en-1-yl]propanoate

CAS Registry Number

Not Available

SMILES

COC(=O)CC[C@]1(C)[C@@H](CC[C@H]2C(=C)CC[C@H]3C(C)(C)[C@@H](O)CC[C@]23C)C(C)=CC[C@H]1C(C)(C)O

InChI Identifier

InChI=1S/C31H52O4/c1-20-10-14-24-28(3,4)26(32)16-18-30(24,7)22(20)12-13-23-21(2)11-15-25(29(5,6)34)31(23,8)19-17-27(33)35-9/h11,22-26,32,34H,1,10,12-19H2,2-9H3/t22-,23-,24-,25-,26-,30+,31+/m0/s1

InChI Key

KYHATJJXUGJUJJ-LUFVGXTESA-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, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 252 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 50 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 75 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 101 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 126 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 151 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 176 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 201 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 226 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, H₂O, 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
Lansium domesticum	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as bicyclic monoterpenoids. These are monoterpenoids containing exactly 2 rings, which are fused to each other.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Prenol lipids

Sub Class

Monoterpenoids

Direct Parent

Bicyclic monoterpenoids

Alternative Parents

Substituents

Bicyclic monoterpenoid
P-menthane monoterpenoid
Fatty acid ester
Fatty acyl
Cyclic alcohol
Methyl ester
Tertiary alcohol
Carboxylic acid ester
Secondary alcohol
Carboxylic acid derivative
Monocarboxylic acid or derivatives
Hydrocarbon derivative
Organic oxide
Alcohol
Carbonyl group
Organic oxygen compound
Organooxygen compound
Aliphatic homopolycyclic compound

Molecular Framework

Aliphatic homopolycyclic compounds

External Descriptors

methyl ester (CHEBI:67475 )
diol (CHEBI:67475 )
triterpenoid (CHEBI:67475 )

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	5.85	ChemAxon
pKa (Strongest Acidic)	19.49	ChemAxon
pKa (Strongest Basic)	-0.42	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	3	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	66.76 Å²	ChemAxon
Rotatable Bond Count	8	ChemAxon
Refractivity	143.86 m³·mol⁻¹	ChemAxon
Polarizability	59 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

26333559

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

53262847

PDB ID

Not Available

ChEBI ID

67475

Good Scents ID

Not Available

References

General References

Dong SH, Zhang CR, Dong L, Wu Y, Yue JM: Onoceranoid-type triterpenoids from Lansium domesticum. J Nat Prod. 2011 May 27;74(5):1042-8. doi: 10.1021/np100943x. Epub 2011 Mar 14. [PubMed:21401117 ]
Fadhilah K, Wahyuono S, Astuti P: A bioactive compound isolated from Duku ( Lansium domesticum Corr) fruit peels exhibits cytotoxicity against T47D cell line. F1000Res. 2020 Jan 6;9:3. doi: 10.12688/f1000research.21072.2. eCollection 2020. [PubMed:34136135 ]
LOTUS database [Link]

Showing NP-Card for lamesticumin b (NP0279988)

MOL for NP0279988 (lamesticumin b)

3D MOL for NP0279988 (lamesticumin b)

3D SDF for NP0279988 (lamesticumin b)

3D-SDF for NP0279988 (lamesticumin b)

PDB for NP0279988 (lamesticumin b)

3D PDB for NP0279988 (lamesticumin b)

SMILES for NP0279988 (lamesticumin b)

INCHI for NP0279988 (lamesticumin b)

Structure for NP0279988 (lamesticumin b)

3D Structure for NP0279988 (lamesticumin b)