NP-MRD: Showing NP-Card for [4S-(4alpha,5alpha,6beta)]-4,6-dihydroxy-2-(hydroxymethyl)-5-(1-methylethyl)-2-Cyclohexen-1-one (NP0057768)

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Record Information

Version

2.0

Created at

2022-04-28 03:09:59 UTC

Updated at

2022-04-28 03:09:59 UTC

NP-MRD ID

NP0057768

Secondary Accession Numbers

None

Natural Product Identification

Common Name

[4S-(4alpha,5alpha,6beta)]-4,6-dihydroxy-2-(hydroxymethyl)-5-(1-methylethyl)-2-Cyclohexen-1-one

Description

C10H16O4 belongs to the class of organic compounds known as menthane monoterpenoids. These are monoterpenoids with a structure based on the o-, m-, or p-menthane backbone. P-menthane consists of the cyclohexane ring with a methyl group and a (2-methyl)-propyl group at the 1 and 4 ring position, respectively. The o- and m- menthanes are much rarer, and presumably arise by alkyl migration of p-menthanes. [4S-(4alpha,5alpha,6beta)]-4,6-dihydroxy-2-(hydroxymethyl)-5-(1-methylethyl)-2-Cyclohexen-1-one is found in Sphaeranthus bullatus and Sphaeranthus suaveolens. [4S-(4alpha,5alpha,6beta)]-4,6-dihydroxy-2-(hydroxymethyl)-5-(1-methylethyl)-2-Cyclohexen-1-one was first documented in 2014 (PMID: 24860298). Based on a literature review a small amount of articles have been published on C10H16O4 (PMID: 34636563) (PMID: 33148878) (PMID: 27049168) (PMID: 26396837).

Structure

MOL 3D MOL SDF PDB SMILES InChI

     RDKit          3D

 30 30  0  0  0  0  0  0  0  0999 V2000
   -2.5803   -1.0000   -0.1751 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0548    0.4020   -0.0812 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.7240    1.0508    1.1239 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5715    0.5105    0.0114 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.0750   -0.1430    1.1564 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.3803   -1.4061    1.4749 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.5467   -0.2314    0.9990 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1899    0.0137   -0.1235 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6751   -0.0877   -0.2371 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2532   -0.4593    0.9519 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4265    0.3984   -1.2978 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9940    1.0305   -2.2162 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0048    0.0049   -1.3244 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.7103    0.6098   -2.3499 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6119   -1.5272    0.7851 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6611   -0.8973   -0.4965 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1095   -1.5869   -0.9906 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4392    0.9497   -0.9678 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3332    1.9234    0.8562 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9200    1.4231    1.7999 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3017    0.3173    1.7218 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3141    1.5913    0.0261 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0802    0.4783    2.0888 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2707   -2.0670    0.7507 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.1401   -0.5222    1.8831 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.9546   -0.8040   -1.0238 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.0710    0.9135   -0.5571 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.5645   -1.3892    0.9128 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1162   -1.0741   -1.3395 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7066    1.5785   -2.3008 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  2  4  1  0
  4  5  1  0
  5  6  1  0
  5  7  1  0
  7  8  2  0
  8  9  1  0
  9 10  1  0
  8 11  1  0
 11 12  2  0
 11 13  1  0
 13 14  1  0
 13  4  1  0
  1 15  1  0
  1 16  1  0
  1 17  1  0
  2 18  1  6
  3 19  1  0
  3 20  1  0
  3 21  1  0
  4 22  1  1
  5 23  1  1
  6 24  1  0
  7 25  1  0
  9 26  1  0
  9 27  1  0
 10 28  1  0
 13 29  1  1
 14 30  1  0
M  END


  Mrv1652304282205102D          

 14 14  0  0  1  0            999 V2000
    1.4289    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -0.4125    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   -0.0000    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.0000    0.8250    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.7145    1.2375    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.7145    2.0625    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
   -0.7145    2.0625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4289    0.8250    0.0000 C   0  0  0  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
    2.1434   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579   -0.0000    0.0000 O   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  2  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
  1  7  1  0  0  0  0
  7  8  1  1  0  0  0
  6  9  1  1  0  0  0
  9 10  1  0  0  0  0
  9 11  1  0  0  0  0
  5 12  1  6  0  0  0
  2 13  1  0  0  0  0
 13 14  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0057768

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CC(C)[C@H]1[C@@H](O)C=C(CO)C(=O)[C@@H]1O

> <INCHI_IDENTIFIER>
InChI=1S/C10H16O4/c1-5(2)8-7(12)3-6(4-11)9(13)10(8)14/h3,5,7-8,10-12,14H,4H2,1-2H3/t7-,8-,10+/m0/s1

> <INCHI_KEY>
HPZJQYJGKPNSIZ-OYNCUSHFSA-N

> <FORMULA>
C10H16O4

> <MOLECULAR_WEIGHT>
200.234

> <EXACT_MASS>
200.104858995

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_ATOM_COUNT>
30

> <JCHEM_AVERAGE_POLARIZABILITY>
20.880084173633115

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
(4S,5S,6R)-4,6-dihydroxy-2-(hydroxymethyl)-5-(propan-2-yl)cyclohex-2-en-1-one

> <ALOGPS_LOGP>
-0.37

> <JCHEM_LOGP>
-0.3629625859999995

> <ALOGPS_LOGS>
-0.47

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
14.39756532769238

> <JCHEM_PKA_STRONGEST_ACIDIC>
13.017189561326859

> <JCHEM_PKA_STRONGEST_BASIC>
-2.8212930246558043

> <JCHEM_POLAR_SURFACE_AREA>
77.76

> <JCHEM_REFRACTIVITY>
52.002599999999994

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
6.80e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(4S,5S,6R)-4,6-dihydroxy-2-(hydroxymethyl)-5-isopropylcyclohex-2-en-1-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       2.667   1.540   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       2.667  -0.000   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       1.334  -0.770   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  -0.000   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       0.000   1.540   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       1.334   2.310   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0       1.334   3.850   0.000  0.00  0.00           O+0
HETATM    9  C   UNK     0      -1.334   2.310   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      -1.334   3.850   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      -2.667   1.540   0.000  0.00  0.00           C+0
HETATM   12  O   UNK     0      -1.334  -0.770   0.000  0.00  0.00           O+0
HETATM   13  C   UNK     0       4.001  -0.770   0.000  0.00  0.00           C+0
HETATM   14  O   UNK     0       5.335  -0.000   0.000  0.00  0.00           O+0
CONECT    1    2    7                                                       
CONECT    2    1    3   13                                                  
CONECT    3    2    4    5                                                  
CONECT    4    3                                                            
CONECT    5    3    6   12                                                  
CONECT    6    5    7    9                                                  
CONECT    7    6    1    8                                                  
CONECT    8    7                                                            
CONECT    9    6   10   11                                                  
CONECT   10    9                                                            
CONECT   11    9                                                            
CONECT   12    5                                                            
CONECT   13    2   14                                                       
CONECT   14   13                                                            
MASTER        0    0    0    0    0    0    0    0   14    0   28    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₁₀H₁₆O₄

Average Mass

200.2340 Da

Monoisotopic Mass

200.10486 Da

IUPAC Name

(4S,5S,6R)-4,6-dihydroxy-2-(hydroxymethyl)-5-(propan-2-yl)cyclohex-2-en-1-one

Traditional Name

(4S,5S,6R)-4,6-dihydroxy-2-(hydroxymethyl)-5-isopropylcyclohex-2-en-1-one

CAS Registry Number

Not Available

SMILES

CC(C)[C@H]1[C@@H](O)C=C(CO)C(=O)[C@@H]1O

InChI Identifier

InChI=1S/C10H16O4/c1-5(2)8-7(12)3-6(4-11)9(13)10(8)14/h3,5,7-8,10-12,14H,4H2,1-2H3/t7-,8-,10+/m0/s1

InChI Key

HPZJQYJGKPNSIZ-OYNCUSHFSA-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
Sphaeranthus bullatus	Plant	KNApSAcK
Sphaeranthus suaveolens	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as menthane monoterpenoids. These are monoterpenoids with a structure based on the o-, m-, or p-menthane backbone. P-menthane consists of the cyclohexane ring with a methyl group and a (2-methyl)-propyl group at the 1 and 4 ring position, respectively. The o- and m- menthanes are much rarer, and presumably arise by alkyl migration of p-menthanes.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Prenol lipids

Sub Class

Monoterpenoids

Direct Parent

Menthane monoterpenoids

Alternative Parents

Substituents

P-menthane monoterpenoid
Monocyclic monoterpenoid
Cyclohexenone
Cyclic ketone
Secondary alcohol
Ketone
Organic oxygen compound
Organic oxide
Hydrocarbon derivative
Primary alcohol
Organooxygen compound
Carbonyl group
Alcohol
Aliphatic homomonocyclic compound

Molecular Framework

Aliphatic 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	-0.37	ALOGPS
logP	-0.36	ChemAxon
logS	-0.47	ALOGPS
pKa (Strongest Acidic)	13.02	ChemAxon
pKa (Strongest Basic)	-2.8	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	4	ChemAxon
Hydrogen Donor Count	3	ChemAxon
Polar Surface Area	77.76 Å²	ChemAxon
Rotatable Bond Count	2	ChemAxon
Refractivity	52 m³·mol⁻¹	ChemAxon
Polarizability	20.88 Å³	ChemAxon
Number of Rings	1	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	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

C00000837

Chemspider ID

Not Available

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

C10H16O4

METLIN ID

Not Available

PubChem Compound

14589114

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Berndt T: Peroxy Radical Processes and Product Formation in the OH Radical-Initiated Oxidation of alpha-Pinene for Near-Atmospheric Conditions. J Phys Chem A. 2021 Oct 21;125(41):9151-9160. doi: 10.1021/acs.jpca.1c05576. Epub 2021 Oct 12. [PubMed:34636563 ]
Zhao FH, Li SY, Guo WY, Zhao ZH, Guo XW, Li YS, Fan SQ, Li ZL: Two new Cd(II) MOFs of 1,4-bis(1H-benzimidazol-1-yl)butane and flexible dicarboxylate ligands: luminescence sensing towards Fe(3). Acta Crystallogr C Struct Chem. 2020 Nov 1;76(Pt 11):1024-1033. doi: 10.1107/S2053229620013698. Epub 2020 Oct 22. [PubMed:33148878 ]
Kurten T, Tiusanen K, Roldin P, Rissanen M, Luy JN, Boy M, Ehn M, Donahue N: alpha-Pinene Autoxidation Products May Not Have Extremely Low Saturation Vapor Pressures Despite High O:C Ratios. J Phys Chem A. 2016 Apr 28;120(16):2569-82. doi: 10.1021/acs.jpca.6b02196. Epub 2016 Apr 19. [PubMed:27049168 ]
Macias MA, Suescun L, Pandolfi E, Schapiro V, Tibhe GD, Mombru AW: Crystal structure and absolute configuration of (3aS,4S,5R,7aR)-2,2,7-trimethyl-3a,4,5,7a-tetra-hydro-1,3-benzodioxole-4,5-diol. Acta Crystallogr E Crystallogr Commun. 2015 Aug 6;71(Pt 9):1013-6. doi: 10.1107/S2056989015014590. eCollection 2015 Sep 1. [PubMed:26396837 ]
Giuseppe B, Francesco N, Giovanni G, Alessandro S, Mollica Nardo V: Poly[(mu4-decanedio-ato)cobalt(II)]. Acta Crystallogr Sect E Struct Rep Online. 2014 Apr 2;70(Pt 5):m159. doi: 10.1107/S1600536814006011. eCollection 2014 May 1. [PubMed:24860298 ]

Showing NP-Card for [4S-(4alpha,5alpha,6beta)]-4,6-dihydroxy-2-(hydroxymethyl)-5-(1-methylethyl)-2-Cyclohexen-1-one (NP0057768)

MOL for NP0057768 ([4S-(4alpha,5alpha,6beta)]-4,6-dihydroxy-2-(hydroxymethyl)-5-(1-methylethyl)-2-Cyclohexen-1-one)

3D MOL for NP0057768 ([4S-(4alpha,5alpha,6beta)]-4,6-dihydroxy-2-(hydroxymethyl)-5-(1-methylethyl)-2-Cyclohexen-1-one)

3D SDF for NP0057768 ([4S-(4alpha,5alpha,6beta)]-4,6-dihydroxy-2-(hydroxymethyl)-5-(1-methylethyl)-2-Cyclohexen-1-one)

3D-SDF for NP0057768 ([4S-(4alpha,5alpha,6beta)]-4,6-dihydroxy-2-(hydroxymethyl)-5-(1-methylethyl)-2-Cyclohexen-1-one)

PDB for NP0057768 ([4S-(4alpha,5alpha,6beta)]-4,6-dihydroxy-2-(hydroxymethyl)-5-(1-methylethyl)-2-Cyclohexen-1-one)

3D PDB for NP0057768 ([4S-(4alpha,5alpha,6beta)]-4,6-dihydroxy-2-(hydroxymethyl)-5-(1-methylethyl)-2-Cyclohexen-1-one)

SMILES for NP0057768 ([4S-(4alpha,5alpha,6beta)]-4,6-dihydroxy-2-(hydroxymethyl)-5-(1-methylethyl)-2-Cyclohexen-1-one)

INCHI for NP0057768 ([4S-(4alpha,5alpha,6beta)]-4,6-dihydroxy-2-(hydroxymethyl)-5-(1-methylethyl)-2-Cyclohexen-1-one)

Structure for NP0057768 ([4S-(4alpha,5alpha,6beta)]-4,6-dihydroxy-2-(hydroxymethyl)-5-(1-methylethyl)-2-Cyclohexen-1-one)

3D Structure for NP0057768 ([4S-(4alpha,5alpha,6beta)]-4,6-dihydroxy-2-(hydroxymethyl)-5-(1-methylethyl)-2-Cyclohexen-1-one)