NP-MRD: Showing NP-Card for (1r,2r,4s)-4-[(2s)-1,2-dihydroxypropan-2-yl]-1-methylcyclohexane-1,2-diol (NP0213408)

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Record Information

Version

2.0

Created at

2022-09-05 12:23:26 UTC

Updated at

2022-09-05 12:23:27 UTC

NP-MRD ID

NP0213408

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(1r,2r,4s)-4-[(2s)-1,2-dihydroxypropan-2-yl]-1-methylcyclohexane-1,2-diol

Description

(1R,2R,4S)-4-[(2S)-1,2-dihydroxypropan-2-yl]-1-methylcyclohexane-1,2-diol 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. (1r,2r,4s)-4-[(2s)-1,2-dihydroxypropan-2-yl]-1-methylcyclohexane-1,2-diol is found in Cnidium monnieri. Based on a literature review very few articles have been published on (1R,2R,4S)-4-[(2S)-1,2-dihydroxypropan-2-yl]-1-methylcyclohexane-1,2-diol.

Structure

MOL 3D MOL SDF PDB SMILES InChI

     RDKit          3D

 34 34  0  0  0  0  0  0  0  0999 V2000
   -2.7387   -1.3396    0.8629 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0101   -0.5813   -0.2728 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.5045   -1.2307   -1.4314 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5972    0.7803   -0.2680 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3213    1.5754   -1.3518 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5410   -0.7180   -0.1438 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.1252    0.0282   -1.2594 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6369   -0.1056   -1.2006 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0013    0.6335    0.0911 C   0  0  1  0  0  0  0  0  0  0  0  0
    3.4849    0.7775    0.1072 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4129    1.8918    0.0207 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4722   -0.1071    1.2593 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.2947   -1.2258    1.4577 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0291   -0.4731    1.2029 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3698   -2.3763    0.8430 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5801   -0.8274    1.8214 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8115   -1.3180    0.5653 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4209   -0.6374   -2.2155 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7207    0.6249   -0.2840 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4458    1.3206    0.7120 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2756    2.5214   -1.0294 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3206   -1.8089   -0.3769 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0749    1.1203   -1.2139 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2065   -0.3261   -2.2531 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0444    0.4975   -2.0198 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9801   -1.1397   -1.2023 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.8171    0.9661   -0.9457 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.8552    1.6334    0.6952 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.9854   -0.1796    0.3968 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9088    2.5335    0.6198 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6627    0.5400    2.1681 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8937   -2.0496    1.0817 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1161   -1.3460    1.8784 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5496    0.3459    1.6848 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  6
  2  4  1  0
  4  5  1  0
  2  6  1  0
  6  7  1  0
  7  8  1  0
  8  9  1  0
  9 10  1  0
  9 11  1  6
  9 12  1  0
 12 13  1  0
 12 14  1  0
 14  6  1  0
  1 15  1  0
  1 16  1  0
  1 17  1  0
  3 18  1  0
  4 19  1  0
  4 20  1  0
  5 21  1  0
  6 22  1  6
  7 23  1  0
  7 24  1  0
  8 25  1  0
  8 26  1  0
 10 27  1  0
 10 28  1  0
 10 29  1  0
 11 30  1  0
 12 31  1  1
 13 32  1  0
 14 33  1  0
 14 34  1  0
M  END


  Mrv1652309052214232D          

 14 14  0  0  1  0            999 V2000
    1.5395   -1.2375    0.0000 C   0  0  0  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
   -0.1105   -1.2375    0.0000 O   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   -2.4750    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -0.4125    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.8250    0.0000 C   0  0  0  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
    0.1842    1.8695    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2448    1.8695    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.8250    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.1434    1.2375    0.0000 O   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
  2  1  1  6  0  0  0
  2  3  1  6  0  0  0
  2  4  1  0  0  0  0
  4  5  1  0  0  0  0
  6  2  1  1  0  0  0
  6  7  1  0  0  0  0
  7  8  1  0  0  0  0
  8  9  1  0  0  0  0
  9 10  1  6  0  0  0
  9 11  1  1  0  0  0
  9 12  1  0  0  0  0
 12 13  1  6  0  0  0
 12 14  1  0  0  0  0
  6 14  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0213408

> <DATABASE_NAME>
NP-MRD

> <SMILES>
C[C@@](O)(CO)[C@H]1CC[C@@](C)(O)[C@H](O)C1

> <INCHI_IDENTIFIER>
InChI=1S/C10H20O4/c1-9(13)4-3-7(5-8(9)12)10(2,14)6-11/h7-8,11-14H,3-6H2,1-2H3/t7-,8+,9+,10+/m0/s1

> <INCHI_KEY>
QEFNQQRVZDFDIJ-SGIHWFKDSA-N

> <FORMULA>
C10H20O4

> <MOLECULAR_WEIGHT>
204.266

> <EXACT_MASS>
204.136159124

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_ATOM_COUNT>
34

> <JCHEM_AVERAGE_POLARIZABILITY>
21.781125221732015

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(1R,2R,4S)-4-[(2S)-1,2-dihydroxypropan-2-yl]-1-methylcyclohexane-1,2-diol

> <JCHEM_LOGP>
-0.9350975396666668

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
14.076828736135628

> <JCHEM_PKA_STRONGEST_ACIDIC>
13.49315569244352

> <JCHEM_PKA_STRONGEST_BASIC>
-3.0715866598061323

> <JCHEM_POLAR_SURFACE_AREA>
80.92

> <JCHEM_REFRACTIVITY>
52.276199999999996

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
(1R,2R,4S)-4-[(2S)-1,2-dihydroxypropan-2-yl]-1-methylcyclohexane-1,2-diol

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 05-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   05-SEP-22         0                                  
HETATM    1  C   UNK     0       2.874  -2.310   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       1.334  -2.310   0.000  0.00  0.00           C+0
HETATM    3  O   UNK     0      -0.206  -2.310   0.000  0.00  0.00           O+0
HETATM    4  C   UNK     0       1.334  -3.850   0.000  0.00  0.00           C+0
HETATM    5  O   UNK     0       2.667  -4.620   0.000  0.00  0.00           O+0
HETATM    6  C   UNK     0       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      -0.000   0.000   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       0.000   1.540   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       1.334   2.310   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       0.344   3.490   0.000  0.00  0.00           C+0
HETATM   11  O   UNK     0       2.324   3.490   0.000  0.00  0.00           O+0
HETATM   12  C   UNK     0       2.667   1.540   0.000  0.00  0.00           C+0
HETATM   13  O   UNK     0       4.001   2.310   0.000  0.00  0.00           O+0
HETATM   14  C   UNK     0       2.667  -0.000   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3    4    6                                             
CONECT    3    2                                                            
CONECT    4    2    5                                                       
CONECT    5    4                                                            
CONECT    6    2    7   14                                                  
CONECT    7    6    8                                                       
CONECT    8    7    9                                                       
CONECT    9    8   10   11   12                                             
CONECT   10    9                                                            
CONECT   11    9                                                            
CONECT   12    9   13   14                                                  
CONECT   13   12                                                            
CONECT   14   12    6                                                       
MASTER        0    0    0    0    0    0    0    0   14    0   28    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₁₀H₂₀O₄

Average Mass

204.2660 Da

Monoisotopic Mass

204.13616 Da

IUPAC Name

(1R,2R,4S)-4-[(2S)-1,2-dihydroxypropan-2-yl]-1-methylcyclohexane-1,2-diol

Traditional Name

(1R,2R,4S)-4-[(2S)-1,2-dihydroxypropan-2-yl]-1-methylcyclohexane-1,2-diol

CAS Registry Number

Not Available

SMILES

C[C@@](O)(CO)[C@H]1CC[C@@](C)(O)[C@H](O)C1

InChI Identifier

InChI=1S/C10H20O4/c1-9(13)4-3-7(5-8(9)12)10(2,14)6-11/h7-8,11-14H,3-6H2,1-2H3/t7-,8+,9+,10+/m0/s1

InChI Key

QEFNQQRVZDFDIJ-SGIHWFKDSA-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
Cnidium monnieri	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
Cyclohexanol
Tertiary alcohol
Cyclic alcohol
Secondary alcohol
Organic oxygen compound
Hydrocarbon derivative
Primary alcohol
Organooxygen compound
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	-0.94	ChemAxon
pKa (Strongest Acidic)	13.49	ChemAxon
pKa (Strongest Basic)	-3.1	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	4	ChemAxon
Hydrogen Donor Count	4	ChemAxon
Polar Surface Area	80.92 Å²	ChemAxon
Rotatable Bond Count	2	ChemAxon
Refractivity	52.28 m³·mol⁻¹	ChemAxon
Polarizability	21.78 Å³	ChemAxon
Number of Rings	1	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

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

162976410

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

LOTUS database [Link]

Showing NP-Card for (1r,2r,4s)-4-[(2s)-1,2-dihydroxypropan-2-yl]-1-methylcyclohexane-1,2-diol (NP0213408)

MOL for NP0213408 ((1r,2r,4s)-4-[(2s)-1,2-dihydroxypropan-2-yl]-1-methylcyclohexane-1,2-diol)

3D MOL for NP0213408 ((1r,2r,4s)-4-[(2s)-1,2-dihydroxypropan-2-yl]-1-methylcyclohexane-1,2-diol)

3D SDF for NP0213408 ((1r,2r,4s)-4-[(2s)-1,2-dihydroxypropan-2-yl]-1-methylcyclohexane-1,2-diol)

3D-SDF for NP0213408 ((1r,2r,4s)-4-[(2s)-1,2-dihydroxypropan-2-yl]-1-methylcyclohexane-1,2-diol)

PDB for NP0213408 ((1r,2r,4s)-4-[(2s)-1,2-dihydroxypropan-2-yl]-1-methylcyclohexane-1,2-diol)

3D PDB for NP0213408 ((1r,2r,4s)-4-[(2s)-1,2-dihydroxypropan-2-yl]-1-methylcyclohexane-1,2-diol)

SMILES for NP0213408 ((1r,2r,4s)-4-[(2s)-1,2-dihydroxypropan-2-yl]-1-methylcyclohexane-1,2-diol)

INCHI for NP0213408 ((1r,2r,4s)-4-[(2s)-1,2-dihydroxypropan-2-yl]-1-methylcyclohexane-1,2-diol)

Structure for NP0213408 ((1r,2r,4s)-4-[(2s)-1,2-dihydroxypropan-2-yl]-1-methylcyclohexane-1,2-diol)

3D Structure for NP0213408 ((1r,2r,4s)-4-[(2s)-1,2-dihydroxypropan-2-yl]-1-methylcyclohexane-1,2-diol)