NP-MRD: Showing NP-Card for (1s,4s,5r,6s,7r,11s)-5-chloro-2,10-dioxatricyclo[5.3.1.0⁴,¹¹]undecane-4,6,9-triol (NP0208713)

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Record Information

Version

2.0

Created at

2022-09-05 05:49:25 UTC

Updated at

2022-09-05 05:49:25 UTC

NP-MRD ID

NP0208713

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(1s,4s,5r,6s,7r,11s)-5-chloro-2,10-dioxatricyclo[5.3.1.0⁴,¹¹]undecane-4,6,9-triol

Description

(1S,4S,5R,6S,7R,11S)-5-chloro-2,10-dioxatricyclo[5.3.1.0⁴,¹¹]Undecane-4,6,9-triol belongs to the class of organic compounds known as iridoids and derivatives. These are monoterpenes containing a skeleton structurally characterized by the presence of a cylopentane fused to a pyran ( forming a 4,7-dimethylcyclopenta[c]pyran), or a derivative where the pentane moiety is open. (1s,4s,5r,6s,7r,11s)-5-chloro-2,10-dioxatricyclo[5.3.1.0⁴,¹¹]undecane-4,6,9-triol is found in Rehmannia glutinosa. Based on a literature review very few articles have been published on (1S,4S,5R,6S,7R,11S)-5-chloro-2,10-dioxatricyclo[5.3.1.0⁴,¹¹]Undecane-4,6,9-triol.

Structure

MOL 3D MOL SDF PDB SMILES InChI

     RDKit          3D

 28 30  0  0  0  0  0  0  0  0999 V2000
    2.9146    0.5091   -0.6852 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.3971   -0.0260    0.4821 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.5527   -1.2501    0.2461 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2882   -0.9915   -0.4843 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.8817   -1.6271    0.2337 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.4673   -2.6509   -0.4801 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8338   -0.5212    0.5881 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.8836   -0.2343    2.3524 Cl  0  0  0  0  0  0  0  0  0  0  0  0
   -1.4175    0.7043   -0.1701 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.3322    0.9934   -1.1672 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1800    1.8929    0.7192 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0105    2.5028    0.2972 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.8108    1.4356   -0.0936 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.5262    0.9551    1.0104 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0416    0.4200   -0.7476 C   0  0  1  0  0  0  0  0  0  0  0  0
    3.4814   -0.1132   -1.1887 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.1560   -0.2453    1.2473 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.1976   -2.0291   -0.2280 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3091   -1.6640    1.2611 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3577   -1.5247   -1.4773 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5269   -2.0694    1.1995 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8321   -2.3699   -1.3513 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8781   -0.7833    0.2950 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1104    1.8884   -1.5483 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0514    1.6268    1.7860 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0030    2.6315    0.5582 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5494    1.8808   -0.8088 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0907    0.6591   -1.8457 H   0  0  0  0  0  0  0  0  0  0  0  0
  6  5  1  0
  5  7  1  0
  7  8  1  0
  7  9  1  0
  9 10  1  6
  9 11  1  0
 11 12  1  0
 12 13  1  0
 13 14  1  0
 14  2  1  0
  2  1  1  0
  2  3  1  0
  3  4  1  0
  4 15  1  0
  4  5  1  0
 15  9  1  0
 15 13  1  0
  6 22  1  0
  5 21  1  1
  7 23  1  6
 10 24  1  0
 11 25  1  0
 11 26  1  0
 13 27  1  6
  2 17  1  1
  1 16  1  0
  3 18  1  0
  3 19  1  0
  4 20  1  6
 15 28  1  6
M  END


  Mrv1652309052207492D          

 15 17  0  0  1  0            999 V2000
    4.4084   -0.7317    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.6297   -0.4592    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0044   -0.9973    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2257   -0.7248    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.0605   -0.7849    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.6213   -1.4832    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7420   -0.0239    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.0609    0.1658    0.0000 Cl  0  0  0  0  0  0  0  0  0  0  0  0
    1.3673    0.5143    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.6623    0.9427    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.5569    1.3172    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3792    1.3849    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.6977    0.6239    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    3.4764    0.3514    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.0724    0.0858    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  4  3  1  1  0  0  0
  4  5  1  0  0  0  0
  5  6  1  6  0  0  0
  5  7  1  0  0  0  0
  7  8  1  1  0  0  0
  7  9  1  0  0  0  0
  9 10  1  6  0  0  0
  9 11  1  0  0  0  0
 11 12  1  0  0  0  0
 13 12  1  1  0  0  0
 13 14  1  0  0  0  0
  2 14  1  0  0  0  0
 15 13  1  1  0  0  0
  4 15  1  0  0  0  0
  9 15  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0208713

> <DATABASE_NAME>
NP-MRD

> <SMILES>
O[C@@H]1[C@@H](Cl)[C@@]2(O)CO[C@H]3OC(O)C[C@@H]1[C@@H]23

> <INCHI_IDENTIFIER>
InChI=1S/C9H13ClO5/c10-7-6(12)3-1-4(11)15-8-5(3)9(7,13)2-14-8/h3-8,11-13H,1-2H2/t3-,4?,5-,6+,7-,8+,9-/m1/s1

> <INCHI_KEY>
IRXIOTLCTXBESO-DSTLYXNISA-N

> <FORMULA>
C9H13ClO5

> <MOLECULAR_WEIGHT>
236.65

> <EXACT_MASS>
236.0451512

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_ATOM_COUNT>
28

> <JCHEM_AVERAGE_POLARIZABILITY>
21.32672347380028

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(1S,4S,5R,6S,7R,11S)-5-chloro-2,10-dioxatricyclo[5.3.1.0^{4,11}]undecane-4,6,9-triol

> <JCHEM_LOGP>
-0.9112805606666661

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
12.806546847641613

> <JCHEM_PKA_STRONGEST_ACIDIC>
12.189513222167589

> <JCHEM_PKA_STRONGEST_BASIC>
-3.333223867843719

> <JCHEM_POLAR_SURFACE_AREA>
79.15

> <JCHEM_REFRACTIVITY>
48.87640000000001

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
(1S,4S,5R,6S,7R,11S)-5-chloro-2,10-dioxatricyclo[5.3.1.0^{4,11}]undecane-4,6,9-triol

> <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  O   UNK     0       8.229  -1.366   0.000  0.00  0.00           O+0
HETATM    2  C   UNK     0       6.776  -0.857   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       5.608  -1.862   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       4.155  -1.353   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       1.980  -1.465   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0       1.160  -2.769   0.000  0.00  0.00           O+0
HETATM    7  C   UNK     0       1.385  -0.045   0.000  0.00  0.00           C+0
HETATM    8 Cl   UNK     0      -0.114   0.309   0.000  0.00  0.00          Cl+0
HETATM    9  C   UNK     0       2.552   0.960   0.000  0.00  0.00           C+0
HETATM   10  O   UNK     0       1.236   1.760   0.000  0.00  0.00           O+0
HETATM   11  C   UNK     0       2.906   2.459   0.000  0.00  0.00           C+0
HETATM   12  O   UNK     0       4.441   2.585   0.000  0.00  0.00           O+0
HETATM   13  C   UNK     0       5.036   1.165   0.000  0.00  0.00           C+0
HETATM   14  O   UNK     0       6.489   0.656   0.000  0.00  0.00           O+0
HETATM   15  C   UNK     0       3.868   0.160   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3   14                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5   15                                                  
CONECT    5    4    6    7                                                  
CONECT    6    5                                                            
CONECT    7    5    8    9                                                  
CONECT    8    7                                                            
CONECT    9    7   10   11   15                                             
CONECT   10    9                                                            
CONECT   11    9   12                                                       
CONECT   12   11   13                                                       
CONECT   13   12   14   15                                                  
CONECT   14   13    2                                                       
CONECT   15   13    4    9                                                  
MASTER        0    0    0    0    0    0    0    0   15    0   34    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₉H₁₃ClO₅

Average Mass

236.6500 Da

Monoisotopic Mass

236.04515 Da

IUPAC Name

(1S,4S,5R,6S,7R,11S)-5-chloro-2,10-dioxatricyclo[5.3.1.0^{4,11}]undecane-4,6,9-triol

Traditional Name

(1S,4S,5R,6S,7R,11S)-5-chloro-2,10-dioxatricyclo[5.3.1.0^{4,11}]undecane-4,6,9-triol

CAS Registry Number

Not Available

SMILES

O[C@@H]1[C@@H](Cl)[C@@]2(O)CO[C@H]3OC(O)C[C@@H]1[C@@H]23

InChI Identifier

InChI=1S/C9H13ClO5/c10-7-6(12)3-1-4(11)15-8-5(3)9(7,13)2-14-8/h3-8,11-13H,1-2H2/t3-,4?,5-,6+,7-,8+,9-/m1/s1

InChI Key

IRXIOTLCTXBESO-DSTLYXNISA-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
Rehmannia glutinosa	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as iridoids and derivatives. These are monoterpenes containing a skeleton structurally characterized by the presence of a cylopentane fused to a pyran ( forming a 4,7-dimethylcyclopenta[c]pyran), or a derivative where the pentane moiety is open.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Prenol lipids

Sub Class

Monoterpenoids

Direct Parent

Iridoids and derivatives

Alternative Parents

Substituents

Iridoid-skeleton
Furopyran
Pyran
Oxane
Tetrahydrofuran
Tertiary alcohol
Furan
Cyclic alcohol
Secondary alcohol
Hemiacetal
Halohydrin
Chlorohydrin
Oxacycle
Organoheterocyclic compound
Polyol
Acetal
Organic oxygen compound
Hydrocarbon derivative
Organooxygen compound
Organochloride
Organohalogen compound
Alkyl halide
Alkyl chloride
Alcohol
Aliphatic heteropolycyclic compound

Molecular Framework

Aliphatic heteropolycyclic 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	-0.91	ChemAxon
pKa (Strongest Acidic)	12.19	ChemAxon
pKa (Strongest Basic)	-3.3	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	5	ChemAxon
Hydrogen Donor Count	3	ChemAxon
Polar Surface Area	79.15 Å²	ChemAxon
Rotatable Bond Count	0	ChemAxon
Refractivity	48.88 m³·mol⁻¹	ChemAxon
Polarizability	21.33 Å³	ChemAxon
Number of Rings	3	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

4478855

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

5320904

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

LOTUS database [Link]

Showing NP-Card for (1s,4s,5r,6s,7r,11s)-5-chloro-2,10-dioxatricyclo[5.3.1.0⁴,¹¹]undecane-4,6,9-triol (NP0208713)

MOL for NP0208713 ((1s,4s,5r,6s,7r,11s)-5-chloro-2,10-dioxatricyclo[5.3.1.0⁴,¹¹]undecane-4,6,9-triol)

3D MOL for NP0208713 ((1s,4s,5r,6s,7r,11s)-5-chloro-2,10-dioxatricyclo[5.3.1.0⁴,¹¹]undecane-4,6,9-triol)

3D SDF for NP0208713 ((1s,4s,5r,6s,7r,11s)-5-chloro-2,10-dioxatricyclo[5.3.1.0⁴,¹¹]undecane-4,6,9-triol)

3D-SDF for NP0208713 ((1s,4s,5r,6s,7r,11s)-5-chloro-2,10-dioxatricyclo[5.3.1.0⁴,¹¹]undecane-4,6,9-triol)

PDB for NP0208713 ((1s,4s,5r,6s,7r,11s)-5-chloro-2,10-dioxatricyclo[5.3.1.0⁴,¹¹]undecane-4,6,9-triol)

3D PDB for NP0208713 ((1s,4s,5r,6s,7r,11s)-5-chloro-2,10-dioxatricyclo[5.3.1.0⁴,¹¹]undecane-4,6,9-triol)

SMILES for NP0208713 ((1s,4s,5r,6s,7r,11s)-5-chloro-2,10-dioxatricyclo[5.3.1.0⁴,¹¹]undecane-4,6,9-triol)

INCHI for NP0208713 ((1s,4s,5r,6s,7r,11s)-5-chloro-2,10-dioxatricyclo[5.3.1.0⁴,¹¹]undecane-4,6,9-triol)

Structure for NP0208713 ((1s,4s,5r,6s,7r,11s)-5-chloro-2,10-dioxatricyclo[5.3.1.0⁴,¹¹]undecane-4,6,9-triol)

3D Structure for NP0208713 ((1s,4s,5r,6s,7r,11s)-5-chloro-2,10-dioxatricyclo[5.3.1.0⁴,¹¹]undecane-4,6,9-triol)