NP-MRD: Showing NP-Card for (1s,2s,4r,5r,6r)-5-[(1r)-1-hydroxyethyl]-1-isocyano-3,7-dioxatricyclo[4.1.0.0²,⁴]heptan-5-ol (NP0300230)

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Record Information

Version

2.0

Created at

2022-09-10 12:31:07 UTC

Updated at

2022-09-10 12:31:07 UTC

NP-MRD ID

NP0300230

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(1s,2s,4r,5r,6r)-5-[(1r)-1-hydroxyethyl]-1-isocyano-3,7-dioxatricyclo[4.1.0.0²,⁴]heptan-5-ol

Description

(1S,2S,4R,5R,6R)-5-[(1R)-1-hydroxyethyl]-1-isocyano-3,7-dioxatricyclo[4.1.0.0²,⁴]Heptan-5-ol belongs to the class of organic compounds known as 1,4-dioxepanes. These are dioxepanes with the two ring oxygen atoms at position 1 and 4, respectively. (1s,2s,4r,5r,6r)-5-[(1r)-1-hydroxyethyl]-1-isocyano-3,7-dioxatricyclo[4.1.0.0²,⁴]heptan-5-ol is found in Trichoderma koningii. Based on a literature review very few articles have been published on (1S,2S,4R,5R,6R)-5-[(1R)-1-hydroxyethyl]-1-isocyano-3,7-dioxatricyclo[4.1.0.0²,⁴]Heptan-5-ol.

Structure

MOL SDF PDB SMILES InChI


  Mrv1652309102214312D          

 13 15  0  0  1  0            999 V2000
    2.5712    2.8459    0.0000 C   0  5  0  0  0  0  0  0  0  0  0  0
    2.4850    2.0254    0.0000 N   0  3  0  0  0  0  0  0  0  0  0  0
    2.3987    1.2049    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    3.2057    1.0334    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.6537    0.4203    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.9862   -0.0646    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.5383   -0.6777    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4342   -0.6777    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.6891   -1.4623    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6272   -0.5062    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.3188    0.4203    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.7668    1.0334    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.5737    1.2049    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
  1  2  3  0  0  0  0
  3  2  1  1  0  0  0
  3  4  1  0  0  0  0
  5  4  1  6  0  0  0
  3  5  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  1  6  0  0  0
  6  8  1  1  0  0  0
  8  9  1  0  0  0  0
  8 10  1  1  0  0  0
  6 11  1  0  0  0  0
 11 12  1  6  0  0  0
 13 12  1  6  0  0  0
 11 13  1  0  0  0  0
  3 13  1  0  0  0  0
M  CHG  2   1  -1   2   1
M  END
> <DATABASE_ID>
NP0300230

> <DATABASE_NAME>
NP-MRD

> <SMILES>
C[C@@H](O)[C@@]1(O)[C@@H]2O[C@@H]2[C@@]2(O[C@H]12)[N+]#[C-]

> <INCHI_IDENTIFIER>
InChI=1S/C8H9NO4/c1-3(10)7(11)4-5(12-4)8(9-2)6(7)13-8/h3-6,10-11H,1H3/t3-,4-,5+,6-,7-,8+/m1/s1

> <INCHI_KEY>
GVXPCFBDZAWTNL-RDULZCEMSA-N

> <FORMULA>
C8H9NO4

> <MOLECULAR_WEIGHT>
183.163

> <EXACT_MASS>
183.053157774

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_ATOM_COUNT>
22

> <JCHEM_AVERAGE_POLARIZABILITY>
16.453531775488205

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(1S,2S,4R,5R,6R)-5-[(1R)-1-hydroxyethyl]-1-isocyano-3,7-dioxatricyclo[4.1.0.0^{2,4}]heptan-5-ol

> <JCHEM_LOGP>
-2.8075418152092784

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
1

> <JCHEM_PKA>
14.831431944173044

> <JCHEM_PKA_STRONGEST_ACIDIC>
11.642844650519356

> <JCHEM_PKA_STRONGEST_BASIC>
-3.2049454350381197

> <JCHEM_POLAR_SURFACE_AREA>
69.88000000000001

> <JCHEM_REFRACTIVITY>
48.110600000000005

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
(1S,2S,4R,5R,6R)-5-[(1R)-1-hydroxyethyl]-1-isocyano-3,7-dioxatricyclo[4.1.0.0^{2,4}]heptan-5-ol

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 10-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   10-SEP-22         0                                  
HETATM    1  C   UNK     0       4.800   5.312   0.000  0.00  0.00           C-1
HETATM    2  N   UNK     0       4.639   3.781   0.000  0.00  0.00           N+1
HETATM    3  C   UNK     0       4.478   2.249   0.000  0.00  0.00           C+0
HETATM    4  O   UNK     0       5.984   1.929   0.000  0.00  0.00           O+0
HETATM    5  C   UNK     0       4.954   0.785   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       3.708  -0.121   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0       4.738  -1.265   0.000  0.00  0.00           O+0
HETATM    8  C   UNK     0       2.677  -1.265   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       3.153  -2.730   0.000  0.00  0.00           C+0
HETATM   10  O   UNK     0       1.171  -0.945   0.000  0.00  0.00           O+0
HETATM   11  C   UNK     0       2.462   0.785   0.000  0.00  0.00           C+0
HETATM   12  O   UNK     0       1.431   1.929   0.000  0.00  0.00           O+0
HETATM   13  C   UNK     0       2.938   2.249   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4    5   13                                             
CONECT    4    3    5                                                       
CONECT    5    4    3    6                                                  
CONECT    6    5    7    8   11                                             
CONECT    7    6                                                            
CONECT    8    6    9   10                                                  
CONECT    9    8                                                            
CONECT   10    8                                                            
CONECT   11    6   12   13                                                  
CONECT   12   11   13                                                       
CONECT   13   12   11    3                                                  
MASTER        0    0    0    0    0    0    0    0   13    0   30    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₈H₉NO₄

Average Mass

183.1630 Da

Monoisotopic Mass

183.05316 Da

IUPAC Name

(1S,2S,4R,5R,6R)-5-[(1R)-1-hydroxyethyl]-1-isocyano-3,7-dioxatricyclo[4.1.0.0^{2,4}]heptan-5-ol

Traditional Name

(1S,2S,4R,5R,6R)-5-[(1R)-1-hydroxyethyl]-1-isocyano-3,7-dioxatricyclo[4.1.0.0^{2,4}]heptan-5-ol

CAS Registry Number

Not Available

SMILES

C[C@@H](O)[C@@]1(O)[C@@H]2O[C@@H]2[C@@]2(O[C@H]12)[N+]#[C-]

InChI Identifier

InChI=1S/C8H9NO4/c1-3(10)7(11)4-5(12-4)8(9-2)6(7)13-8/h3-6,10-11H,1H3/t3-,4-,5+,6-,7-,8+/m1/s1

InChI Key

GVXPCFBDZAWTNL-RDULZCEMSA-N

Experimental Spectra

Not Available

Predicted Spectra

Not Available

Chemical Shift Submissions

Not Available

Species

Species of Origin

Species Name	Source	Reference
Trichoderma koningii	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as 1,4-dioxepanes. These are dioxepanes with the two ring oxygen atoms at position 1 and 4, respectively.

Kingdom

Organic compounds

Super Class

Organoheterocyclic compounds

Class

Dioxepanes

Sub Class

1,4-dioxepanes

Direct Parent

1,4-dioxepanes

Alternative Parents

Substituents

1,4-dioxepane
Oxane
Tertiary alcohol
Cyclic alcohol
Secondary alcohol
1,2-diol
Oxacycle
Organic isocyanide
Ether
Oxirane
Dialkyl ether
Organic nitrogen compound
Organic oxygen compound
Organopnictogen compound
Hydrocarbon derivative
Organic zwitterion
Organooxygen compound
Organonitrogen compound
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	-2.8	ChemAxon
pKa (Strongest Acidic)	11.64	ChemAxon
pKa (Strongest Basic)	-3.2	ChemAxon
Physiological Charge	1	ChemAxon
Hydrogen Acceptor Count	4	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	69.88 Å²	ChemAxon
Rotatable Bond Count	1	ChemAxon
Refractivity	48.11 m³·mol⁻¹	ChemAxon
Polarizability	16.45 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

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

163190992

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

LOTUS database [Link]

Showing NP-Card for (1s,2s,4r,5r,6r)-5-[(1r)-1-hydroxyethyl]-1-isocyano-3,7-dioxatricyclo[4.1.0.0²,⁴]heptan-5-ol (NP0300230)

MOL for NP0300230 ((1s,2s,4r,5r,6r)-5-[(1r)-1-hydroxyethyl]-1-isocyano-3,7-dioxatricyclo[4.1.0.0²,⁴]heptan-5-ol)

3D MOL for NP0300230 ((1s,2s,4r,5r,6r)-5-[(1r)-1-hydroxyethyl]-1-isocyano-3,7-dioxatricyclo[4.1.0.0²,⁴]heptan-5-ol)

3D SDF for NP0300230 ((1s,2s,4r,5r,6r)-5-[(1r)-1-hydroxyethyl]-1-isocyano-3,7-dioxatricyclo[4.1.0.0²,⁴]heptan-5-ol)

3D-SDF for NP0300230 ((1s,2s,4r,5r,6r)-5-[(1r)-1-hydroxyethyl]-1-isocyano-3,7-dioxatricyclo[4.1.0.0²,⁴]heptan-5-ol)

PDB for NP0300230 ((1s,2s,4r,5r,6r)-5-[(1r)-1-hydroxyethyl]-1-isocyano-3,7-dioxatricyclo[4.1.0.0²,⁴]heptan-5-ol)

3D PDB for NP0300230 ((1s,2s,4r,5r,6r)-5-[(1r)-1-hydroxyethyl]-1-isocyano-3,7-dioxatricyclo[4.1.0.0²,⁴]heptan-5-ol)

SMILES for NP0300230 ((1s,2s,4r,5r,6r)-5-[(1r)-1-hydroxyethyl]-1-isocyano-3,7-dioxatricyclo[4.1.0.0²,⁴]heptan-5-ol)

INCHI for NP0300230 ((1s,2s,4r,5r,6r)-5-[(1r)-1-hydroxyethyl]-1-isocyano-3,7-dioxatricyclo[4.1.0.0²,⁴]heptan-5-ol)

Structure for NP0300230 ((1s,2s,4r,5r,6r)-5-[(1r)-1-hydroxyethyl]-1-isocyano-3,7-dioxatricyclo[4.1.0.0²,⁴]heptan-5-ol)

3D Structure for NP0300230 ((1s,2s,4r,5r,6r)-5-[(1r)-1-hydroxyethyl]-1-isocyano-3,7-dioxatricyclo[4.1.0.0²,⁴]heptan-5-ol)