NP-MRD: Showing NP-Card for Conduritol B epoxide (NP0340045)

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Record Information

Version

2.0

Created at

2024-09-12 01:09:58 UTC

Updated at

2024-09-12 01:09:58 UTC

NP-MRD ID

NP0340045

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Conduritol B epoxide

Description

Conduritol B epoxide was first documented in 1977 (PMID: 560212).

Structure

MOL SDF PDB SMILES InChI


  Mrv1652304032019062D          

 17 18  0  0  1  0            999 V2000
    2.8579    0.8250    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.8579    1.6500    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.1434    0.4125    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.1434    2.0625    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.4289    0.8250    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.4289    1.6500    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    3.5724    0.4125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724    2.0625    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -0.4125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434    2.8875    0.0000 O   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
    3.5724    1.2375    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579    2.4750    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.0000    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434    1.2375    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    0.4125    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.0164    2.3645    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  0  0  0  0
  3  1  1  0  0  0  0
  4  2  1  0  0  0  0
  5  3  1  0  0  0  0
  6  4  1  0  0  0  0
  6  5  1  0  0  0  0
  1  7  1  6  0  0  0
  2  8  1  1  0  0  0
  3  9  1  1  0  0  0
  4 10  1  1  0  0  0
 11  5  1  0  0  0  0
 11  6  1  0  0  0  0
  1 12  1  1  0  0  0
  2 13  1  6  0  0  0
  3 14  1  6  0  0  0
  4 15  1  1  0  0  0
  5 16  1  1  0  0  0
  6 17  1  1  0  0  0
M  END
> <DATABASE_ID>
NP0340045

> <DATABASE_NAME>
NP-MRD

> <SMILES>
[H][C@]12O[C@@]1([H])[C@]([H])(O)[C@@]([H])(O)[C@]([H])(O)[C@@]2([H])O

> <INCHI_IDENTIFIER>
InChI=1S/C6H10O5/c7-1-2(8)4(10)6-5(11-6)3(1)9/h1-10H/t1-,2-,3+,4+,5-,6+/m0/s1

> <INCHI_KEY>
ZHMWOVGZCINIHW-FTYOSCRSSA-N

> <FORMULA>
C6H10O5

> <MOLECULAR_WEIGHT>
162.141

> <EXACT_MASS>
162.052823422

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_ATOM_COUNT>
21

> <JCHEM_AVERAGE_POLARIZABILITY>
14.301351261405713

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(1R,2R,3S,4S,5R,6S)-7-oxabicyclo[4.1.0]heptane-2,3,4,5-tetrol

> <ALOGPS_LOGP>
-2.72

> <JCHEM_LOGP>
-2.6203060796666673

> <ALOGPS_LOGS>
0.90

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
13.17814845560562

> <JCHEM_PKA_STRONGEST_ACIDIC>
12.455655518319112

> <JCHEM_PKA_STRONGEST_BASIC>
-3.646002117912589

> <JCHEM_POLAR_SURFACE_AREA>
93.45

> <JCHEM_REFRACTIVITY>
32.2649

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.29e+03 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(1R,2R,3S,4S,5R,6S)-7-oxabicyclo[4.1.0]heptane-2,3,4,5-tetrol

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 03-APR-20   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   03-APR-20         0                                  
HETATM    1  C   UNK     0       5.335   1.540   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       5.335   3.080   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       4.001   0.770   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       4.001   3.850   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       2.667   1.540   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       2.667   3.080   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0       6.668   0.770   0.000  0.00  0.00           O+0
HETATM    8  O   UNK     0       6.668   3.850   0.000  0.00  0.00           O+0
HETATM    9  O   UNK     0       4.001  -0.770   0.000  0.00  0.00           O+0
HETATM   10  O   UNK     0       4.001   5.390   0.000  0.00  0.00           O+0
HETATM   11  O   UNK     0       1.334   2.310   0.000  0.00  0.00           O+0
HETATM   12  H   UNK     0       6.668   2.310   0.000  0.00  0.00           H+0
HETATM   13  H   UNK     0       5.335   4.620   0.000  0.00  0.00           H+0
HETATM   14  H   UNK     0       2.667   0.000   0.000  0.00  0.00           H+0
HETATM   15  H   UNK     0       4.001   2.310   0.000  0.00  0.00           H+0
HETATM   16  H   UNK     0       1.334   0.770   0.000  0.00  0.00           H+0
HETATM   17  H   UNK     0       1.897   4.414   0.000  0.00  0.00           H+0
CONECT    1    2    3    7   12                                             
CONECT    2    1    4    8   13                                             
CONECT    3    1    5    9   14                                             
CONECT    4    2    6   10   15                                             
CONECT    5    3    6   11   16                                             
CONECT    6    4    5   11   17                                             
CONECT    7    1                                                            
CONECT    8    2                                                            
CONECT    9    3                                                            
CONECT   10    4                                                            
CONECT   11    5    6                                                       
CONECT   12    1                                                            
CONECT   13    2                                                            
CONECT   14    3                                                            
CONECT   15    4                                                            
CONECT   16    5                                                            
CONECT   17    6                                                            
MASTER        0    0    0    0    0    0    0    0   17    0   36    0
END

View in JSmol

Synonyms

Value	Source
(+)-(1R,2R,3S,4S,5R,6S)-2,3,4,5-Tetraol-7-oxabicyclo[4.1.0]heptane	ChEBI
(1R,2R,3S,4S,5R,6S)-2,3,4,5-Tetraol-7-oxabicyclo[4.1.0]heptane	ChEBI
1D-Conduritol b epoxide	ChEBI
Conduritol C epoxide	MeSH
Conduritol epoxide	MeSH
Conduritol b-epoxide	MeSH

Chemical Formula

C₆H₁₀O₅

Average Mass

162.1410 Da

Monoisotopic Mass

162.05282 Da

IUPAC Name

(1R,2R,3S,4S,5R,6S)-7-oxabicyclo[4.1.0]heptane-2,3,4,5-tetrol

Traditional Name

(1R,2R,3S,4S,5R,6S)-7-oxabicyclo[4.1.0]heptane-2,3,4,5-tetrol

CAS Registry Number

Not Available

SMILES

[H][C@]12O[C@@]1([H])[C@]([H])(O)[C@@]([H])(O)[C@]([H])(O)[C@@]2([H])O

InChI Identifier

InChI=1S/C6H10O5/c7-1-2(8)4(10)6-5(11-6)3(1)9/h1-10H/t1-,2-,3+,4+,5-,6+/m0/s1

InChI Key

ZHMWOVGZCINIHW-FTYOSCRSSA-N

Experimental Spectra

Not Available

Predicted Spectra

Not Available

Chemical Shift Submissions

Not Available

Species

Species of Origin

Not Available

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as oxepanes. Oxepanes are compounds containing an oxepane ring, which is a seven-member saturated aliphatic heterocycle with one oxygen and six carbon atoms.

Kingdom

Organic compounds

Super Class

Organoheterocyclic compounds

Class

Oxepanes

Sub Class

Not Available

Direct Parent

Oxepanes

Alternative Parents

Substituents

Oxepane
Cyclitol or derivatives
Cyclic alcohol
Secondary alcohol
Oxacycle
Polyol
Ether
Oxirane
Dialkyl ether
Organic oxygen compound
Hydrocarbon derivative
Organooxygen compound
Alcohol
Aliphatic heteropolycyclic compound

Molecular Framework

Aliphatic heteropolycyclic compounds

External Descriptors

conduritol epoxide (CHEBI:67233 )

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	-2.7	ALOGPS
logP	-2.6	ChemAxon
logS	0.9	ALOGPS
pKa (Strongest Acidic)	12.46	ChemAxon
pKa (Strongest Basic)	-3.6	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	5	ChemAxon
Hydrogen Donor Count	4	ChemAxon
Polar Surface Area	93.45 Å²	ChemAxon
Rotatable Bond Count	0	ChemAxon
Refractivity	32.26 m³·mol⁻¹	ChemAxon
Polarizability	14.3 Å³	ChemAxon
Number of Rings	2	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

119054

PDB ID

Not Available

ChEBI ID

67233

Good Scents ID

Not Available

References

General References

Braun H, Legler G, Deshusses J, Semenza G: Stereospecific ring opening of conduritol-B-epoxide by an active site asparatate residue of sucrase-isomaltase. Biochim Biophys Acta. 1977 Jul 8;483(1):135-40. doi: 10.1016/0005-2744(77)90015-8. [PubMed:560212 ]

Showing NP-Card for Conduritol B epoxide (NP0340045)

MOL for NP0340045 (Conduritol B epoxide)

3D MOL for NP0340045 (Conduritol B epoxide)

3D SDF for NP0340045 (Conduritol B epoxide)

3D-SDF for NP0340045 (Conduritol B epoxide)

PDB for NP0340045 (Conduritol B epoxide)

3D PDB for NP0340045 (Conduritol B epoxide)

SMILES for NP0340045 (Conduritol B epoxide)

INCHI for NP0340045 (Conduritol B epoxide)

Structure for NP0340045 (Conduritol B epoxide)

3D Structure for NP0340045 (Conduritol B epoxide)