NP-MRD: Showing NP-Card for (1r,2r,3r,4s,5s,6s)-6-{[(2r,3s,4r,5s,6r)-3-amino-4,5-dihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}cyclohexane-1,2,3,4,5-pentol (NP0223277)

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Record Information

Version

2.0

Created at

2022-09-06 01:19:16 UTC

Updated at

2022-09-06 01:19:17 UTC

NP-MRD ID

NP0223277

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(1r,2r,3r,4s,5s,6s)-6-{[(2r,3s,4r,5s,6r)-3-amino-4,5-dihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}cyclohexane-1,2,3,4,5-pentol

Description

(1r,2r,3r,4s,5s,6s)-6-{[(2r,3s,4r,5s,6r)-3-amino-4,5-dihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}cyclohexane-1,2,3,4,5-pentol is found in Micromonospora echinospora.

Structure

MOL SDF PDB SMILES InChI


  Mrv1652309062203192D          

 23 24  0  0  1  0            999 V2000
   -0.7145   -0.4125    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145   -1.2375    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.4289   -1.6500    0.0000 C   0  0  1  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
   -2.8579   -1.6500    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.8579   -2.4750    0.0000 C   0  0  1  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
   -3.5724   -2.8875    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -3.5724   -3.7125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2868   -2.4750    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -5.0013   -2.8875    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2868   -1.6500    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -5.0013   -1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5724   -1.2375    0.0000 C   0  0  1  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
   -1.4289   -2.4750    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145   -2.8875    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.7145   -3.7125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4289   -4.1250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000   -2.4750    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.7145   -2.8875    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000   -1.6500    0.0000 C   0  0  2  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
  2  1  1  1  0  0  0
  2  3  1  0  0  0  0
  3  4  1  6  0  0  0
  5  4  1  1  0  0  0
  5  6  1  0  0  0  0
  6  7  1  1  0  0  0
  6  8  1  0  0  0  0
  8  9  1  1  0  0  0
  8 10  1  0  0  0  0
 10 11  1  1  0  0  0
 10 12  1  0  0  0  0
 12 13  1  1  0  0  0
 12 14  1  0  0  0  0
  5 14  1  0  0  0  0
 14 15  1  1  0  0  0
  3 16  1  0  0  0  0
 16 17  1  0  0  0  0
 17 18  1  1  0  0  0
 18 19  1  0  0  0  0
 17 20  1  0  0  0  0
 20 21  1  6  0  0  0
 20 22  1  0  0  0  0
  2 22  1  0  0  0  0
 22 23  1  1  0  0  0
M  END
> <DATABASE_ID>
NP0223277

> <DATABASE_NAME>
NP-MRD

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

> <INCHI_IDENTIFIER>
InChI=1S/C12H23NO10/c13-3-5(16)4(15)2(1-14)22-12(3)23-11-9(20)7(18)6(17)8(19)10(11)21/h2-12,14-21H,1,13H2/t2-,3+,4-,5-,6-,7+,8-,9+,10-,11+,12-/m1/s1

> <INCHI_KEY>
HEPUIGACZYVUCD-GUMWOQCNSA-N

> <FORMULA>
C12H23NO10

> <MOLECULAR_WEIGHT>
341.313

> <EXACT_MASS>
341.132195945

> <JCHEM_ACCEPTOR_COUNT>
11

> <JCHEM_ATOM_COUNT>
46

> <JCHEM_AVERAGE_POLARIZABILITY>
31.53126042507073

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
9

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(1R,2R,3r,4S,5S,6s)-6-{[(2R,3S,4R,5S,6R)-3-amino-4,5-dihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}cyclohexane-1,2,3,4,5-pentol

> <JCHEM_LOGP>
-5.659727094333334

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
1

> <JCHEM_PKA>
12.755366603409957

> <JCHEM_PKA_STRONGEST_ACIDIC>
12.250867384470688

> <JCHEM_PKA_STRONGEST_BASIC>
8.12572819649635

> <JCHEM_POLAR_SURFACE_AREA>
206.31999999999996

> <JCHEM_REFRACTIVITY>
69.8458

> <JCHEM_ROTATABLE_BOND_COUNT>
3

> <JCHEM_RULE_OF_FIVE>
0

> <JCHEM_TRADITIONAL_IUPAC>
(1R,2R,3r,4S,5S,6s)-6-{[(2R,3S,4R,5S,6R)-3-amino-4,5-dihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}cyclohexane-1,2,3,4,5-pentol

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 06-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   06-SEP-22         0                                  
HETATM    1  N   UNK     0      -1.334  -0.770   0.000  0.00  0.00           N+0
HETATM    2  C   UNK     0      -1.334  -2.310   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -2.667  -3.080   0.000  0.00  0.00           C+0
HETATM    4  O   UNK     0      -4.001  -2.310   0.000  0.00  0.00           O+0
HETATM    5  C   UNK     0      -5.335  -3.080   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      -5.335  -4.620   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0      -4.001  -5.390   0.000  0.00  0.00           O+0
HETATM    8  C   UNK     0      -6.668  -5.390   0.000  0.00  0.00           C+0
HETATM    9  O   UNK     0      -6.668  -6.930   0.000  0.00  0.00           O+0
HETATM   10  C   UNK     0      -8.002  -4.620   0.000  0.00  0.00           C+0
HETATM   11  O   UNK     0      -9.336  -5.390   0.000  0.00  0.00           O+0
HETATM   12  C   UNK     0      -8.002  -3.080   0.000  0.00  0.00           C+0
HETATM   13  O   UNK     0      -9.336  -2.310   0.000  0.00  0.00           O+0
HETATM   14  C   UNK     0      -6.668  -2.310   0.000  0.00  0.00           C+0
HETATM   15  O   UNK     0      -6.668  -0.770   0.000  0.00  0.00           O+0
HETATM   16  O   UNK     0      -2.667  -4.620   0.000  0.00  0.00           O+0
HETATM   17  C   UNK     0      -1.334  -5.390   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0      -1.334  -6.930   0.000  0.00  0.00           C+0
HETATM   19  O   UNK     0      -2.667  -7.700   0.000  0.00  0.00           O+0
HETATM   20  C   UNK     0       0.000  -4.620   0.000  0.00  0.00           C+0
HETATM   21  O   UNK     0       1.334  -5.390   0.000  0.00  0.00           O+0
HETATM   22  C   UNK     0       0.000  -3.080   0.000  0.00  0.00           C+0
HETATM   23  O   UNK     0       1.334  -2.310   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3   22                                                  
CONECT    3    2    4   16                                                  
CONECT    4    3    5                                                       
CONECT    5    4    6   14                                                  
CONECT    6    5    7    8                                                  
CONECT    7    6                                                            
CONECT    8    6    9   10                                                  
CONECT    9    8                                                            
CONECT   10    8   11   12                                                  
CONECT   11   10                                                            
CONECT   12   10   13   14                                                  
CONECT   13   12                                                            
CONECT   14   12    5   15                                                  
CONECT   15   14                                                            
CONECT   16    3   17                                                       
CONECT   17   16   18   20                                                  
CONECT   18   17   19                                                       
CONECT   19   18                                                            
CONECT   20   17   21   22                                                  
CONECT   21   20                                                            
CONECT   22   20    2   23                                                  
CONECT   23   22                                                            
MASTER        0    0    0    0    0    0    0    0   23    0   48    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₁₂H₂₃NO₁₀

Average Mass

341.3130 Da

Monoisotopic Mass

341.13220 Da

IUPAC Name

(1R,2R,3r,4S,5S,6s)-6-{[(2R,3S,4R,5S,6R)-3-amino-4,5-dihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}cyclohexane-1,2,3,4,5-pentol

Traditional Name

(1R,2R,3r,4S,5S,6s)-6-{[(2R,3S,4R,5S,6R)-3-amino-4,5-dihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}cyclohexane-1,2,3,4,5-pentol

CAS Registry Number

Not Available

SMILES

N[C@H]1[C@@H](O)[C@H](O)[C@@H](CO)O[C@@H]1O[C@H]1[C@@H](O)[C@@H](O)[C@@H](O)[C@@H](O)[C@H]1O

InChI Identifier

InChI=1S/C12H23NO10/c13-3-5(16)4(15)2(1-14)22-12(3)23-11-9(20)7(18)6(17)8(19)10(11)21/h2-12,14-21H,1,13H2/t2-,3+,4-,5-,6-,7+,8-,9+,10-,11+,12-/m1/s1

InChI Key

HEPUIGACZYVUCD-GUMWOQCNSA-N

Experimental Spectra

Not Available

Predicted Spectra

Not Available

Chemical Shift Submissions

Not Available

Species

Species of Origin

Species Name	Source	Reference
Micromonospora echinospora	LOTUS Database	35616633

Chemical Taxonomy

Classification

Not classified

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	-5.7	ChemAxon
pKa (Strongest Acidic)	12.25	ChemAxon
pKa (Strongest Basic)	8.13	ChemAxon
Physiological Charge	1	ChemAxon
Hydrogen Acceptor Count	11	ChemAxon
Hydrogen Donor Count	9	ChemAxon
Polar Surface Area	206.32 Å²	ChemAxon
Rotatable Bond Count	3	ChemAxon
Refractivity	69.85 m³·mol⁻¹	ChemAxon
Polarizability	31.53 Å³	ChemAxon
Number of Rings	2	ChemAxon
Bioavailability	No	ChemAxon
Rule of Five	No	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

External Links

Not Available

References

General References

LOTUS database [Link]

Showing NP-Card for (1r,2r,3r,4s,5s,6s)-6-{[(2r,3s,4r,5s,6r)-3-amino-4,5-dihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}cyclohexane-1,2,3,4,5-pentol (NP0223277)

MOL for NP0223277 ((1r,2r,3r,4s,5s,6s)-6-{[(2r,3s,4r,5s,6r)-3-amino-4,5-dihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}cyclohexane-1,2,3,4,5-pentol)

3D MOL for NP0223277 ((1r,2r,3r,4s,5s,6s)-6-{[(2r,3s,4r,5s,6r)-3-amino-4,5-dihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}cyclohexane-1,2,3,4,5-pentol)

3D SDF for NP0223277 ((1r,2r,3r,4s,5s,6s)-6-{[(2r,3s,4r,5s,6r)-3-amino-4,5-dihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}cyclohexane-1,2,3,4,5-pentol)

3D-SDF for NP0223277 ((1r,2r,3r,4s,5s,6s)-6-{[(2r,3s,4r,5s,6r)-3-amino-4,5-dihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}cyclohexane-1,2,3,4,5-pentol)

PDB for NP0223277 ((1r,2r,3r,4s,5s,6s)-6-{[(2r,3s,4r,5s,6r)-3-amino-4,5-dihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}cyclohexane-1,2,3,4,5-pentol)

3D PDB for NP0223277 ((1r,2r,3r,4s,5s,6s)-6-{[(2r,3s,4r,5s,6r)-3-amino-4,5-dihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}cyclohexane-1,2,3,4,5-pentol)

SMILES for NP0223277 ((1r,2r,3r,4s,5s,6s)-6-{[(2r,3s,4r,5s,6r)-3-amino-4,5-dihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}cyclohexane-1,2,3,4,5-pentol)

INCHI for NP0223277 ((1r,2r,3r,4s,5s,6s)-6-{[(2r,3s,4r,5s,6r)-3-amino-4,5-dihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}cyclohexane-1,2,3,4,5-pentol)

Structure for NP0223277 ((1r,2r,3r,4s,5s,6s)-6-{[(2r,3s,4r,5s,6r)-3-amino-4,5-dihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}cyclohexane-1,2,3,4,5-pentol)

3D Structure for NP0223277 ((1r,2r,3r,4s,5s,6s)-6-{[(2r,3s,4r,5s,6r)-3-amino-4,5-dihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}cyclohexane-1,2,3,4,5-pentol)