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Showing NP-Card for 25,26-Dihydroxyvitamin D3 (NP0334064)

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Record Information
Version2.0
Created at2024-09-09 21:53:11 UTC
Updated at2024-09-09 21:53:12 UTC
NP-MRD IDNP0334064
Secondary Accession NumbersNone
Natural Product Identification
Common Name25,26-Dihydroxyvitamin D3
Description25,26-(OH)2D3 is a renal microsomal 25-OH-D3 metabolite, whose plasma concentration increases during vitamin D excess concomitantly with an increase in the concentration of lactone. This observation considered with the related structural features of 25,26-(OH)2D3 and lactone (both are oxidized at (C-26) suggested that 25,26(OH)2D3, a metabolite of unknown function, could be a precursor to lactone. In fact, it has been reported that functionalization of C-26 and subsequent lactone formation occurs exclusively in kidney. However, rigorous examination has unambiguously excluded 25S,26-(OH)2D3, the naturally occurring form as a significant lactone precursor. (PMID: 6286629 ) [HMDB]
Structure
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MOLSDFPDBSMILESInChI

MOL for NP0334064 (25,26-Dihydroxyvitamin D3)


  Mrv2104 05252300252D          

 32 34  0  0  0  0            999 V2000
    3.3523   -1.3646    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4358    3.5881    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0247    4.6324    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8371    2.7559    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1781    3.9312    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3523    1.9354    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0768    3.1465    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3523    1.1104    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6378   -2.6021    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6378   -0.1271    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9233   -0.5396    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9233   -3.0146    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6538    1.5229    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1387    0.8555    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9851    4.1027    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6378    2.3479    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2089   -1.7771    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4950    5.6719    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6378   -1.7771    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8838    2.9750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6378    0.6979    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9233   -1.3646    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2089   -2.6021    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1387    2.1904    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9233    1.1104    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2400    4.8873    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9233    1.9354    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3020    5.8434    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.4944   -3.0146    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4554    5.1422    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.3523   -0.5396    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2089   -0.1271    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  1 19  2  0  0  0  0
  2 20  1  0  0  0  0
  3 26  1  0  0  0  0
  4 27  1  0  0  0  0
  5  7  1  0  0  0  0
  5 15  1  0  0  0  0
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  6 16  1  0  0  0  0
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 15 26  1  0  0  0  0
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 17 22  1  0  0  0  0
 17 23  1  0  0  0  0
 18 26  1  0  0  0  0
 18 28  1  0  0  0  0
 19 22  1  0  0  0  0
 20 24  1  0  0  0  0
 21 25  1  0  0  0  0
 23 29  1  0  0  0  0
 24 27  1  0  0  0  0
 25 27  1  0  0  0  0
 26 30  1  0  0  0  0
M  END
Download

3D MOL for NP0334064 (25,26-Dihydroxyvitamin D3)

Download
3D SDF for NP0334064 (25,26-Dihydroxyvitamin D3)

  Mrv2104 05252300252D          

 32 34  0  0  0  0            999 V2000
    3.3523   -1.3646    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4358    3.5881    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0247    4.6324    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8371    2.7559    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1781    3.9312    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3523    1.9354    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0768    3.1465    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3523    1.1104    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6378   -2.6021    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6378   -0.1271    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9233   -0.5396    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9233   -3.0146    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6538    1.5229    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1387    0.8555    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9851    4.1027    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6378    2.3479    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2089   -1.7771    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4950    5.6719    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6378   -1.7771    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8838    2.9750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6378    0.6979    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9233   -1.3646    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2089   -2.6021    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1387    2.1904    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9233    1.1104    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2400    4.8873    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9233    1.9354    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3020    5.8434    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.4944   -3.0146    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4554    5.1422    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.3523   -0.5396    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2089   -0.1271    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  1 19  2  0  0  0  0
  2 20  1  0  0  0  0
  3 26  1  0  0  0  0
  4 27  1  0  0  0  0
  5  7  1  0  0  0  0
  5 15  1  0  0  0  0
  6  8  1  0  0  0  0
  6 16  1  0  0  0  0
  7 20  1  0  0  0  0
  8 21  1  0  0  0  0
  9 12  1  0  0  0  0
  9 19  1  0  0  0  0
 10 31  1  0  0  0  0
 10 11  1  0  0  0  0
 10 21  2  0  0  0  0
 11 32  1  0  0  0  0
 11 22  2  0  0  0  0
 12 23  1  0  0  0  0
 13 14  1  0  0  0  0
 13 24  1  0  0  0  0
 14 25  1  0  0  0  0
 15 26  1  0  0  0  0
 16 27  1  0  0  0  0
 17 22  1  0  0  0  0
 17 23  1  0  0  0  0
 18 26  1  0  0  0  0
 18 28  1  0  0  0  0
 19 22  1  0  0  0  0
 20 24  1  0  0  0  0
 21 25  1  0  0  0  0
 23 29  1  0  0  0  0
 24 27  1  0  0  0  0
 25 27  1  0  0  0  0
 26 30  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0334064

> <DATABASE_NAME>
NP-MRD

> <SMILES>
[H]\C(\C(\[H])=C1\CC(O)CCC1=C)=C1/CCCC2(C)C(CCC12)C(C)CCCC(C)(O)CO

> <INCHI_IDENTIFIER>
InChI=1/C27H44O3/c1-19-9-12-23(29)17-22(19)11-10-21-8-6-16-27(4)24(13-14-25(21)27)20(2)7-5-15-26(3,30)18-28/h10-11,20,23-25,28-30H,1,5-9,12-18H2,2-4H3/b21-10-,22-11-

> <INCHI_KEY>
QOWCBCXATJITSI-BIAOHPHYNA-N

> <FORMULA>
C27H44O3

> <MOLECULAR_WEIGHT>
416.646

> <EXACT_MASS>
416.329045277

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_ATOM_COUNT>
74

> <JCHEM_AVERAGE_POLARIZABILITY>
51.09513801261384

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
6-[(4Z)-4-{2-[(1Z)-5-hydroxy-2-methylidenecyclohexylidene]ethylidene}-7a-methyl-octahydroinden-1-yl]-2-methylheptane-1,2-diol

> <JCHEM_LOGP>
4.607436103000002

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
15.485651631254557

> <JCHEM_PKA_STRONGEST_ACIDIC>
14.038375924925708

> <JCHEM_PKA_STRONGEST_BASIC>
-1.3184890847799178

> <JCHEM_POLAR_SURFACE_AREA>
60.69

> <JCHEM_REFRACTIVITY>
126.60429999999995

> <JCHEM_ROTATABLE_BOND_COUNT>
7

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
6-[(4Z)-4-{2-[(1Z)-5-hydroxy-2-methylidenecyclohexylidene]ethylidene}-7a-methyl-hexahydro-1H-inden-1-yl]-2-methylheptane-1,2-diol

> <JCHEM_VEBER_RULE>
0

$$$$

Download
3D-SDF for NP0334064 (25,26-Dihydroxyvitamin D3)
Download
PDB for NP0334064 (25,26-Dihydroxyvitamin D3)
HEADER    PROTEIN                                 25-MAY-23   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   25-MAY-23         0                                  
HETATM    1  C   UNK     0       6.258  -2.547   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       2.680   6.698   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -3.779   8.647   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       3.429   5.144   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      -0.333   7.338   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       6.258   3.613   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       0.143   5.874   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       6.258   2.073   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       4.924  -4.857   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       4.924  -0.237   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       3.590  -1.007   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       3.590  -5.627   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       1.220   2.843   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       2.126   1.597   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0      -1.839   7.658   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       4.924   4.383   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       2.257  -3.317   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0      -2.791  10.588   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       4.924  -3.317   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       1.650   5.553   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0       4.924   1.303   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0       3.590  -2.547   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0       2.257  -4.857   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0       2.126   4.089   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0       3.590   2.073   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0      -2.315   9.123   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0       3.590   3.613   0.000  0.00  0.00           C+0
HETATM   28  O   UNK     0      -4.297  10.908   0.000  0.00  0.00           O+0
HETATM   29  O   UNK     0       0.923  -5.627   0.000  0.00  0.00           O+0
HETATM   30  O   UNK     0      -0.850   9.599   0.000  0.00  0.00           O+0
HETATM   31  H   UNK     0       6.258  -1.007   0.000  0.00  0.00           H+0
HETATM   32  H   UNK     0       2.257  -0.237   0.000  0.00  0.00           H+0
CONECT    1   19                                                            
CONECT    2   20                                                            
CONECT    3   26                                                            
CONECT    4   27                                                            
CONECT    5    7   15                                                       
CONECT    6    8   16                                                       
CONECT    7    5   20                                                       
CONECT    8    6   21                                                       
CONECT    9   12   19                                                       
CONECT   10   31   11   21                                                  
CONECT   11   10   32   22                                                  
CONECT   12    9   23                                                       
CONECT   13   14   24                                                       
CONECT   14   13   25                                                       
CONECT   15    5   26                                                       
CONECT   16    6   27                                                       
CONECT   17   22   23                                                       
CONECT   18   26   28                                                       
CONECT   19    1    9   22                                                  
CONECT   20    2    7   24                                                  
CONECT   21    8   10   25                                                  
CONECT   22   11   17   19                                                  
CONECT   23   12   17   29                                                  
CONECT   24   13   20   27                                                  
CONECT   25   14   21   27                                                  
CONECT   26    3   15   18   30                                             
CONECT   27    4   16   24   25                                             
CONECT   28   18                                                            
CONECT   29   23                                                            
CONECT   30   26                                                            
CONECT   31   10                                                            
CONECT   32   11                                                            
MASTER        0    0    0    0    0    0    0    0   32    0   68    0
END

Download
3D PDB for NP0334064 (25,26-Dihydroxyvitamin D3)
Download
SMILES for NP0334064 (25,26-Dihydroxyvitamin D3)
[H]\C(\C(\[H])=C1\CC(O)CCC1=C)=C1/CCCC2(C)C(CCC12)C(C)CCCC(C)(O)CO
Download
INCHI for NP0334064 (25,26-Dihydroxyvitamin D3)
InChI=1/C27H44O3/c1-19-9-12-23(29)17-22(19)11-10-21-8-6-16-27(4)24(13-14-25(21)27)20(2)7-5-15-26(3,30)18-28/h10-11,20,23-25,28-30H,1,5-9,12-18H2,2-4H3/b21-10-,22-11-
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View in JSmol
SynonymsNot Available
Chemical FormulaC27H44O3
Average Mass416.6460 Da
Monoisotopic Mass416.32905 Da
IUPAC Name6-[(4Z)-4-{2-[(1Z)-5-hydroxy-2-methylidenecyclohexylidene]ethylidene}-7a-methyl-octahydroinden-1-yl]-2-methylheptane-1,2-diol
Traditional Name6-[(4Z)-4-{2-[(1Z)-5-hydroxy-2-methylidenecyclohexylidene]ethylidene}-7a-methyl-hexahydro-1H-inden-1-yl]-2-methylheptane-1,2-diol
CAS Registry NumberNot Available
SMILES
[H]\C(\C(\[H])=C1\CC(O)CCC1=C)=C1/CCCC2(C)C(CCC12)C(C)CCCC(C)(O)CO
InChI Identifier
InChI=1/C27H44O3/c1-19-9-12-23(29)17-22(19)11-10-21-8-6-16-27(4)24(13-14-25(21)27)20(2)7-5-15-26(3,30)18-28/h10-11,20,23-25,28-30H,1,5-9,12-18H2,2-4H3/b21-10-,22-11-
InChI KeyQOWCBCXATJITSI-BIAOHPHYNA-N
Experimental Spectra
Not Available
Predicted Spectra
Not Available
Chemical Shift Submissions
Not Available
Species
Species of OriginNot Available
Chemical Taxonomy
DescriptionThis compound belongs to the class of organic compounds known as vitamin d and derivatives. These are compounds containing a secosteroid backbone, usually secoergostane or secocholestane.
KingdomOrganic compounds  
Super ClassLipids and lipid-like molecules  
ClassSteroids and steroid derivatives  
Sub ClassVitamin D and derivatives  
Direct ParentVitamin D and derivatives  
Alternative Parents
Substituents
  • Triterpenoid
    • 

  • Fatty alcohol
    • 

  • Fatty acyl
    • 

  • Tertiary alcohol
    • 

  • Cyclic alcohol
    • 

  • Secondary alcohol
    • 

  • Organic oxygen compound
    • 

  • Hydrocarbon derivative
    • 

  • Organooxygen compound
    • 

  • Alcohol
    • 

  • Aliphatic homopolycyclic compound
Molecular FrameworkAliphatic homopolycyclic compounds
External DescriptorsNot Available
Physical Properties
StateNot Available
Experimental Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Predicted Properties
PropertyValueSource
logP4.61ChemAxon
pKa (Strongest Acidic)14.04ChemAxon
pKa (Strongest Basic)-1.3ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count3ChemAxon
Hydrogen Donor Count3ChemAxon
Polar Surface Area60.69 ŲChemAxon
Rotatable Bond Count7ChemAxon
Refractivity126.6 m³·mol⁻¹ChemAxon
Polarizability51.1 ųChemAxon
Number of Rings3ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleYesChemAxon
HMDB IDNot Available
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FoodDB IDNot Available
KNApSAcK IDNot Available
Chemspider IDNot Available
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem CompoundNot Available
PDB IDNot Available
ChEBI IDNot Available
Good Scents IDNot Available
References
General References
  1. Zelzer S, Meinitzer A, Enko D, Simstich S, Le Goff C, Cavalier E, Herrmann M, Goessler W: Simultaneous determination of 24,25- and 25,26-dihydroxyvitamin D3 in serum samples with liquid-chromatography mass spectrometry - A useful tool for the assessment of vitamin D metabolism. J Chromatogr B Analyt Technol Biomed Life Sci. 2020 Nov 20;1158:122394. doi:  10.1016/j.jchromb.2020.122394. Epub 2020 Oct 6. [PubMed:33091679  ]