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

Jump To Section:

Identification Spectra BioTaxonomy ChemoTaxonomy Physical properties Links References XML

Record Information

Version

2.0

Created at

2024-09-09 21:53:11 UTC

Updated at

2024-09-09 21:53:12 UTC

NP-MRD ID

NP0334064

Secondary Accession Numbers

None

Natural Product Identification

Common Name

25,26-Dihydroxyvitamin D3

Description

25,26-(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

MOL SDF PDB SMILES InChI


  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


  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

$$$$

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

View in JSmol

Synonyms

Not Available

Chemical Formula

C₂₇H₄₄O₃

Average Mass

416.6460 Da

Monoisotopic Mass

416.32905 Da

IUPAC Name

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

Traditional Name

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

CAS Registry Number

Not 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 Key

QOWCBCXATJITSI-BIAOHPHYNA-N

Experimental Spectra

Not Available

Predicted Spectra

Not Available

Chemical Shift Submissions

Not Available

Species

Species of Origin

Not Available

Chemical Taxonomy

Description

This 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.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Steroids and steroid derivatives

Sub Class

Vitamin D and derivatives

Direct Parent

Vitamin 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 Framework

Aliphatic homopolycyclic 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	4.61	ChemAxon
pKa (Strongest Acidic)	14.04	ChemAxon
pKa (Strongest Basic)	-1.3	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	3	ChemAxon
Hydrogen Donor Count	3	ChemAxon
Polar Surface Area	60.69 Å²	ChemAxon
Rotatable Bond Count	7	ChemAxon
Refractivity	126.6 m³·mol⁻¹	ChemAxon
Polarizability	51.1 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	Yes	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

Not Available

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

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

MOL for NP0334064 (25,26-Dihydroxyvitamin D3)

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

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

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

PDB for NP0334064 (25,26-Dihydroxyvitamin D3)

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

SMILES for NP0334064 (25,26-Dihydroxyvitamin D3)

INCHI for NP0334064 (25,26-Dihydroxyvitamin D3)

Structure for NP0334064 (25,26-Dihydroxyvitamin D3)

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