NP-MRD: Showing NP-Card for 24,25-Dihydroxyvitamin D (NP0334642)

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Record Information

Version

2.0

Created at

2024-09-10 19:16:47 UTC

Updated at

2024-09-10 19:16:48 UTC

NP-MRD ID

NP0334642

Secondary Accession Numbers

None

Natural Product Identification

Common Name

24,25-Dihydroxyvitamin D

Description

24,25-Dihydroxyvitamin D belongs to the class of organic compounds known as vitamin d and derivatives. Vitamin D and derivatives are compounds containing a secosteroid backbone, usually secoergostane or secocholestane. 24,25-Dihydroxyvitamin D was first documented in 2023 (PMID: 37798100). Based on a literature review a significant number of articles have been published on 24,25-Dihydroxyvitamin D (PMID: 39134205) (PMID: 38890759) (PMID: 38756523) (PMID: 38588969) (PMID: 38481375) (PMID: 38158723).

Structure

MOL SDF PDB SMILES InChI

24,25-Dihydroxyvitamin D.mol
  Mrv2104 05252321492D          

 31 33  0  0  0  0            999 V2000
   -2.7493   -2.8669    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.3349   -3.5802    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5099   -3.5780    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3387   -2.1491    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5137   -2.1491    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1012   -1.4346    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2762   -1.4346    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1363   -0.7201    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9594   -0.7168    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.5130   -1.3284    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2658   -0.9909    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1774   -0.1706    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.7890    0.3831    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.6153    1.1896    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1987    1.7729    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9851    2.5698    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1883    2.7833    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3914    2.9969    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9747    1.9864    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5743    0.1302    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3700   -0.0013    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.8531    0.6675    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9555    0.7121    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1305    0.7099    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2800   -0.0057    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0993   -2.8624    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2743   -2.8624    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5743   -2.8669    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.5685    3.1532    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.4018    3.5802    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.6258   -1.4714    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  1  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  2  0  0  0  0
  6  7  1  0  0  0  0
  7  8  2  0  0  0  0
  8  9  1  0  0  0  0
  9 10  1  0  0  0  0
 10 11  1  0  0  0  0
 12 11  1  1  0  0  0
 12 13  1  0  0  0  0
 13 14  1  0  0  0  0
 14 15  1  0  0  0  0
 15 16  1  0  0  0  0
 16 17  1  0  0  0  0
 17 18  1  0  0  0  0
 17 19  1  0  0  0  0
 13 20  1  1  0  0  0
 12 21  1  0  0  0  0
  9 21  1  0  0  0  0
 21 22  1  1  0  0  0
 21 23  1  0  0  0  0
 23 24  1  0  0  0  0
 24 25  1  0  0  0  0
  8 25  1  0  0  0  0
  3 26  1  0  0  0  0
  5 26  1  0  0  0  0
 26 27  2  0  0  0  0
  1 28  1  1  0  0  0
 16 29  1  0  0  0  0
 17 30  1  0  0  0  0
  9 31  1  6  0  0  0
M  END

24,25-Dihydroxyvitamin D.mol
  Mrv2104 05252321492D          

 31 33  0  0  0  0            999 V2000
   -2.7493   -2.8669    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.3349   -3.5802    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5099   -3.5780    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3387   -2.1491    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5137   -2.1491    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1012   -1.4346    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2762   -1.4346    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1363   -0.7201    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9594   -0.7168    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.5130   -1.3284    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2658   -0.9909    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1774   -0.1706    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.7890    0.3831    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.6153    1.1896    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1987    1.7729    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9851    2.5698    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1883    2.7833    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3914    2.9969    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9747    1.9864    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5743    0.1302    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3700   -0.0013    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.8531    0.6675    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9555    0.7121    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1305    0.7099    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2800   -0.0057    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0993   -2.8624    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2743   -2.8624    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5743   -2.8669    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.5685    3.1532    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.4018    3.5802    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.6258   -1.4714    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  1  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  2  0  0  0  0
  6  7  1  0  0  0  0
  7  8  2  0  0  0  0
  8  9  1  0  0  0  0
  9 10  1  0  0  0  0
 10 11  1  0  0  0  0
 12 11  1  1  0  0  0
 12 13  1  0  0  0  0
 13 14  1  0  0  0  0
 14 15  1  0  0  0  0
 15 16  1  0  0  0  0
 16 17  1  0  0  0  0
 17 18  1  0  0  0  0
 17 19  1  0  0  0  0
 13 20  1  1  0  0  0
 12 21  1  0  0  0  0
  9 21  1  0  0  0  0
 21 22  1  1  0  0  0
 21 23  1  0  0  0  0
 23 24  1  0  0  0  0
 24 25  1  0  0  0  0
  8 25  1  0  0  0  0
  3 26  1  0  0  0  0
  5 26  1  0  0  0  0
 26 27  2  0  0  0  0
  1 28  1  1  0  0  0
 16 29  1  0  0  0  0
 17 30  1  0  0  0  0
  9 31  1  6  0  0  0
M  END
> <DATABASE_ID>
NP0334642

> <DATABASE_NAME>
NP-MRD

> <SMILES>
[H][C@@]12CC[C@H]([C@H](C)CCC(O)C(C)(C)O)[C@@]1(C)CCC\C2=C/C=C1/C[C@H](O)CCC1=C

> <INCHI_IDENTIFIER>
InChI=1/C27H44O3/c1-18-8-12-22(28)17-21(18)11-10-20-7-6-16-27(5)23(13-14-24(20)27)19(2)9-15-25(29)26(3,4)30/h10-11,19,22-25,28-30H,1,6-9,12-17H2,2-5H3/b20-10+,21-11-/t19-,22-,23-,24+,25?,27-/s2

> <INCHI_KEY>
FCKJYANJHNLEEP-ZGCDCWRANA-N

> <FORMULA>
C27H44O3

> <MOLECULAR_WEIGHT>
416.646

> <EXACT_MASS>
416.329045277

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_ATOM_COUNT>
74

> <JCHEM_AVERAGE_POLARIZABILITY>
50.979796762510205

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(6R)-6-[(1R,3aS,4E,7aR)-4-{2-[(1Z,5R)-5-hydroxy-2-methylidenecyclohexylidene]ethylidene}-7a-methyl-octahydro-1H-inden-1-yl]-2-methylheptane-2,3-diol

> <JCHEM_LOGP>
4.579442462666668

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
15.325111733971047

> <JCHEM_PKA_STRONGEST_ACIDIC>
13.849642780244134

> <JCHEM_PKA_STRONGEST_BASIC>
-1.3184890847799178

> <JCHEM_POLAR_SURFACE_AREA>
60.69

> <JCHEM_REFRACTIVITY>
126.4221

> <JCHEM_ROTATABLE_BOND_COUNT>
6

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
24,25-dihydroxyvitamin D

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 25-MAY-23   NONE
TITLE     NULL                                                        
COMPND    MOLECULE: 24,25-Dihydroxyvitamin D.mol                      
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   25-MAY-23         0                                  
HETATM    1  C   UNK     0      -5.132  -5.352   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -4.358  -6.683   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -2.818  -6.679   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -4.366  -4.012   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      -2.826  -4.012   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      -2.056  -2.678   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      -0.516  -2.678   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       0.254  -1.344   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       1.791  -1.338   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       2.824  -2.480   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       4.229  -1.850   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       4.064  -0.318   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       5.206   0.715   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       4.882   2.221   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       5.971   3.309   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       5.572   4.797   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       4.085   5.195   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       2.597   5.594   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       3.686   3.708   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       6.672   0.243   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0       2.557  -0.002   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0       3.459   1.246   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0       1.784   1.329   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0       0.244   1.325   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0      -0.523  -0.011   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0      -2.052  -5.343   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0      -0.512  -5.343   0.000  0.00  0.00           C+0
HETATM   28  O   UNK     0      -6.672  -5.352   0.000  0.00  0.00           O+0
HETATM   29  O   UNK     0       6.661   5.886   0.000  0.00  0.00           O+0
HETATM   30  O   UNK     0       4.483   6.683   0.000  0.00  0.00           O+0
HETATM   31  H   UNK     0       1.168  -2.747   0.000  0.00  0.00           H+0
CONECT    1    2    4   28                                                  
CONECT    2    1    3                                                       
CONECT    3    2   26                                                       
CONECT    4    1    5                                                       
CONECT    5    4    6   26                                                  
CONECT    6    5    7                                                       
CONECT    7    6    8                                                       
CONECT    8    7    9   25                                                  
CONECT    9    8   10   21   31                                             
CONECT   10    9   11                                                       
CONECT   11   10   12                                                       
CONECT   12   11   13   21                                                  
CONECT   13   12   14   20                                                  
CONECT   14   13   15                                                       
CONECT   15   14   16                                                       
CONECT   16   15   17   29                                                  
CONECT   17   16   18   19   30                                             
CONECT   18   17                                                            
CONECT   19   17                                                            
CONECT   20   13                                                            
CONECT   21   12    9   22   23                                             
CONECT   22   21                                                            
CONECT   23   21   24                                                       
CONECT   24   23   25                                                       
CONECT   25   24    8                                                       
CONECT   26    3    5   27                                                  
CONECT   27   26                                                            
CONECT   28    1                                                            
CONECT   29   16                                                            
CONECT   30   17                                                            
CONECT   31    9                                                            
MASTER        0    0    0    0    0    0    0    0   31    0   66    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₂₇H₄₄O₃

Average Mass

416.6460 Da

Monoisotopic Mass

416.32905 Da

IUPAC Name

(6R)-6-[(1R,3aS,4E,7aR)-4-{2-[(1Z,5R)-5-hydroxy-2-methylidenecyclohexylidene]ethylidene}-7a-methyl-octahydro-1H-inden-1-yl]-2-methylheptane-2,3-diol

Traditional Name

24,25-dihydroxyvitamin D

CAS Registry Number

Not Available

SMILES

[H][C@@]12CC[C@H]([C@H](C)CCC(O)C(C)(C)O)[C@@]1(C)CCC\C2=C/C=C1/C[C@H](O)CCC1=C

InChI Identifier

InChI=1/C27H44O3/c1-18-8-12-22(28)17-21(18)11-10-20-7-6-16-27(5)23(13-14-24(20)27)19(2)9-15-25(29)26(3,4)30/h10-11,19,22-25,28-30H,1,6-9,12-17H2,2-5H3/b20-10+,21-11-/t19-,22-,23-,24+,25?,27-/s2

InChI Key

FCKJYANJHNLEEP-ZGCDCWRANA-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
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	4.58	ChemAxon
pKa (Strongest Acidic)	13.85	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	6	ChemAxon
Refractivity	126.42 m³·mol⁻¹	ChemAxon
Polarizability	50.98 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

Shadid ILC, Guchelaar HJ, Weiss ST, Mirzakhani H: Vitamin D beyond the blood: Tissue distribution of vitamin D metabolites after supplementation. Life Sci. 2024 Oct 15;355:122942. doi: 10.1016/j.lfs.2024.122942. Epub 2024 Aug 10. [PubMed:39134205 ]
Herrmann M, Keppel MH, Zelzer S, Alonso N, Cavalier E, Kleber M, Enko D, Scharnagl H, Pilz S, Marz W: The role of functional vitamin D deficiency and low vitamin D reservoirs in relation to cardiovascular health and mortality. Clin Chem Lab Med. 2024 Jun 19. doi: 10.1515/cclm-2024-0391. [PubMed:38890759 ]
Backus RC, Ueda DC: Age-dependent changes in plasma concentrations of 25-hydroxyvitamin D may complicate vitamin D status assessment of immature cats. Front Vet Sci. 2024 May 2;11:1365204. doi: 10.3389/fvets.2024.1365204. eCollection 2024. [PubMed:38756523 ]
Lu Y, Chen H, Chen Y, Zhao L, Hou S: Accumulated LPS induced by colitis altered the activities of vitamin D-metabolizing hydroxylases and decreased the generation of 25-hydroxyvitamin D. Chem Biol Interact. 2024 May 25;395:110997. doi: 10.1016/j.cbi.2024.110997. Epub 2024 Apr 6. [PubMed:38588969 ]
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Showing NP-Card for 24,25-Dihydroxyvitamin D (NP0334642)

MOL for NP0334642 (24,25-Dihydroxyvitamin D)

3D MOL for NP0334642 (24,25-Dihydroxyvitamin D)

3D SDF for NP0334642 (24,25-Dihydroxyvitamin D)

3D-SDF for NP0334642 (24,25-Dihydroxyvitamin D)

PDB for NP0334642 (24,25-Dihydroxyvitamin D)

3D PDB for NP0334642 (24,25-Dihydroxyvitamin D)

SMILES for NP0334642 (24,25-Dihydroxyvitamin D)

INCHI for NP0334642 (24,25-Dihydroxyvitamin D)

Structure for NP0334642 (24,25-Dihydroxyvitamin D)

3D Structure for NP0334642 (24,25-Dihydroxyvitamin D)