NP-MRD: Showing NP-Card for 1beta,3alpha,7beta-Trihydroxy-5beta-cholanoic acid (NP0339200)

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Record Information

Version

2.0

Created at

2024-09-11 20:22:22 UTC

Updated at

2024-09-11 20:22:22 UTC

NP-MRD ID

NP0339200

Secondary Accession Numbers

None

Natural Product Identification

Common Name

1beta,3alpha,7beta-Trihydroxy-5beta-cholanoic acid

Description

PGP(18:3(6Z,9Z,12Z)/20:3(5Z,8Z,11Z)), also known as PGP(18:3/20:3) Or PGP(38:6), Belongs to the class of organic compounds known as phosphatidylglycerophosphates. These are glycerophosphoglycerophosphates in which two fatty acids are bonded to the 1-glycerol moiety through ester linkages. It is a glycerophospholipid in which a phosphoglycerol moiety occupies a glycerol substitution site followed by another phosphate moiety. PGP(18:3(6Z,9Z,12Z)/20:3(5Z,8Z,11Z)) is an extremely weak basic (essentially neutral) compound (based on its pKa). Phosphatidylglycerol is formed from phosphatidic acid by a sequence of enzymatic reactions that proceeds via the intermediate, cytidine diphosphate diacylglycerol (CDP-diacylglycerol). Finally, phosphatidylglycerol is formed by the action of specific phosphatases. Phosphatidylglycerolphosphate is present at a level of 1-2% in most animal tissues, but it can be the second most abundant phospholipid in lung surfactant at up to 11% of the total.

Structure

MOL SDF PDB SMILES InChI


  Mrv0541 02251208182D          

 30 33  0  0  1  0            999 V2000
   10.9027  -10.6803    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   10.9027  -11.5053    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.1882  -10.2678    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   10.1882  -11.9178    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.4738  -10.6803    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.4738  -11.5053    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   12.3317  -10.6803    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.3317  -11.5053    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   11.6172  -10.2678    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.6172  -11.9178    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   13.0462   -9.4428    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   13.0462  -10.2678    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.3317   -9.0303    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.6172   -9.4428    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   13.8308   -9.1878    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   14.3157   -9.8553    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   13.8310  -10.5227    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   14.0858   -8.4032    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   14.8928   -8.2317    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   13.5338   -7.7901    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   15.4448   -8.8448    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   16.2518   -8.6734    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   16.8038   -9.2865    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   17.6108   -9.1149    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   16.5488  -10.0711    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   10.9027   -9.8553    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   13.1325   -8.6223    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.1882   -9.4428    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    8.7593  -11.9178    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   13.0462  -11.9178    0.0000 O   0  0  0  0  0  0  0  0  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
  8  7  1  0  0  0  0
 10  8  1  0  0  0  0
  1  9  1  0  0  0  0
  2 10  1  0  0  0  0
  2  1  1  0  0  0  0
 13 11  1  0  0  0  0
  7 12  1  0  0  0  0
 14 13  1  0  0  0  0
  9  7  1  0  0  0  0
  9 14  1  0  0  0  0
 15 11  1  0  0  0  0
 12 11  1  0  0  0  0
 16 15  1  0  0  0  0
 17 12  1  0  0  0  0
 17 16  1  0  0  0  0
 18 15  1  0  0  0  0
 19 18  1  0  0  0  0
 18 20  1  6  0  0  0
 21 19  1  0  0  0  0
 22 21  1  0  0  0  0
 23 22  1  0  0  0  0
 24 23  1  0  0  0  0
 25 23  2  0  0  0  0
  1 26  1  1  0  0  0
 11 27  1  1  0  0  0
  3 28  1  1  0  0  0
  6 29  1  6  0  0  0
  8 30  1  1  0  0  0
M  END


  Mrv0541 02251208182D          

 30 33  0  0  1  0            999 V2000
   10.9027  -10.6803    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   10.9027  -11.5053    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.1882  -10.2678    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   10.1882  -11.9178    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.4738  -10.6803    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.4738  -11.5053    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   12.3317  -10.6803    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.3317  -11.5053    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   11.6172  -10.2678    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.6172  -11.9178    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   13.0462   -9.4428    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   13.0462  -10.2678    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.3317   -9.0303    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.6172   -9.4428    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   13.8308   -9.1878    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   14.3157   -9.8553    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   13.8310  -10.5227    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   14.0858   -8.4032    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   14.8928   -8.2317    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   13.5338   -7.7901    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   15.4448   -8.8448    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   16.2518   -8.6734    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   16.8038   -9.2865    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   17.6108   -9.1149    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   16.5488  -10.0711    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   10.9027   -9.8553    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   13.1325   -8.6223    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.1882   -9.4428    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    8.7593  -11.9178    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   13.0462  -11.9178    0.0000 O   0  0  0  0  0  0  0  0  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
  8  7  1  0  0  0  0
 10  8  1  0  0  0  0
  1  9  1  0  0  0  0
  2 10  1  0  0  0  0
  2  1  1  0  0  0  0
 13 11  1  0  0  0  0
  7 12  1  0  0  0  0
 14 13  1  0  0  0  0
  9  7  1  0  0  0  0
  9 14  1  0  0  0  0
 15 11  1  0  0  0  0
 12 11  1  0  0  0  0
 16 15  1  0  0  0  0
 17 12  1  0  0  0  0
 17 16  1  0  0  0  0
 18 15  1  0  0  0  0
 19 18  1  0  0  0  0
 18 20  1  6  0  0  0
 21 19  1  0  0  0  0
 22 21  1  0  0  0  0
 23 22  1  0  0  0  0
 24 23  1  0  0  0  0
 25 23  2  0  0  0  0
  1 26  1  1  0  0  0
 11 27  1  1  0  0  0
  3 28  1  1  0  0  0
  6 29  1  6  0  0  0
  8 30  1  1  0  0  0
M  END
> <DATABASE_ID>
NP0339200

> <DATABASE_NAME>
NP-MRD

> <SMILES>
C[C@]12CCC3C(C1CCC2[C@H](O)CCCC(O)=O)[C@@H](O)CC1C[C@H](O)C[C@@H](O)[C@]31C

> <INCHI_IDENTIFIER>
InChI=1S/C24H40O6/c1-23-9-8-17-22(16(23)7-6-15(23)18(26)4-3-5-21(29)30)19(27)11-13-10-14(25)12-20(28)24(13,17)2/h13-20,22,25-28H,3-12H2,1-2H3,(H,29,30)/t13?,14-,15?,16?,17?,18+,19-,20+,22?,23+,24-/m0/s1

> <INCHI_KEY>
TVLHFFLEOSSHFT-QVLZICSDSA-N

> <FORMULA>
C24H40O6

> <MOLECULAR_WEIGHT>
424.5708

> <EXACT_MASS>
424.282489012

> <JCHEM_ACCEPTOR_COUNT>
6

> <JCHEM_AVERAGE_POLARIZABILITY>
48.688094436865164

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
5

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
(5R)-5-hydroxy-5-[(2S,3R,5S,9S,15S)-3,5,9-trihydroxy-2,15-dimethyltetracyclo[8.7.0.0²,⁷.0¹¹,¹⁵]heptadecan-14-yl]pentanoic acid

> <ALOGPS_LOGP>
1.42

> <JCHEM_LOGP>
1.258485222333334

> <ALOGPS_LOGS>
-3.25

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
4

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
14.503984784746944

> <JCHEM_PKA_STRONGEST_ACIDIC>
4.614626553395153

> <JCHEM_PKA_STRONGEST_BASIC>
-0.3042595111468859

> <JCHEM_POLAR_SURFACE_AREA>
118.22000000000001

> <JCHEM_REFRACTIVITY>
112.39059999999998

> <JCHEM_ROTATABLE_BOND_COUNT>
5

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
2.41e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(5R)-5-hydroxy-5-[(2S,3R,5S,9S,15S)-3,5,9-trihydroxy-2,15-dimethyltetracyclo[8.7.0.0²,⁷.0¹¹,¹⁵]heptadecan-14-yl]pentanoic acid

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 25-FEB-12   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   25-FEB-12         0                                  
HETATM    1  C   UNK     0      20.352 -19.937   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      20.352 -21.477   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      19.018 -19.167   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      19.018 -22.247   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      17.684 -19.937   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      17.684 -21.477   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      23.019 -19.937   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      23.019 -21.477   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      21.685 -19.167   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      21.685 -22.247   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      24.353 -17.627   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      24.353 -19.167   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      23.019 -16.857   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      21.685 -17.627   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0      25.817 -17.151   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0      26.723 -18.397   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0      25.818 -19.642   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0      26.293 -15.686   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0      27.800 -15.366   0.000  0.00  0.00           C+0
HETATM   20  O   UNK     0      25.263 -14.542   0.000  0.00  0.00           O+0
HETATM   21  C   UNK     0      28.830 -16.510   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0      30.337 -16.190   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0      31.367 -17.335   0.000  0.00  0.00           C+0
HETATM   24  O   UNK     0      32.873 -17.014   0.000  0.00  0.00           O+0
HETATM   25  O   UNK     0      30.891 -18.799   0.000  0.00  0.00           O+0
HETATM   26  C   UNK     0      20.352 -18.397   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0      24.514 -16.095   0.000  0.00  0.00           C+0
HETATM   28  O   UNK     0      19.018 -17.627   0.000  0.00  0.00           O+0
HETATM   29  O   UNK     0      16.351 -22.247   0.000  0.00  0.00           O+0
HETATM   30  O   UNK     0      24.353 -22.247   0.000  0.00  0.00           O+0
CONECT    1    3    9    2   26                                             
CONECT    2    4   10    1                                                  
CONECT    3    1    5   28                                                  
CONECT    4    2    6                                                       
CONECT    5    3    6                                                       
CONECT    6    4    5   29                                                  
CONECT    7    8   12    9                                                  
CONECT    8    7   10   30                                                  
CONECT    9    1    7   14                                                  
CONECT   10    8    2                                                       
CONECT   11   13   15   12   27                                             
CONECT   12    7   11   17                                                  
CONECT   13   11   14                                                       
CONECT   14   13    9                                                       
CONECT   15   11   16   18                                                  
CONECT   16   15   17                                                       
CONECT   17   12   16                                                       
CONECT   18   15   19   20                                                  
CONECT   19   18   21                                                       
CONECT   20   18                                                            
CONECT   21   19   22                                                       
CONECT   22   21   23                                                       
CONECT   23   22   24   25                                                  
CONECT   24   23                                                            
CONECT   25   23                                                            
CONECT   26    1                                                            
CONECT   27   11                                                            
CONECT   28    3                                                            
CONECT   29    6                                                            
CONECT   30    8                                                            
MASTER        0    0    0    0    0    0    0    0   30    0   66    0
END

View in JSmol

Synonyms

Value	Source
1-g-Linolenoyl-2-meadoyl-sn-glycero-3-phospho-(1'-sn-glycerol-3'-phosphate)	HMDB
1-gamma-Linolenoyl-2-meadoyl-sn-glycero-3-phospho-(1'-sn-glycerol-3'-phosphate)	HMDB
3-sn-Phosphatidyl-1'-sn-glycerol 3'-phosphoric acid	HMDB
PGP(18:3/20:3)	HMDB
PGP(18:3n6/20:3n9)	HMDB
PGP(18:3W6/20:3W9)	HMDB
PGP(38:6)	HMDB
1-(6Z,9Z,12Z-Octadecatrienoyl)-2-(5Z,8Z,11Z-eicosatrienoyl)-sn-glycero-3-phospho-(1'-sn-glycerol-3'-phosphate)	HMDB
1b,3a,7b-Trihydroxy-5b-cholanate	HMDB
1b,3a,7b-Trihydroxy-5b-cholanic acid	HMDB
1b,3a,7b-Trihydroxy-5b-cholanoate	HMDB, Generator
7b-Hydroxyisocholate	HMDB
7b-Hydroxyisocholic acid	HMDB
Lagocholate	HMDB
Lagocholic acid	HMDB
(5R)-5-Hydroxy-5-[(2S,3R,5S,9S,15S)-3,5,9-trihydroxy-2,15-dimethyltetracyclo[8.7.0.0²,⁷.0¹¹,¹⁵]heptadecan-14-yl]pentanoate	Generator

Chemical Formula

C₂₄H₄₀O₆

Average Mass

424.5708 Da

Monoisotopic Mass

424.28249 Da

IUPAC Name

(5R)-5-hydroxy-5-[(2S,3R,5S,9S,15S)-3,5,9-trihydroxy-2,15-dimethyltetracyclo[8.7.0.0²,⁷.0¹¹,¹⁵]heptadecan-14-yl]pentanoic acid

Traditional Name

(5R)-5-hydroxy-5-[(2S,3R,5S,9S,15S)-3,5,9-trihydroxy-2,15-dimethyltetracyclo[8.7.0.0²,⁷.0¹¹,¹⁵]heptadecan-14-yl]pentanoic acid

CAS Registry Number

Not Available

SMILES

C[C@]12CCC3C(C1CCC2[C@H](O)CCCC(O)=O)[C@@H](O)CC1C[C@H](O)C[C@@H](O)[C@]31C

InChI Identifier

InChI=1S/C24H40O6/c1-23-9-8-17-22(16(23)7-6-15(23)18(26)4-3-5-21(29)30)19(27)11-13-10-14(25)12-20(28)24(13,17)2/h13-20,22,25-28H,3-12H2,1-2H3,(H,29,30)/t13?,14-,15?,16?,17?,18+,19-,20+,22?,23+,24-/m0/s1

InChI Key

TVLHFFLEOSSHFT-QVLZICSDSA-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 phosphatidylglycerophosphates. These are glycerophosphoglycerophosphates in which two fatty acids are bonded to the 1-glycerol moiety through ester linkages.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Glycerophospholipids

Sub Class

Glycerophosphoglycerophosphates

Direct Parent

Phosphatidylglycerophosphates

Alternative Parents

Substituents

Diacylglycerophosphoglycerophosphate
Sn-glycerol-3-phosphate
Fatty acid ester
Monoalkyl phosphate
Dialkyl phosphate
Dicarboxylic acid or derivatives
Organic phosphoric acid derivative
Phosphoric acid ester
Alkyl phosphate
Fatty acyl
Secondary alcohol
Carboxylic acid ester
Carboxylic acid derivative
Organooxygen compound
Organic oxide
Organic oxygen compound
Alcohol
Carbonyl group
Hydrocarbon derivative
Aliphatic acyclic compound

Molecular Framework

Aliphatic acyclic 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	1.42	ALOGPS
logP	1.26	ChemAxon
logS	-3.2	ALOGPS
pKa (Strongest Acidic)	4.61	ChemAxon
pKa (Strongest Basic)	-0.3	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	6	ChemAxon
Hydrogen Donor Count	5	ChemAxon
Polar Surface Area	118.22 Å²	ChemAxon
Rotatable Bond Count	5	ChemAxon
Refractivity	112.39 m³·mol⁻¹	ChemAxon
Polarizability	48.69 Å³	ChemAxon
Number of Rings	4	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

External Links

HMDB ID

HMDB0013570

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

FDB029570

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

53481888

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Showing NP-Card for 1beta,3alpha,7beta-Trihydroxy-5beta-cholanoic acid (NP0339200)

MOL for NP0339200 (1beta,3alpha,7beta-Trihydroxy-5beta-cholanoic acid)

3D MOL for NP0339200 (1beta,3alpha,7beta-Trihydroxy-5beta-cholanoic acid)

3D SDF for NP0339200 (1beta,3alpha,7beta-Trihydroxy-5beta-cholanoic acid)

3D-SDF for NP0339200 (1beta,3alpha,7beta-Trihydroxy-5beta-cholanoic acid)

PDB for NP0339200 (1beta,3alpha,7beta-Trihydroxy-5beta-cholanoic acid)

3D PDB for NP0339200 (1beta,3alpha,7beta-Trihydroxy-5beta-cholanoic acid)

SMILES for NP0339200 (1beta,3alpha,7beta-Trihydroxy-5beta-cholanoic acid)

INCHI for NP0339200 (1beta,3alpha,7beta-Trihydroxy-5beta-cholanoic acid)

Structure for NP0339200 (1beta,3alpha,7beta-Trihydroxy-5beta-cholanoic acid)

3D Structure for NP0339200 (1beta,3alpha,7beta-Trihydroxy-5beta-cholanoic acid)