NP-MRD: Showing NP-Card for PGH3 (NP0339163)

Jump To Section:

Identification Spectra BioTaxonomy ChemoTaxonomy Physical properties Links References XML

Record Information

Version

2.0

Created at

2024-09-11 19:59:42 UTC

Updated at

2024-09-11 19:59:42 UTC

NP-MRD ID

NP0339163

Secondary Accession Numbers

None

Natural Product Identification

Common Name

PGH3

Description

PGH3 belongs to the class of organic compounds known as prostaglandins and related compounds. These are unsaturated carboxylic acids consisting of a 20 carbon skeleton that also contains a five member ring, and are based upon the fatty acid arachidonic acid. PGH3 is an extremely weak basic (essentially neutral) compound (based on its pKa).

Structure

MOL SDF PDB SMILES InChI


  Mrv0541 02251208152D          

 25 26  0  0  1  0            999 V2000
   13.8552  -12.1879    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   13.8552  -11.3629    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   14.5697  -10.9504    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   14.5697  -10.1254    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   13.8552   -9.7129    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   13.8552   -8.8879    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   14.5697   -8.4754    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   13.1408   -8.4754    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.4262   -8.8879    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.7118   -8.4754    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   10.9973   -8.8879    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   10.5210   -8.0629    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.9973   -7.2379    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   10.2828   -7.6504    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   10.2828   -8.4754    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   11.7118   -7.6504    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   12.4262   -7.2379    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   13.1408   -7.6504    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   13.8552   -7.2379    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   13.8552   -6.4129    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   14.5697   -6.0003    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   14.5697   -5.1753    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   15.2842   -4.7628    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   15.9986   -5.1753    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   15.2842   -3.9378    0.0000 O   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
  3  4  2  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  1  6  0  0  0
  6  8  1  0  0  0  0
  8  9  2  0  0  0  0
 10  9  1  1  0  0  0
 10 11  1  0  0  0  0
 10 16  1  0  0  0  0
 11 12  1  1  0  0  0
 11 15  1  0  0  0  0
 13 12  1  1  0  0  0
 13 14  1  0  0  0  0
 13 16  1  0  0  0  0
 14 15  1  0  0  0  0
 16 17  1  6  0  0  0
 17 18  1  0  0  0  0
 18 19  2  0  0  0  0
 19 20  1  0  0  0  0
 20 21  1  0  0  0  0
 21 22  1  0  0  0  0
 22 23  1  0  0  0  0
 23 24  1  0  0  0  0
 23 25  2  0  0  0  0
M  END
> <DATABASE_ID>
NP0339163

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CC\C=C/C[C@@H](O)\C=C\[C@H]1[C@H]2C[C@H](OO2)[C@@H]1C\C=C/CCCC(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C20H30O5/c1-2-3-6-9-15(21)12-13-17-16(18-14-19(17)25-24-18)10-7-4-5-8-11-20(22)23/h3-4,6-7,12-13,15-19,21H,2,5,8-11,14H2,1H3,(H,22,23)/b6-3-,7-4-,13-12+/t15-,16-,17-,18+,19-/m1/s1

> <INCHI_KEY>
PVTQTOGPOPGQGE-LWAFXZDQSA-N

> <FORMULA>
C20H30O5

> <MOLECULAR_WEIGHT>
350.4492

> <EXACT_MASS>
350.20932407

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_AVERAGE_POLARIZABILITY>
38.96897394849502

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
(5Z)-7-[(1R,4S,5R,6R)-6-[(1E,3R,5Z)-3-hydroxyocta-1,5-dien-1-yl]-2,3-dioxabicyclo[2.2.1]heptan-5-yl]hept-5-enoic acid

> <ALOGPS_LOGP>
4.22

> <JCHEM_LOGP>
3.5950059293333325

> <ALOGPS_LOGS>
-3.93

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
17.591508496208274

> <JCHEM_PKA_STRONGEST_ACIDIC>
4.355294010270015

> <JCHEM_PKA_STRONGEST_BASIC>
-1.664976579097757

> <JCHEM_POLAR_SURFACE_AREA>
75.99000000000001

> <JCHEM_REFRACTIVITY>
99.15849999999999

> <JCHEM_ROTATABLE_BOND_COUNT>
11

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
4.13e-02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(5Z)-7-[(1R,4S,5R,6R)-6-[(1E,3R,5Z)-3-hydroxyocta-1,5-dien-1-yl]-2,3-dioxabicyclo[2.2.1]heptan-5-yl]hept-5-enoic 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      25.863 -22.751   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      25.863 -21.211   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      27.197 -20.441   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      27.197 -18.901   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      25.863 -18.131   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      25.863 -16.591   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0      27.197 -15.821   0.000  0.00  0.00           O+0
HETATM    8  C   UNK     0      24.529 -15.821   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      23.196 -16.591   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      21.862 -15.821   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      20.528 -16.591   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      19.639 -15.051   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      20.528 -13.511   0.000  0.00  0.00           C+0
HETATM   14  O   UNK     0      19.195 -14.281   0.000  0.00  0.00           O+0
HETATM   15  O   UNK     0      19.195 -15.821   0.000  0.00  0.00           O+0
HETATM   16  C   UNK     0      21.862 -14.281   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0      23.196 -13.511   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0      24.529 -14.281   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0      25.863 -13.511   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0      25.863 -11.971   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0      27.197 -11.201   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0      27.197  -9.661   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0      28.531  -8.891   0.000  0.00  0.00           C+0
HETATM   24  O   UNK     0      29.864  -9.661   0.000  0.00  0.00           O+0
HETATM   25  O   UNK     0      28.531  -7.351   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4    6                                                       
CONECT    6    5    7    8                                                  
CONECT    7    6                                                            
CONECT    8    6    9                                                       
CONECT    9    8   10                                                       
CONECT   10    9   11   16                                                  
CONECT   11   10   12   15                                                  
CONECT   12   11   13                                                       
CONECT   13   12   14   16                                                  
CONECT   14   13   15                                                       
CONECT   15   11   14                                                       
CONECT   16   10   13   17                                                  
CONECT   17   16   18                                                       
CONECT   18   17   19                                                       
CONECT   19   18   20                                                       
CONECT   20   19   21                                                       
CONECT   21   20   22                                                       
CONECT   22   21   23                                                       
CONECT   23   22   24   25                                                  
CONECT   24   23                                                            
CONECT   25   23                                                            
MASTER        0    0    0    0    0    0    0    0   25    0   52    0
END

View in JSmol

Synonyms

Value	Source
Prostaglandin H(,3)	HMDB

Chemical Formula

C₂₀H₃₀O₅

Average Mass

350.4492 Da

Monoisotopic Mass

350.20932 Da

IUPAC Name

(5Z)-7-[(1R,4S,5R,6R)-6-[(1E,3R,5Z)-3-hydroxyocta-1,5-dien-1-yl]-2,3-dioxabicyclo[2.2.1]heptan-5-yl]hept-5-enoic acid

Traditional Name

(5Z)-7-[(1R,4S,5R,6R)-6-[(1E,3R,5Z)-3-hydroxyocta-1,5-dien-1-yl]-2,3-dioxabicyclo[2.2.1]heptan-5-yl]hept-5-enoic acid

CAS Registry Number

Not Available

SMILES

CC\C=C/C[C@@H](O)\C=C\[C@H]1[C@H]2C[C@H](OO2)[C@@H]1C\C=C/CCCC(O)=O

InChI Identifier

InChI=1S/C20H30O5/c1-2-3-6-9-15(21)12-13-17-16(18-14-19(17)25-24-18)10-7-4-5-8-11-20(22)23/h3-4,6-7,12-13,15-19,21H,2,5,8-11,14H2,1H3,(H,22,23)/b6-3-,7-4-,13-12+/t15-,16-,17-,18+,19-/m1/s1

InChI Key

PVTQTOGPOPGQGE-LWAFXZDQSA-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 prostaglandins and related compounds. These are unsaturated carboxylic acids consisting of a 20 carbon skeleton that also contains a five member ring, and are based upon the fatty acid arachidonic acid.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Fatty Acyls

Sub Class

Eicosanoids

Direct Parent

Prostaglandins and related compounds

Alternative Parents

Substituents

Prostaglandin skeleton
Long-chain fatty acid
Heterocyclic fatty acid
Hydroxy fatty acid
Ortho-dioxane
Fatty acid
Unsaturated fatty acid
Ortho-dioxolane
Dialkyl peroxide
Secondary alcohol
Carboxylic acid derivative
Carboxylic acid
Oxacycle
Organoheterocyclic compound
Monocarboxylic acid or derivatives
Organic oxide
Organic oxygen compound
Hydrocarbon derivative
Alcohol
Carbonyl group
Organooxygen compound
Aliphatic heteropolycyclic compound

Molecular Framework

Aliphatic heteropolycyclic 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	4.22	ALOGPS
logP	3.6	ChemAxon
logS	-3.9	ALOGPS
pKa (Strongest Acidic)	4.36	ChemAxon
pKa (Strongest Basic)	-1.7	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	5	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	75.99 Å²	ChemAxon
Rotatable Bond Count	11	ChemAxon
Refractivity	99.16 m³·mol⁻¹	ChemAxon
Polarizability	38.97 Å³	ChemAxon
Number of Rings	2	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

Not Available

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

FDB029265

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

53481592

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Not Available

Showing NP-Card for PGH3 (NP0339163)

MOL for NP0339163 (PGH3)

3D MOL for NP0339163 (PGH3)

3D SDF for NP0339163 (PGH3)

3D-SDF for NP0339163 (PGH3)

PDB for NP0339163 (PGH3)

3D PDB for NP0339163 (PGH3)

SMILES for NP0339163 (PGH3)

INCHI for NP0339163 (PGH3)

Structure for NP0339163 (PGH3)

3D Structure for NP0339163 (PGH3)