NP-MRD: Showing NP-Card for prostaglandin-b1 (NP0301254)

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Record Information

Version

2.0

Created at

2022-09-10 14:05:46 UTC

Updated at

2022-09-10 14:05:46 UTC

NP-MRD ID

NP0301254

Secondary Accession Numbers

None

Natural Product Identification

Common Name

prostaglandin-b1

Description

Prostaglandin B1, also known as PGB1, 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. Thus, prostaglandin B1 is considered to be an eicosanoid lipid molecule. Prostaglandin B1 blocks S-phase DNA synthesis; inhibition of DNA synthesis does not appear to require elevated levels of cAMP. Prostaglandin B1 is a very hydrophobic molecule, practically insoluble (in water), and relatively neutral. PGE1 is a prostanoid. Prostaglandin B1 exists in all living organisms, ranging from bacteria to humans. The PGs and TXs are collectively identified as prostanoids. prostaglandin-b1 is found in Homo sapiens and Larix sibirica. prostaglandin-b1 was first documented in 1983 (PMID: 6635328). Prostaglandin B1 has the ability to enhance peripheral vascular resistance and elevate blood pressure (PMID: 7667505) (PMID: 1477202) (PMID: 2129000) (PMID: 2597672).

Structure

MOL SDF PDB SMILES InChI


  Mrv0541 02231219372D          

 24 24  0  0  1  0            999 V2000
   20.4808  -14.6060    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   21.3783  -10.1940    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   15.1198  -14.3424    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   15.5614  -12.9833    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   20.7108  -13.1540    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   19.9262  -12.8990    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   21.3783  -12.6691    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   19.3131  -13.4511    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   22.0457  -13.1540    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   21.7908  -13.9386    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   18.5284  -13.1962    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   20.9658  -13.9386    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   17.9153  -13.7482    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   21.3783  -11.8440    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   22.8072  -10.1940    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   22.0927  -10.6065    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   17.1307  -13.4933    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   22.8072   -9.3690    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   22.0927  -11.4315    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   23.5218   -8.9565    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   16.5176  -14.0453    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   23.5218   -8.1315    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   24.2362   -7.7190    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   15.7329  -13.7903    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1 12  2  0  0  0  0
 16  2  1  1  0  0  0
  3 24  1  0  0  0  0
  4 24  2  0  0  0  0
  5  6  1  0  0  0  0
  5  7  2  0  0  0  0
  5 12  1  0  0  0  0
  6  8  1  0  0  0  0
  7  9  1  0  0  0  0
  7 14  1  0  0  0  0
  8 11  1  0  0  0  0
  9 10  1  0  0  0  0
 10 12  1  0  0  0  0
 11 13  1  0  0  0  0
 13 17  1  0  0  0  0
 14 19  2  0  0  0  0
 15 16  1  0  0  0  0
 15 18  1  0  0  0  0
 16 19  1  0  0  0  0
 17 21  1  0  0  0  0
 18 20  1  0  0  0  0
 20 22  1  0  0  0  0
 21 24  1  0  0  0  0
 22 23  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0301254

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CCCCC[C@H](O)\C=C\C1=C(CCCCCCC(O)=O)C(=O)CC1

> <INCHI_IDENTIFIER>
InChI=1S/C20H32O4/c1-2-3-6-9-17(21)14-12-16-13-15-19(22)18(16)10-7-4-5-8-11-20(23)24/h12,14,17,21H,2-11,13,15H2,1H3,(H,23,24)/b14-12+/t17-/m0/s1

> <INCHI_KEY>
YBHMPNRDOVPQIN-VSOYFRJCSA-N

> <FORMULA>
C20H32O4

> <MOLECULAR_WEIGHT>
336.4657

> <EXACT_MASS>
336.230059512

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_AVERAGE_POLARIZABILITY>
40.72246864158204

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
7-{2-[(1E,3S)-3-hydroxyoct-1-en-1-yl]-5-oxocyclopent-1-en-1-yl}heptanoic acid

> <ALOGPS_LOGP>
3.99

> <JCHEM_LOGP>
4.546779006666667

> <ALOGPS_LOGS>
-4.38

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
17.769121357059053

> <JCHEM_PKA_STRONGEST_ACIDIC>
4.303507240331283

> <JCHEM_PKA_STRONGEST_BASIC>
-1.5872915354101118

> <JCHEM_POLAR_SURFACE_AREA>
74.6

> <JCHEM_REFRACTIVITY>
97.4893

> <JCHEM_ROTATABLE_BOND_COUNT>
13

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.39e-02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
prostaglandin-B1

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 23-FEB-12   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   23-FEB-12         0                                  
HETATM    1  O   UNK     0      38.231 -27.265   0.000  0.00  0.00           O+0
HETATM    2  O   UNK     0      39.906 -19.029   0.000  0.00  0.00           O+0
HETATM    3  O   UNK     0      28.224 -26.772   0.000  0.00  0.00           O+0
HETATM    4  O   UNK     0      29.048 -24.235   0.000  0.00  0.00           O+0
HETATM    5  C   UNK     0      38.660 -24.554   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      37.196 -24.078   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      39.906 -23.649   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      36.051 -25.109   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      41.152 -24.554   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      40.676 -26.019   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      34.586 -24.633   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      39.136 -26.019   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      33.442 -25.663   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      39.906 -22.109   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0      42.573 -19.029   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0      41.240 -19.799   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0      31.977 -25.187   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0      42.573 -17.489   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0      41.240 -21.339   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0      43.907 -16.719   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0      30.833 -26.218   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0      43.907 -15.179   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0      45.241 -14.409   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0      29.368 -25.742   0.000  0.00  0.00           C+0
CONECT    1   12                                                            
CONECT    2   16                                                            
CONECT    3   24                                                            
CONECT    4   24                                                            
CONECT    5    6    7   12                                                  
CONECT    6    5    8                                                       
CONECT    7    5    9   14                                                  
CONECT    8    6   11                                                       
CONECT    9    7   10                                                       
CONECT   10    9   12                                                       
CONECT   11    8   13                                                       
CONECT   12    1    5   10                                                  
CONECT   13   11   17                                                       
CONECT   14    7   19                                                       
CONECT   15   16   18                                                       
CONECT   16    2   15   19                                                  
CONECT   17   13   21                                                       
CONECT   18   15   20                                                       
CONECT   19   14   16                                                       
CONECT   20   18   22                                                       
CONECT   21   17   24                                                       
CONECT   22   20   23                                                       
CONECT   23   22                                                            
CONECT   24    3    4   21                                                  
MASTER        0    0    0    0    0    0    0    0   24    0   48    0
END

View in JSmol

Synonyms

Value	Source
PGB1	ChEBI
(13E,15S)-15-Hydroxy-9-oxoprosta-8(12),13-dien-1-Oate	HMDB
(13E,15S)-15-Hydroxy-9-oxoprosta-8(12),13-dien-1-Oic acid	HMDB
9-oxo-15S-Hydroxy-8(12),13E-prostadienoate	HMDB
9-oxo-15S-Hydroxy-8(12),13E-prostadienoic acid	HMDB
Prostaglandin-b1	HMDB
Prostaglandin b1	MeSH

Chemical Formula

C₂₀H₃₂O₄

Average Mass

336.4657 Da

Monoisotopic Mass

336.23006 Da

IUPAC Name

7-{2-[(1E,3S)-3-hydroxyoct-1-en-1-yl]-5-oxocyclopent-1-en-1-yl}heptanoic acid

Traditional Name

prostaglandin-B1

CAS Registry Number

Not Available

SMILES

CCCCC[C@H](O)\C=C\C1=C(CCCCCCC(O)=O)C(=O)CC1

InChI Identifier

InChI=1S/C20H32O4/c1-2-3-6-9-17(21)14-12-16-13-15-19(22)18(16)10-7-4-5-8-11-20(23)24/h12,14,17,21H,2-11,13,15H2,1H3,(H,23,24)/b14-12+/t17-/m0/s1

InChI Key

YBHMPNRDOVPQIN-VSOYFRJCSA-N

Experimental Spectra

Not Available

Predicted Spectra

Not Available

Chemical Shift Submissions

Not Available

Species

Species of Origin

Species Name	Source	Reference
Homo sapiens	LOTUS Database	35616633
Larix sibirica	LOTUS Database	35616633

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
Fatty alcohol
Hydroxy fatty acid
Ketone
Cyclic ketone
Secondary alcohol
Monocarboxylic acid or derivatives
Carboxylic acid
Carboxylic acid derivative
Hydrocarbon derivative
Alcohol
Organic oxide
Organic oxygen compound
Organooxygen compound
Carbonyl group
Aliphatic homomonocyclic compound

Molecular Framework

Aliphatic homomonocyclic compounds

External Descriptors

prostaglandins B (CHEBI:27624 )
Prostaglandins (C00959 )
Prostaglandins (LMFA03010131 )

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	3.99	ALOGPS
logP	4.55	ChemAxon
logS	-4.4	ALOGPS
pKa (Strongest Acidic)	4.3	ChemAxon
pKa (Strongest Basic)	-1.6	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	4	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	74.6 Å²	ChemAxon
Rotatable Bond Count	13	ChemAxon
Refractivity	97.49 m³·mol⁻¹	ChemAxon
Polarizability	40.72 Å³	ChemAxon
Number of Rings	1	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

HMDB0002982

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

FDB023088

KNApSAcK ID

Not Available

Chemspider ID

4444076

KEGG Compound ID

C00959

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

408

PubChem Compound

5280388

PDB ID

Not Available

ChEBI ID

27624

Good Scents ID

Not Available

References

General References

Hishinuma T, Nakamura H, Itoh K, Ohyama Y, Ishibashi M, Mizugaki M: Microdetermination of the prostaglandin B1 in human plasma by gas chromatography/selected ion monitoring using [18O]prostaglandin B1 as an internal standard. Prostaglandins. 1995 Apr;49(4):239-46. doi: 10.1016/0090-6980(95)00016-4. [PubMed:7667505 ]
Fry MR, Ghosh SS, East JM, Franson RC: Role of human sperm phospholipase A2 in fertilization: effects of a novel inhibitor of phospholipase A2 activity on membrane perturbations and oocyte penetration. Biol Reprod. 1992 Nov;47(5):751-9. doi: 10.1095/biolreprod47.5.751. [PubMed:1477202 ]
Franson R, Raghupathi R, Fry M, Saal J, Vishwanath B, Ghosh SS, Rosenthal MD: Inhibition of human phospholipases A2 by cis-unsaturated fatty acids and oligomers of prostaglandin B1. Adv Exp Med Biol. 1990;279:219-30. doi: 10.1007/978-1-4613-0651-1_15. [PubMed:2129000 ]
Franson RC, Rosenthal MD: Oligomers of prostaglandin B1 inhibit in vitro phospholipase A2 activity. Biochim Biophys Acta. 1989 Dec 18;1006(3):272-7. doi: 10.1016/0005-2760(89)90013-1. [PubMed:2597672 ]
Himori N, Burkman AM: Prostaglandin B1 can modify the pressor responses to sympathetic nerve stimulation. Res Commun Chem Pathol Pharmacol. 1983 Sep;41(3):397-405. [PubMed:6635328 ]
LOTUS database [Link]

Showing NP-Card for prostaglandin-b1 (NP0301254)

MOL for NP0301254 (prostaglandin-b1)

3D MOL for NP0301254 (prostaglandin-b1)

3D SDF for NP0301254 (prostaglandin-b1)

3D-SDF for NP0301254 (prostaglandin-b1)

PDB for NP0301254 (prostaglandin-b1)

3D PDB for NP0301254 (prostaglandin-b1)

SMILES for NP0301254 (prostaglandin-b1)

INCHI for NP0301254 (prostaglandin-b1)

Structure for NP0301254 (prostaglandin-b1)

3D Structure for NP0301254 (prostaglandin-b1)