NP-MRD: Showing NP-Card for (5s,6r,7e,9e,11z,14z)-6-{[(2r)-2-amino-2-(carboxymethyl-c-hydroxycarbonimidoyl)ethyl]sulfanyl}-5-hydroxyicosa-7,9,11,14-tetraenoic acid (NP0175932)

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Record Information

Version

2.0

Created at

2022-09-03 13:30:39 UTC

Updated at

2022-09-03 13:30:39 UTC

NP-MRD ID

NP0175932

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(5s,6r,7e,9e,11z,14z)-6-{[(2r)-2-amino-2-(carboxymethyl-c-hydroxycarbonimidoyl)ethyl]sulfanyl}-5-hydroxyicosa-7,9,11,14-tetraenoic acid

Description

Leukotriene D4, also known as LTD4, belongs to the class of organic compounds known as leukotrienes. These are eicosanoids containing a hydroxyl group attached to the aliphatic chain of an arachidonic acid. Leukotrienes have four double bonds, three (and only three) of which are conjugated. Thus, leukotriene D4 is considered to be an eicosanoid lipid molecule. Leukotriene D4 is a very hydrophobic molecule, practically insoluble (in water), and relatively neutral. Leukotriene D4 and L-glutamic acid can be biosynthesized from leukotriene C4; which is catalyzed by the enzyme Gamma-glutamyltranspeptidase 1. In humans, leukotriene D4 is involved in mefenamic acid action pathway. (5s,6r,7e,9e,11z,14z)-6-{[(2r)-2-amino-2-(carboxymethyl-c-hydroxycarbonimidoyl)ethyl]sulfanyl}-5-hydroxyicosa-7,9,11,14-tetraenoic acid is found in Homo sapiens and Mus musculus. (5s,6r,7e,9e,11z,14z)-6-{[(2r)-2-amino-2-(carboxymethyl-c-hydroxycarbonimidoyl)ethyl]sulfanyl}-5-hydroxyicosa-7,9,11,14-tetraenoic acid was first documented in 1989 (PMID: 2573348). A leukotriene that is (7E,9E,11Z,14Z)-icosa-7,9,11,14-tetraenoic acid substituted by a hydroxy group at position 5 (5S) and a L-cysteinylglycinyl group at position 6 (6R) (PMID: 9406280) (PMID: 1492107) (PMID: 9820300) (PMID: 7894671).

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652303121822302D          

 34 33  0  0  0  0            999 V2000
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M  END

     RDKit          3D

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M  END


  Mrv1652303121822302D          

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 15 16  1  0  0  0  0
 16 17  1  0  0  0  0
 17 18  1  0  0  0  0
 17 19  2  0  0  0  0
 21 22  2  0  0  0  0
 22 23  1  0  0  0  0
 23 24  2  0  0  0  0
 24 25  1  0  0  0  0
 25 26  2  0  0  0  0
 26 27  1  0  0  0  0
 27 28  1  0  0  0  0
 28 29  2  0  0  0  0
 29 30  1  0  0  0  0
 30 31  1  0  0  0  0
 31 32  1  0  0  0  0
 32 33  1  0  0  0  0
 33 34  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0175932

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CCCCC\C=C/C\C=C/C=C/C=C/[C@@H](SC[C@H](N)C(=O)NCC(O)=O)[C@@H](O)CCCC(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C25H40N2O6S/c1-2-3-4-5-6-7-8-9-10-11-12-13-16-22(21(28)15-14-17-23(29)30)34-19-20(26)25(33)27-18-24(31)32/h6-7,9-13,16,20-22,28H,2-5,8,14-15,17-19,26H2,1H3,(H,27,33)(H,29,30)(H,31,32)/b7-6-,10-9-,12-11+,16-13+/t20-,21-,22+/m0/s1

> <INCHI_KEY>
YEESKJGWJFYOOK-IJHYULJSSA-N

> <FORMULA>
C25H40N2O6S

> <MOLECULAR_WEIGHT>
496.66

> <EXACT_MASS>
496.26070819

> <JCHEM_ACCEPTOR_COUNT>
7

> <JCHEM_ATOM_COUNT>
74

> <JCHEM_AVERAGE_POLARIZABILITY>
56.08299633054518

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
5

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(5S,6R,7E,9E,11Z,14Z)-6-{[(2R)-2-amino-2-[(carboxymethyl)carbamoyl]ethyl]sulfanyl}-5-hydroxyicosa-7,9,11,14-tetraenoic acid

> <ALOGPS_LOGP>
1.17

> <JCHEM_LOGP>
0.7629385429743649

> <ALOGPS_LOGS>
-5.28

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
4.215832547861241

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.290179717912459

> <JCHEM_PKA_STRONGEST_BASIC>
8.049653171894935

> <JCHEM_POLAR_SURFACE_AREA>
149.95

> <JCHEM_REFRACTIVITY>
140.42320000000004

> <JCHEM_ROTATABLE_BOND_COUNT>
20

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
2.58e-03 g/l

> <JCHEM_TRADITIONAL_IUPAC>
leukotriene D4

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 12-MAR-18   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   12-MAR-18         0                                  
HETATM    1  C   UNK     0    8719.2638726.707   0.000  0.00  0.00           C+0
HETATM    2  S   UNK     0    8719.2638725.162   0.000  0.00  0.00           S+0
HETATM    3  C   UNK     0    8717.9398724.371   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0    8717.9398722.829   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0    8719.2788722.056   0.000  0.00  0.00           C+0
HETATM    6  N   UNK     0    8720.6148722.829   0.000  0.00  0.00           N+0
HETATM    7  C   UNK     0    8721.9498722.056   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0    8723.2848722.829   0.000  0.00  0.00           C+0
HETATM    9  O   UNK     0    8724.6208722.056   0.000  0.00  0.00           O+0
HETATM   10  O   UNK     0    8723.2848724.371   0.000  0.00  0.00           O+0
HETATM   11  O   UNK     0    8719.2788720.515   0.000  0.00  0.00           O+0
HETATM   12  N   UNK     0    8716.6088722.056   0.000  0.00  0.00           N+0
HETATM   13  C   UNK     0    8717.9288727.474   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0    8716.5938726.707   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0    8715.2578727.474   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0    8713.9228726.707   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0    8712.5878727.474   0.000  0.00  0.00           C+0
HETATM   18  O   UNK     0    8711.2478726.707   0.000  0.00  0.00           O+0
HETATM   19  O   UNK     0    8712.5878729.014   0.000  0.00  0.00           O+0
HETATM   20  O   UNK     0    8717.9288729.014   0.000  0.00  0.00           O+0
HETATM   21  C   UNK     0    8720.5998727.474   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0    8721.9348726.707   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0    8723.2698727.474   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0    8724.6058726.707   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0    8725.9408727.474   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0    8727.4818727.474   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0    8728.8188726.707   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0    8730.1508727.474   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0    8731.6958727.474   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0    8733.0288726.707   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0    8734.3658727.474   0.000  0.00  0.00           C+0
HETATM   32  C   UNK     0    8735.7028726.707   0.000  0.00  0.00           C+0
HETATM   33  C   UNK     0    8737.0358727.474   0.000  0.00  0.00           C+0
HETATM   34  C   UNK     0    8738.3758726.707   0.000  0.00  0.00           C+0
CONECT    1    2   13   21                                                  
CONECT    2    1    3                                                       
CONECT    3    2    4                                                       
CONECT    4    3    5   12                                                  
CONECT    5    4    6   11                                                  
CONECT    6    5    7                                                       
CONECT    7    6    8                                                       
CONECT    8    7    9   10                                                  
CONECT    9    8                                                            
CONECT   10    8                                                            
CONECT   11    5                                                            
CONECT   12    4                                                            
CONECT   13    1   14   20                                                  
CONECT   14   13   15                                                       
CONECT   15   14   16                                                       
CONECT   16   15   17                                                       
CONECT   17   16   18   19                                                  
CONECT   18   17                                                            
CONECT   19   17                                                            
CONECT   20   13                                                            
CONECT   21    1   22                                                       
CONECT   22   21   23                                                       
CONECT   23   22   24                                                       
CONECT   24   23   25                                                       
CONECT   25   24   26                                                       
CONECT   26   25   27                                                       
CONECT   27   26   28                                                       
CONECT   28   27   29                                                       
CONECT   29   28   30                                                       
CONECT   30   29   31                                                       
CONECT   31   30   32                                                       
CONECT   32   31   33                                                       
CONECT   33   32   34                                                       
CONECT   34   33                                                            
MASTER        0    0    0    0    0    0    0    0   34    0   66    0
END

View in JSmol

Synonyms

Value	Source
(R-(R,s-(e,e,Z,Z)))-N-(S-(1-(4-carboxy-1-hydroxybutyl)-2,4,6,9-pentadecatetraenyl)-L-cysteinyl)glycine	ChEBI
5S-Hydroxy-6R-(S-cysteinylglycinyl)-7E,9E,11E,14Z-eicosatetraenoic acid	ChEBI
LTD4	ChEBI
5S-Hydroxy-6R-(S-cysteinylglycinyl)-7E,9E,11E,14Z-eicosatetraenoate	Generator
Leukotriene D	HMDB
Leukotriene D-4	HMDB
Leukotrienes D	HMDB
Leukotriene D 4	HMDB

Chemical Formula

C₂₅H₄₀N₂O₆S

Average Mass

496.6600 Da

Monoisotopic Mass

496.26071 Da

IUPAC Name

(5S,6R,7E,9E,11Z,14Z)-6-{[(2R)-2-amino-2-[(carboxymethyl)carbamoyl]ethyl]sulfanyl}-5-hydroxyicosa-7,9,11,14-tetraenoic acid

Traditional Name

leukotriene D4

CAS Registry Number

Not Available

SMILES

CCCCC\C=C/C\C=C/C=C/C=C/[C@@H](SC[C@H](N)C(=O)NCC(O)=O)[C@@H](O)CCCC(O)=O

InChI Identifier

InChI=1S/C25H40N2O6S/c1-2-3-4-5-6-7-8-9-10-11-12-13-16-22(21(28)15-14-17-23(29)30)34-19-20(26)25(33)27-18-24(31)32/h6-7,9-13,16,20-22,28H,2-5,8,14-15,17-19,26H2,1H3,(H,27,33)(H,29,30)(H,31,32)/b7-6-,10-9-,12-11+,16-13+/t20-,21-,22+/m0/s1

InChI Key

YEESKJGWJFYOOK-IJHYULJSSA-N

Experimental Spectra

Not Available

Predicted Spectra

Spectrum Type	Description	Depositor ID	Depositor Organization	Depositor	Deposition Date	View
1D NMR	¹³C NMR Spectrum (1D, 25 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 252 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 50 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 75 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 101 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 126 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 151 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 176 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 201 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 226 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum

Chemical Shift Submissions

Not Available

Species

Species of Origin

Species Name	Source	Reference
Homo sapiens	LOTUS Database	35616633
Mus musculus	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as leukotrienes. These are eicosanoids containing a hydroxyl group attached to the aliphatic chain of an arachidonic acid. Leukotrienes have four double bonds, three (and only three) of which are conjugated.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Fatty Acyls

Sub Class

Eicosanoids

Direct Parent

Leukotrienes

Alternative Parents

Substituents

Leukotriene
Hydroxyeicosatetraenoic acid
Alpha-dipeptide
Alpha peptide
Long-chain fatty acid
N-acyl-alpha amino acid or derivatives
N-acyl-alpha-amino acid
Alpha-amino acid amide
Cysteine or derivatives
Alpha-amino acid or derivatives
Hydroxy fatty acid
Thia fatty acid
Dicarboxylic acid or derivatives
Fatty acid
Unsaturated fatty acid
Secondary alcohol
Secondary carboxylic acid amide
Amino acid
Carboxamide group
Amino acid or derivatives
Carboxylic acid derivative
Carboxylic acid
Dialkylthioether
Sulfenyl compound
Thioether
Amine
Organic oxygen compound
Organic nitrogen compound
Hydrocarbon derivative
Alcohol
Organic oxide
Carbonyl group
Organopnictogen compound
Primary amine
Primary aliphatic amine
Organosulfur compound
Organooxygen compound
Organonitrogen compound
Aliphatic acyclic compound

Molecular Framework

Aliphatic acyclic compounds

External Descriptors

organic sulfide (CHEBI:28666 )
leukotriene (CHEBI:28666 )
Leukotrienes (C05951 )
Leukotrienes (LMFA03020006 )

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	1.17	ALOGPS
logP	0.76	ChemAxon
logS	-5.3	ALOGPS
pKa (Strongest Acidic)	3.29	ChemAxon
pKa (Strongest Basic)	8.05	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	7	ChemAxon
Hydrogen Donor Count	5	ChemAxon
Polar Surface Area	149.95 Å²	ChemAxon
Rotatable Bond Count	20	ChemAxon
Refractivity	140.42 m³·mol⁻¹	ChemAxon
Polarizability	56.08 Å³	ChemAxon
Number of Rings	0	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

External Links

HMDB ID

HMDB0003080

DrugBank ID

DB11858

Phenol Explorer Compound ID

Not Available

FoodDB ID

FDB023105

KNApSAcK ID

Not Available

Chemspider ID

Not Available

KEGG Compound ID

C05951

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Leukotriene_D4

METLIN ID

Not Available

PubChem Compound

5280878

PDB ID

Not Available

ChEBI ID

28666

Good Scents ID

Not Available

References

General References

Beckh K, Dirks A, Koop I, Koop H, Adler G: Impairment of hepatic transport processes in perfused rat liver by the specific CCK receptor antagonist loxiglumide. Res Exp Med (Berl). 1997;197(3):125-35. doi: 10.1007/s004330050062. [PubMed:9406280 ]
Card GL, Li Y, Miller S, Wright BE: Carbonate inhibition of leukotriene D4-dipeptidase in human serum. Prostaglandins Leukot Essent Fatty Acids. 1992 Dec;47(4):301-5. doi: 10.1016/0952-3278(92)90202-t. [PubMed:1492107 ]
Mayatepek E, Flock B: Leukotriene C4-synthesis deficiency: a new inborn error of metabolism linked to a fatal developmental syndrome. Lancet. 1998 Nov 7;352(9139):1514-7. doi: 10.1016/S0140-6736(98)01186-6. [PubMed:9820300 ]
Card GL, Unnithan T, Rhodes MJ, Wright BE: Leukotriene metabolism and hypersensitivity in man and mouse. Biochem Biophys Res Commun. 1989 Oct 31;164(2):626-30. doi: 10.1016/0006-291x(89)91506-4. [PubMed:2573348 ]
Hsieh JY, Lin C, Matuszewski BK: Robotic sample preparation and high-performance liquid chromatographic analysis of verlukast in human plasma. J Chromatogr B Biomed Appl. 1994 Nov 18;661(2):307-12. doi: 10.1016/0378-4347(94)00367-x. [PubMed:7894671 ]
LOTUS database [Link]

Showing NP-Card for (5s,6r,7e,9e,11z,14z)-6-{[(2r)-2-amino-2-(carboxymethyl-c-hydroxycarbonimidoyl)ethyl]sulfanyl}-5-hydroxyicosa-7,9,11,14-tetraenoic acid (NP0175932)

MOL for NP0175932 ((5s,6r,7e,9e,11z,14z)-6-{[(2r)-2-amino-2-(carboxymethyl-c-hydroxycarbonimidoyl)ethyl]sulfanyl}-5-hydroxyicosa-7,9,11,14-tetraenoic acid)

3D MOL for NP0175932 ((5s,6r,7e,9e,11z,14z)-6-{[(2r)-2-amino-2-(carboxymethyl-c-hydroxycarbonimidoyl)ethyl]sulfanyl}-5-hydroxyicosa-7,9,11,14-tetraenoic acid)

3D SDF for NP0175932 ((5s,6r,7e,9e,11z,14z)-6-{[(2r)-2-amino-2-(carboxymethyl-c-hydroxycarbonimidoyl)ethyl]sulfanyl}-5-hydroxyicosa-7,9,11,14-tetraenoic acid)

3D-SDF for NP0175932 ((5s,6r,7e,9e,11z,14z)-6-{[(2r)-2-amino-2-(carboxymethyl-c-hydroxycarbonimidoyl)ethyl]sulfanyl}-5-hydroxyicosa-7,9,11,14-tetraenoic acid)

PDB for NP0175932 ((5s,6r,7e,9e,11z,14z)-6-{[(2r)-2-amino-2-(carboxymethyl-c-hydroxycarbonimidoyl)ethyl]sulfanyl}-5-hydroxyicosa-7,9,11,14-tetraenoic acid)

3D PDB for NP0175932 ((5s,6r,7e,9e,11z,14z)-6-{[(2r)-2-amino-2-(carboxymethyl-c-hydroxycarbonimidoyl)ethyl]sulfanyl}-5-hydroxyicosa-7,9,11,14-tetraenoic acid)

SMILES for NP0175932 ((5s,6r,7e,9e,11z,14z)-6-{[(2r)-2-amino-2-(carboxymethyl-c-hydroxycarbonimidoyl)ethyl]sulfanyl}-5-hydroxyicosa-7,9,11,14-tetraenoic acid)

INCHI for NP0175932 ((5s,6r,7e,9e,11z,14z)-6-{[(2r)-2-amino-2-(carboxymethyl-c-hydroxycarbonimidoyl)ethyl]sulfanyl}-5-hydroxyicosa-7,9,11,14-tetraenoic acid)

Structure for NP0175932 ((5s,6r,7e,9e,11z,14z)-6-{[(2r)-2-amino-2-(carboxymethyl-c-hydroxycarbonimidoyl)ethyl]sulfanyl}-5-hydroxyicosa-7,9,11,14-tetraenoic acid)

3D Structure for NP0175932 ((5s,6r,7e,9e,11z,14z)-6-{[(2r)-2-amino-2-(carboxymethyl-c-hydroxycarbonimidoyl)ethyl]sulfanyl}-5-hydroxyicosa-7,9,11,14-tetraenoic acid)