NP-MRD: Showing NP-Card for (5s,6r)-6-{[(2r)-2-amino-2-(carboxymethyl-c-hydroxycarbonimidoyl)ethyl]sulfanyl}-5-hydroxyicosa-7,9,11,14-tetraenoic acid (NP0257272)

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Record Information

Version

2.0

Created at

2022-09-07 22:21:23 UTC

Updated at

2022-09-07 22:21:23 UTC

NP-MRD ID

NP0257272

Secondary Accession Numbers

None

Natural Product Identification

Common Name

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

Description

(5S,6R)-6-{[(2R)-2-amino-2-[(carboxymethyl)-C-hydroxycarbonimidoyl]ethyl]sulfanyl}-5-hydroxyicosa-7,9,11,14-tetraenoic acid belongs to the class of organic compounds known as hydroxyeicosatetraenoic acids. These are eicosanoic acids with an attached hydroxyl group and four CC double bonds. (5s,6r)-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. Based on a literature review very few articles have been published on (5S,6R)-6-{[(2R)-2-amino-2-[(carboxymethyl)-C-hydroxycarbonimidoyl]ethyl]sulfanyl}-5-hydroxyicosa-7,9,11,14-tetraenoic acid.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652309082200212D          

 34 33  0  0  1  0            999 V2000
    9.6535    9.7573    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.1134    9.1336    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.3033    9.2895    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.7632    8.6659    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.9530    8.8218    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.4129    8.1982    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.6028    8.3541    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0627    7.7304    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.3328    6.9509    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.7927    6.3272    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0627    5.5477    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.5226    4.9241    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.7927    4.1445    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2526    3.5209    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.5226    2.7413    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    3.9825    2.1177    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
    4.2526    1.3381    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7125    0.7145    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    3.9825   -0.0651    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
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    0.7420    2.7413    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.0922    3.2090    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.3328    2.5854    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    5.8729    3.2090    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
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    7.4931    0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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    7.7632   -0.0651    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
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 30 31  1  0  0  0  0
 31 32  1  0  0  0  0
 32 33  2  0  0  0  0
 32 34  1  0  0  0  0
M  END

     RDKit          3D

 74 73  0  0  0  0  0  0  0  0999 V2000
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   -6.1221   -1.5543    1.9258 N   0  0  0  0  0  0  0  0  0  0  0  0
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M  END


  Mrv1652309082200212D          

 34 33  0  0  1  0            999 V2000
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M  END
> <DATABASE_ID>
NP0257272

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CCCCCC=CCC=CC=CC=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)/t20-,21-,22+/m0/s1

> <INCHI_KEY>
YEESKJGWJFYOOK-FDFHNCONSA-N

> <FORMULA>
C25H40N2O6S

> <MOLECULAR_WEIGHT>
496.66

> <EXACT_MASS>
496.26070819

> <JCHEM_ACCEPTOR_COUNT>
8

> <JCHEM_ATOM_COUNT>
74

> <JCHEM_AVERAGE_POLARIZABILITY>
55.93198762307353

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
5

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

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

> <JCHEM_LOGP>
1.4726525619791506

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
3.9079171104760517

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.228349884186795

> <JCHEM_PKA_STRONGEST_BASIC>
9.199176958304562

> <JCHEM_POLAR_SURFACE_AREA>
153.44

> <JCHEM_REFRACTIVITY>
140.94490000000005

> <JCHEM_ROTATABLE_BOND_COUNT>
20

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
(5S,6R)-6-{[(2R)-2-amino-2-(carboxymethyl-C-hydroxycarbonimidoyl)ethyl]sulfanyl}-5-hydroxyicosa-7,9,11,14-tetraenoic acid

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 08-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   08-SEP-22         0                                  
HETATM    1  C   UNK     0      18.020  18.214   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      17.012  17.049   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      15.499  17.340   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      14.491  16.176   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      12.979  16.467   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      11.971  15.303   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      10.459  15.594   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       9.450  14.430   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       9.954  12.975   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       8.946  11.811   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       9.450  10.356   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       8.442   9.192   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       8.946   7.736   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       7.938   6.572   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       8.442   5.117   0.000  0.00  0.00           C+0
HETATM   16  S   UNK     0       7.434   3.953   0.000  0.00  0.00           S+0
HETATM   17  C   UNK     0       7.938   2.498   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       6.930   1.334   0.000  0.00  0.00           C+0
HETATM   19  N   UNK     0       7.434  -0.121   0.000  0.00  0.00           N+0
HETATM   20  C   UNK     0       5.418   1.625   0.000  0.00  0.00           C+0
HETATM   21  O   UNK     0       4.410   0.461   0.000  0.00  0.00           O+0
HETATM   22  N   UNK     0       4.914   3.080   0.000  0.00  0.00           N+0
HETATM   23  C   UNK     0       3.401   3.371   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0       2.897   4.826   0.000  0.00  0.00           C+0
HETATM   25  O   UNK     0       1.385   5.117   0.000  0.00  0.00           O+0
HETATM   26  O   UNK     0       3.906   5.990   0.000  0.00  0.00           O+0
HETATM   27  C   UNK     0       9.954   4.826   0.000  0.00  0.00           C+0
HETATM   28  O   UNK     0      10.963   5.990   0.000  0.00  0.00           O+0
HETATM   29  C   UNK     0      10.459   3.371   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0      11.971   3.080   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0      12.475   1.625   0.000  0.00  0.00           C+0
HETATM   32  C   UNK     0      13.987   1.334   0.000  0.00  0.00           C+0
HETATM   33  O   UNK     0      14.995   2.498   0.000  0.00  0.00           O+0
HETATM   34  O   UNK     0      14.491  -0.121   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                                                       
CONECT    7    6    8                                                       
CONECT    8    7    9                                                       
CONECT    9    8   10                                                       
CONECT   10    9   11                                                       
CONECT   11   10   12                                                       
CONECT   12   11   13                                                       
CONECT   13   12   14                                                       
CONECT   14   13   15                                                       
CONECT   15   14   16   27                                                  
CONECT   16   15   17                                                       
CONECT   17   16   18                                                       
CONECT   18   17   19   20                                                  
CONECT   19   18                                                            
CONECT   20   18   21   22                                                  
CONECT   21   20                                                            
CONECT   22   20   23                                                       
CONECT   23   22   24                                                       
CONECT   24   23   25   26                                                  
CONECT   25   24                                                            
CONECT   26   24                                                            
CONECT   27   15   28   29                                                  
CONECT   28   27                                                            
CONECT   29   27   30                                                       
CONECT   30   29   31                                                       
CONECT   31   30   32                                                       
CONECT   32   31   33   34                                                  
CONECT   33   32                                                            
CONECT   34   32                                                            
MASTER        0    0    0    0    0    0    0    0   34    0   66    0
END

View in JSmol

Synonyms

Value	Source
(5S,6R)-6-{[(2R)-2-amino-2-[(carboxymethyl)-C-hydroxycarbonimidoyl]ethyl]sulfanyl}-5-hydroxyicosa-7,9,11,14-tetraenoate	Generator
(5S,6R)-6-{[(2R)-2-amino-2-[(carboxymethyl)-C-hydroxycarbonimidoyl]ethyl]sulphanyl}-5-hydroxyicosa-7,9,11,14-tetraenoate	Generator
(5S,6R)-6-{[(2R)-2-amino-2-[(carboxymethyl)-C-hydroxycarbonimidoyl]ethyl]sulphanyl}-5-hydroxyicosa-7,9,11,14-tetraenoic acid	Generator

Chemical Formula

C₂₅H₄₀N₂O₆S

Average Mass

496.6600 Da

Monoisotopic Mass

496.26071 Da

IUPAC Name

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

Traditional Name

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

CAS Registry Number

Not Available

SMILES

CCCCCC=CCC=CC=CC=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)/t20-,21-,22+/m0/s1

InChI Key

YEESKJGWJFYOOK-FDFHNCONSA-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 hydroxyeicosatetraenoic acids. These are eicosanoic acids with an attached hydroxyl group and four CC double bonds.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Fatty Acyls

Sub Class

Eicosanoids

Direct Parent

Hydroxyeicosatetraenoic acids

Alternative Parents

Substituents

Hydroxyeicosatetraenoic acid
Alpha peptide
Long-chain fatty acid
N-acyl-alpha amino acid or derivatives
N-acyl-alpha-amino acid
Alpha-amino acid or derivatives
Thia fatty acid
Hydroxy fatty acid
Fatty acid
Unsaturated fatty acid
Dicarboxylic acid or derivatives
Amino acid
Secondary alcohol
Amino acid or derivatives
Dialkylthioether
Organic 1,3-dipolar compound
Propargyl-type 1,3-dipolar organic compound
Sulfenyl compound
Thioether
Carboxylic acid
Carboxylic acid derivative
Carboximidic acid derivative
Carboximidic acid
Organic nitrogen compound
Organic oxygen compound
Organopnictogen compound
Organic oxide
Hydrocarbon derivative
Primary amine
Organosulfur compound
Organooxygen compound
Organonitrogen compound
Primary aliphatic amine
Carbonyl group
Amine
Alcohol
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	1.47	ChemAxon
pKa (Strongest Acidic)	3.23	ChemAxon
pKa (Strongest Basic)	9.2	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	8	ChemAxon
Hydrogen Donor Count	5	ChemAxon
Polar Surface Area	153.44 Å²	ChemAxon
Rotatable Bond Count	20	ChemAxon
Refractivity	140.94 m³·mol⁻¹	ChemAxon
Polarizability	55.93 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

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

440856

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

LOTUS database [Link]

Showing NP-Card for (5s,6r)-6-{[(2r)-2-amino-2-(carboxymethyl-c-hydroxycarbonimidoyl)ethyl]sulfanyl}-5-hydroxyicosa-7,9,11,14-tetraenoic acid (NP0257272)

MOL for NP0257272 ((5s,6r)-6-{[(2r)-2-amino-2-(carboxymethyl-c-hydroxycarbonimidoyl)ethyl]sulfanyl}-5-hydroxyicosa-7,9,11,14-tetraenoic acid)

3D MOL for NP0257272 ((5s,6r)-6-{[(2r)-2-amino-2-(carboxymethyl-c-hydroxycarbonimidoyl)ethyl]sulfanyl}-5-hydroxyicosa-7,9,11,14-tetraenoic acid)

3D SDF for NP0257272 ((5s,6r)-6-{[(2r)-2-amino-2-(carboxymethyl-c-hydroxycarbonimidoyl)ethyl]sulfanyl}-5-hydroxyicosa-7,9,11,14-tetraenoic acid)

3D-SDF for NP0257272 ((5s,6r)-6-{[(2r)-2-amino-2-(carboxymethyl-c-hydroxycarbonimidoyl)ethyl]sulfanyl}-5-hydroxyicosa-7,9,11,14-tetraenoic acid)

PDB for NP0257272 ((5s,6r)-6-{[(2r)-2-amino-2-(carboxymethyl-c-hydroxycarbonimidoyl)ethyl]sulfanyl}-5-hydroxyicosa-7,9,11,14-tetraenoic acid)

3D PDB for NP0257272 ((5s,6r)-6-{[(2r)-2-amino-2-(carboxymethyl-c-hydroxycarbonimidoyl)ethyl]sulfanyl}-5-hydroxyicosa-7,9,11,14-tetraenoic acid)

SMILES for NP0257272 ((5s,6r)-6-{[(2r)-2-amino-2-(carboxymethyl-c-hydroxycarbonimidoyl)ethyl]sulfanyl}-5-hydroxyicosa-7,9,11,14-tetraenoic acid)

INCHI for NP0257272 ((5s,6r)-6-{[(2r)-2-amino-2-(carboxymethyl-c-hydroxycarbonimidoyl)ethyl]sulfanyl}-5-hydroxyicosa-7,9,11,14-tetraenoic acid)

Structure for NP0257272 ((5s,6r)-6-{[(2r)-2-amino-2-(carboxymethyl-c-hydroxycarbonimidoyl)ethyl]sulfanyl}-5-hydroxyicosa-7,9,11,14-tetraenoic acid)

3D Structure for NP0257272 ((5s,6r)-6-{[(2r)-2-amino-2-(carboxymethyl-c-hydroxycarbonimidoyl)ethyl]sulfanyl}-5-hydroxyicosa-7,9,11,14-tetraenoic acid)