NP-MRD: Showing NP-Card for Leukotriene D5 (NP0339141)

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Record Information

Version

2.0

Created at

2024-09-11 19:52:37 UTC

Updated at

2024-09-11 19:52:38 UTC

NP-MRD ID

NP0339141

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Leukotriene D5

Description

Leukotriene D5, also known as LTD(,5), belongs to the class of organic compounds known as oligosaccharides. These are carbohydrates made up of 3 to 10 monosaccharide units linked to each other through glycosidic bonds. Thus, leukotriene D5 is considered to be an eicosanoid lipid molecule. These molecules are extremely potent, able to cause profound physiological effects at very dilute concentrations. All eicosanoids function locally at the site of synthesis, through receptor-mediated G-protein linked signalling pathways. Leukotriene D5 is a very hydrophobic molecule, practically insoluble (in water), and relatively neutral. The eicosanoids consist of the prostaglandins (PGs), thromboxanes (TXs), leukotrienes (LTs), and lipoxins (LXs). Leukotrienes are eicosanoids.

Structure

MOL SDF PDB SMILES InChI


  Mrv1652303102016482D          

 34 33  0  0  1  0            999 V2000
   13.1201  -11.3696    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.4056  -11.7821    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.6911  -11.3696    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.9766  -11.7821    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.9766  -12.6071    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.2622  -13.0196    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.2622  -13.8446    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.9766  -14.2571    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.9766  -15.0821    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.6911  -15.4946    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.4056  -15.0821    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   13.1201  -15.4946    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   13.8346  -15.0821    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   14.5490  -15.4946    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   15.2635  -15.0821    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   15.9780  -15.4946    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
   15.9780  -16.3196    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   16.6924  -16.7321    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   17.4069  -16.3196    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   16.6924  -17.5572    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   15.9780  -17.9697    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   17.4069  -17.9697    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   18.1214  -17.5572    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   18.8359  -17.9697    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   18.8359  -18.7947    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   19.5504  -17.5572    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   15.2635  -14.2571    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   14.5490  -13.8446    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   15.9780  -13.8446    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   16.6924  -14.2571    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   17.4069  -13.8446    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   18.1214  -14.2571    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   18.1214  -15.0821    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   18.8359  -13.8446    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  2  0  0  0  0
  7  8  1  0  0  0  0
  8  9  1  0  0  0  0
  9 10  2  0  0  0  0
 10 11  1  0  0  0  0
 11 12  2  0  0  0  0
 12 13  1  0  0  0  0
 13 14  2  0  0  0  0
 14 15  1  0  0  0  0
 15 16  1  0  0  0  0
 15 27  1  1  0  0  0
 16 17  1  0  0  0  0
 17 18  1  0  0  0  0
 18 19  1  6  0  0  0
 18 20  1  0  0  0  0
 20 21  2  0  0  0  0
 20 22  1  0  0  0  0
 22 23  1  0  0  0  0
 23 24  1  0  0  0  0
 24 25  1  0  0  0  0
 24 26  2  0  0  0  0
 27 28  1  6  0  0  0
 27 29  1  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
 32 34  2  0  0  0  0
M  END


  Mrv1652303102016482D          

 34 33  0  0  1  0            999 V2000
   13.1201  -11.3696    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.4056  -11.7821    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.6911  -11.3696    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.9766  -11.7821    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.9766  -12.6071    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.2622  -13.0196    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.2622  -13.8446    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.9766  -14.2571    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.9766  -15.0821    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.6911  -15.4946    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.4056  -15.0821    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   13.1201  -15.4946    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   13.8346  -15.0821    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   14.5490  -15.4946    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   15.2635  -15.0821    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   15.9780  -15.4946    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
   15.9780  -16.3196    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   16.6924  -16.7321    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   17.4069  -16.3196    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   16.6924  -17.5572    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   15.9780  -17.9697    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   17.4069  -17.9697    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   18.1214  -17.5572    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   18.8359  -17.9697    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   18.8359  -18.7947    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   19.5504  -17.5572    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   15.2635  -14.2571    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   14.5490  -13.8446    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   15.9780  -13.8446    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   16.6924  -14.2571    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   17.4069  -13.8446    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   18.1214  -14.2571    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   18.1214  -15.0821    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   18.8359  -13.8446    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  2  0  0  0  0
  7  8  1  0  0  0  0
  8  9  1  0  0  0  0
  9 10  2  0  0  0  0
 10 11  1  0  0  0  0
 11 12  2  0  0  0  0
 12 13  1  0  0  0  0
 13 14  2  0  0  0  0
 14 15  1  0  0  0  0
 15 16  1  0  0  0  0
 15 27  1  1  0  0  0
 16 17  1  0  0  0  0
 17 18  1  0  0  0  0
 18 19  1  6  0  0  0
 18 20  1  0  0  0  0
 20 21  2  0  0  0  0
 20 22  1  0  0  0  0
 22 23  1  0  0  0  0
 23 24  1  0  0  0  0
 24 25  1  0  0  0  0
 24 26  2  0  0  0  0
 27 28  1  6  0  0  0
 27 29  1  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
 32 34  2  0  0  0  0
M  END
> <DATABASE_ID>
NP0339141

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CC\C=C/C\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/C25H38N2O6S/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/h3-4,6-7,9-13,16,20-22,28H,2,5,8,14-15,17-19,26H2,1H3,(H,27,33)(H,29,30)(H,31,32)/b4-3-,7-6-,10-9-,12-11+,16-13+/t20-,21+,22-/m0/s1

> <INCHI_KEY>
RWLDHKGRPLNPBN-DSJHTHEWSA-N

> <FORMULA>
C25H38N2O6S

> <MOLECULAR_WEIGHT>
494.644

> <EXACT_MASS>
494.245057648

> <JCHEM_ACCEPTOR_COUNT>
7

> <JCHEM_ATOM_COUNT>
72

> <JCHEM_AVERAGE_POLARIZABILITY>
54.94686698723376

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
5

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(5R,6S,7E,9E,11Z,14Z,17Z)-6-{[(2R)-2-amino-2-[(carboxymethyl)carbamoyl]ethyl]sulfanyl}-5-hydroxyicosa-7,9,11,14,17-pentaenoic acid

> <ALOGPS_LOGP>
0.90

> <JCHEM_LOGP>
0.40101688630769766

> <ALOGPS_LOGS>
-5.25

> <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>
149.95000000000002

> <JCHEM_REFRACTIVITY>
141.53980000000004

> <JCHEM_ROTATABLE_BOND_COUNT>
19

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
2.81e-03 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(5R,6S,7E,9E,11Z,14Z,17Z)-6-{[(2R)-2-amino-2-(carboxymethylcarbamoyl)ethyl]sulfanyl}-5-hydroxyicosa-7,9,11,14,17-pentaenoic acid

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 10-MAR-20   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   10-MAR-20         0                                  
HETATM    1  C   UNK     0      24.491 -21.223   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      23.157 -21.993   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      21.823 -21.223   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      20.490 -21.993   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      20.490 -23.533   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      19.156 -24.303   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      19.156 -25.843   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      20.490 -26.613   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      20.490 -28.153   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      21.823 -28.923   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      23.157 -28.153   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      24.491 -28.923   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      25.825 -28.153   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      27.158 -28.923   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0      28.492 -28.153   0.000  0.00  0.00           C+0
HETATM   16  S   UNK     0      29.826 -28.923   0.000  0.00  0.00           S+0
HETATM   17  C   UNK     0      29.826 -30.463   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0      31.159 -31.233   0.000  0.00  0.00           C+0
HETATM   19  N   UNK     0      32.493 -30.463   0.000  0.00  0.00           N+0
HETATM   20  C   UNK     0      31.159 -32.773   0.000  0.00  0.00           C+0
HETATM   21  O   UNK     0      29.826 -33.543   0.000  0.00  0.00           O+0
HETATM   22  N   UNK     0      32.493 -33.543   0.000  0.00  0.00           N+0
HETATM   23  C   UNK     0      33.827 -32.773   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0      35.160 -33.543   0.000  0.00  0.00           C+0
HETATM   25  O   UNK     0      35.160 -35.083   0.000  0.00  0.00           O+0
HETATM   26  O   UNK     0      36.494 -32.773   0.000  0.00  0.00           O+0
HETATM   27  C   UNK     0      28.492 -26.613   0.000  0.00  0.00           C+0
HETATM   28  O   UNK     0      27.158 -25.843   0.000  0.00  0.00           O+0
HETATM   29  C   UNK     0      29.826 -25.843   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0      31.159 -26.613   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0      32.493 -25.843   0.000  0.00  0.00           C+0
HETATM   32  C   UNK     0      33.827 -26.613   0.000  0.00  0.00           C+0
HETATM   33  O   UNK     0      33.827 -28.153   0.000  0.00  0.00           O+0
HETATM   34  O   UNK     0      35.160 -25.843   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
LTD(,5)	HMDB

Chemical Formula

C₂₅H₃₈N₂O₆S

Average Mass

494.6440 Da

Monoisotopic Mass

494.24506 Da

IUPAC Name

(5R,6S,7E,9E,11Z,14Z,17Z)-6-{[(2R)-2-amino-2-[(carboxymethyl)carbamoyl]ethyl]sulfanyl}-5-hydroxyicosa-7,9,11,14,17-pentaenoic acid

Traditional Name

(5R,6S,7E,9E,11Z,14Z,17Z)-6-{[(2R)-2-amino-2-(carboxymethylcarbamoyl)ethyl]sulfanyl}-5-hydroxyicosa-7,9,11,14,17-pentaenoic acid

CAS Registry Number

Not Available

SMILES

CC\C=C/C\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/C25H38N2O6S/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/h3-4,6-7,9-13,16,20-22,28H,2,5,8,14-15,17-19,26H2,1H3,(H,27,33)(H,29,30)(H,31,32)/b4-3-,7-6-,10-9-,12-11+,16-13+/t20-,21+,22-/m0/s1

InChI Key

RWLDHKGRPLNPBN-DSJHTHEWSA-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 oligosaccharides. These are carbohydrates made up of 3 to 10 monosaccharide units linked to each other through glycosidic bonds.

Kingdom

Organic compounds

Super Class

Organic oxygen compounds

Class

Organooxygen compounds

Sub Class

Carbohydrates and carbohydrate conjugates

Direct Parent

Oligosaccharides

Alternative Parents

Substituents

Oligosaccharide
O-glycosyl compound
Glycosyl compound
Oxane
Secondary alcohol
Hemiacetal
Oxacycle
Organoheterocyclic compound
Polyol
Acetal
Hydrocarbon derivative
Primary alcohol
Alcohol
Aliphatic heteromonocyclic compound

Molecular Framework

Aliphatic heteromonocyclic 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	0.9	ALOGPS
logP	0.4	ChemAxon
logS	-5.2	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	19	ChemAxon
Refractivity	141.54 m³·mol⁻¹	ChemAxon
Polarizability	54.95 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

HMDB0012994

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

FDB029238

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

53481571

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Showing NP-Card for Leukotriene D5 (NP0339141)

MOL for NP0339141 (Leukotriene D5)

3D MOL for NP0339141 (Leukotriene D5)

3D SDF for NP0339141 (Leukotriene D5)

3D-SDF for NP0339141 (Leukotriene D5)

PDB for NP0339141 (Leukotriene D5)

3D PDB for NP0339141 (Leukotriene D5)

SMILES for NP0339141 (Leukotriene D5)

INCHI for NP0339141 (Leukotriene D5)

Structure for NP0339141 (Leukotriene D5)

3D Structure for NP0339141 (Leukotriene D5)