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Showing metabocard for PE-NMe(13M5/9D5) (HMDB0113808)

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Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2017-09-09 00:10:10 UTC
Update Date2022-11-30 19:25:16 UTC
HMDB IDHMDB0113808
Secondary Accession NumbersNone
Metabolite Identification
Common NamePE-NMe(13M5/9D5)
DescriptionPE-NMe(13M5/9D5) is a monomethylphosphatidylethanolamine. It is a glycerophospholipid, and it is formed by sequential methylation of phosphatidylethanolamine as part of a mechanism for biosynthesis of phosphatidylcholine. Monomethylphosphatidylethanolamines are usually found at trace levels in animal or plant tissues. They can have many different combinations of fatty acids of varying lengths and saturation attached at the C-1 and C-2 positions. PE-NMe(13M5/9D5), in particular, consists of one chain of 13-(3-methyl-5-pentylfuran-2-yl)tridecanoic acid at the C-1 position and one chain of 9-(3,4-dimethyl-5-pentylfuran-2-yl)nonanoic acid at the C-2 position. Fatty acids containing 16, 18 and 20 carbons are the most common. Phospholipids are ubiquitous in nature. They are key components of the cell lipid bilayer and are involved in metabolism and signaling.
Structure
Data?1563873409
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0113808 (PE-NMe(13M5/9D5))


  Mrv1652309091702102D          

 62 63  0  0  1  0            999 V2000
   25.1058    1.4642    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3602    1.1866    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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    7.3978    5.0309    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   24.2853    1.5505    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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 44 62  1  6  0  0  0
M  END
Download

3D MOL for HMDB0113808 (PE-NMe(13M5/9D5))

HMDB0113808
     RDKit          3D
PE-NMe(13M5/9D5)
147148  0  0  0  0  0  0  0  0999 V2000
   -1.4375   -7.4255   -0.4524 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3451   -6.6275   -1.7338 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0247   -5.8692   -1.7546 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1027   -5.0593   -3.0077 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4241   -4.2856   -3.0379 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5045   -3.4899   -4.2885 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5142   -3.4959   -5.2553 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9570   -2.6466   -6.2383 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2576   -2.3012   -7.5105 C   0  0  0  0  0  0  0  0  0  0  0  0
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    3.2198    1.0729   -7.4688 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7512    2.4821   -7.4906 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9233    3.1821   -6.1900 C   0  0  0  0  0  0  0  0  0  0  0  0
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    4.0477    3.4138   -3.3548 C   0  0  0  0  0  0  0  0  0  0  0  0
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    3.6742    5.5961   -2.1816 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1600    5.4934   -2.2345 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6308    4.8656   -0.9785 C   0  0  0  0  0  0  0  0  0  0  0  0
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    2.4711   -2.6907   -4.6700 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3011   -8.0958   -0.4315 H   0  0  0  0  0  0  0  0  0  0  0  0
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   -0.4724   -7.9509   -0.3006 H   0  0  0  0  0  0  0  0  0  0  0  0
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   -1.3380   -7.3278   -2.5946 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8307   -6.5577   -1.5987 H   0  0  0  0  0  0  0  0  0  0  0  0
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    0.0220   -5.7051   -3.9141 H   0  0  0  0  0  0  0  0  0  0  0  0
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    1.4801   -3.6379   -2.1413 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4215   -4.0701   -5.2241 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4111   -1.4215   -7.2850 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9434   -2.1251   -8.3473 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3632   -3.1902   -7.8107 H   0  0  0  0  0  0  0  0  0  0  0  0
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    2.9094   -1.4566   -7.7309 H   0  0  0  0  0  0  0  0  0  0  0  0
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    1.3316    0.2034   -6.7656 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.1339    0.5717   -8.4654 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.2827    0.9317   -7.1802 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6650    2.4732   -7.7661 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.2424    3.0490   -8.3319 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.3126    2.6728   -5.4312 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5282    4.2321   -6.2570 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.8448    3.9126   -6.6513 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.8989    2.3142   -5.8572 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.7494    4.1222   -4.4561 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.2676    5.0871   -4.7416 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.5414    2.4347   -3.2019 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.9659    3.2176   -3.4556 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.4101    4.3918   -2.0465 H   0  0  0  0  0  0  0  0  0  0  0  0
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M  END
Download

3D SDF for HMDB0113808 (PE-NMe(13M5/9D5))


  Mrv1652309091702102D          

 62 63  0  0  1  0            999 V2000
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M  END
> <DATABASE_ID>
HMDB0113808

> <DATABASE_NAME>
hmdb

> <SMILES>
[H][C@@](COC(=O)CCCCCCCCCCCCC1=C(C)C=C(CCCCC)O1)(COP(O)(=O)OCCNC)OC(=O)CCCCCCCCC1=C(C)C(C)=C(CCCCC)O1

> <INCHI_IDENTIFIER>
InChI=1S/C49H86NO10P/c1-7-9-23-29-43-37-40(3)45(58-43)30-25-19-15-13-11-12-14-16-21-27-33-48(51)55-38-44(39-57-61(53,54)56-36-35-50-6)59-49(52)34-28-22-18-17-20-26-32-47-42(5)41(4)46(60-47)31-24-10-8-2/h37,44,50H,7-36,38-39H2,1-6H3,(H,53,54)/t44-/m1/s1

> <INCHI_KEY>
JXJKWUVOPUIDMJ-USYZEHPZSA-N

> <FORMULA>
C49H86NO10P

> <MOLECULAR_WEIGHT>
880.198

> <EXACT_MASS>
879.598934971

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_ATOM_COUNT>
147

> <JCHEM_AVERAGE_POLARIZABILITY>
107.6346382608788

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
[(2R)-2-{[9-(3,4-dimethyl-5-pentylfuran-2-yl)nonanoyl]oxy}-3-{[13-(3-methyl-5-pentylfuran-2-yl)tridecanoyl]oxy}propoxy][2-(methylamino)ethoxy]phosphinic acid

> <ALOGPS_LOGP>
7.95

> <JCHEM_LOGP>
12.846178092698024

> <ALOGPS_LOGS>
-5.56

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.856206920799949

> <JCHEM_PKA_STRONGEST_BASIC>
10.045225536700068

> <JCHEM_POLAR_SURFACE_AREA>
146.67000000000002

> <JCHEM_REFRACTIVITY>
246.32730000000006

> <JCHEM_ROTATABLE_BOND_COUNT>
42

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
2.42e-03 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(2R)-2-{[9-(3,4-dimethyl-5-pentylfuran-2-yl)nonanoyl]oxy}-3-{[13-(3-methyl-5-pentylfuran-2-yl)tridecanoyl]oxy}propoxy(2-(methylamino)ethoxy)phosphinic acid

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for HMDB0113808 (PE-NMe(13M5/9D5))

HMDB0113808
     RDKit          3D
PE-NMe(13M5/9D5)
147148  0  0  0  0  0  0  0  0999 V2000
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M  END
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PDB for HMDB0113808 (PE-NMe(13M5/9D5))

HEADER    PROTEIN                                 09-SEP-17   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   09-SEP-17         0                                  
HETATM    1  C   UNK     0      46.864   2.733   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -6.272   2.215   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      37.038   2.768   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -0.281  -3.822   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       2.996  -3.126   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      13.809   9.391   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      45.333   2.894   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      -4.741   2.054   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      44.427   1.648   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      -4.114   0.647   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      30.020   0.206   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      28.686  -0.564   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      31.353  -0.564   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      27.352   0.206   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0      32.687   0.206   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0      26.019  -0.564   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       7.347  -0.564   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       8.681   0.206   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0      34.021  -0.564   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       6.013   0.206   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0      24.685   0.206   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0      10.015  -0.564   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0      42.896   1.809   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0      -2.583   0.486   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0      35.354   0.206   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0       4.680  -0.564   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0      23.351  -0.564   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0      11.348   0.206   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0      41.991   0.563   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0      36.688  -0.564   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0      -1.956  -0.921   0.000  0.00  0.00           C+0
HETATM   32  C   UNK     0       3.346   0.206   0.000  0.00  0.00           C+0
HETATM   33  C   UNK     0      22.018   0.206   0.000  0.00  0.00           C+0
HETATM   34  C   UNK     0      12.682  -0.564   0.000  0.00  0.00           C+0
HETATM   35  C   UNK     0      13.809   6.724   0.000  0.00  0.00           C+0
HETATM   36  C   UNK     0      13.039   5.390   0.000  0.00  0.00           C+0
HETATM   37  C   UNK     0      39.689   2.058   0.000  0.00  0.00           C+0
HETATM   38  C   UNK     0      18.017  -0.564   0.000  0.00  0.00           C+0
HETATM   39  C   UNK     0      16.683   1.746   0.000  0.00  0.00           C+0
HETATM   40  C   UNK     0      38.183   1.738   0.000  0.00  0.00           C+0
HETATM   41  C   UNK     0       0.345  -2.415   0.000  0.00  0.00           C+0
HETATM   42  C   UNK     0       1.851  -2.095   0.000  0.00  0.00           C+0
HETATM   43  C   UNK     0      40.459   0.724   0.000  0.00  0.00           C+0
HETATM   44  C   UNK     0      16.683   0.206   0.000  0.00  0.00           C+0
HETATM   45  C   UNK     0      38.022   0.206   0.000  0.00  0.00           C+0
HETATM   46  C   UNK     0      -0.425  -1.082   0.000  0.00  0.00           C+0
HETATM   47  C   UNK     0       2.012  -0.564   0.000  0.00  0.00           C+0
HETATM   48  C   UNK     0      20.684  -0.564   0.000  0.00  0.00           C+0
HETATM   49  C   UNK     0      14.016   0.206   0.000  0.00  0.00           C+0
HETATM   50  N   UNK     0      13.039   8.057   0.000  0.00  0.00           N+0
HETATM   51  O   UNK     0      20.684  -2.104   0.000  0.00  0.00           O+0
HETATM   52  O   UNK     0      14.016   1.746   0.000  0.00  0.00           O+0
HETATM   53  O   UNK     0      16.889   4.056   0.000  0.00  0.00           O+0
HETATM   54  O   UNK     0      15.349   5.596   0.000  0.00  0.00           O+0
HETATM   55  O   UNK     0      19.350   0.206   0.000  0.00  0.00           O+0
HETATM   56  O   UNK     0      13.809   4.056   0.000  0.00  0.00           O+0
HETATM   57  O   UNK     0      15.349   2.516   0.000  0.00  0.00           O+0
HETATM   58  O   UNK     0      39.429  -0.420   0.000  0.00  0.00           O+0
HETATM   59  O   UNK     0      15.349  -0.564   0.000  0.00  0.00           O+0
HETATM   60  O   UNK     0       0.606   0.063   0.000  0.00  0.00           O+0
HETATM   61  P   UNK     0      15.349   4.056   0.000  0.00  0.00           P+0
HETATM   62  H   UNK     0      18.017   0.976   0.000  0.00  0.00           H+0
CONECT    1    7                                                            
CONECT    2    8                                                            
CONECT    3   40                                                            
CONECT    4   41                                                            
CONECT    5   42                                                            
CONECT    6   50                                                            
CONECT    7    1    9                                                       
CONECT    8    2   10                                                       
CONECT    9    7   23                                                       
CONECT   10    8   24                                                       
CONECT   11   12   13                                                       
CONECT   12   11   14                                                       
CONECT   13   11   15                                                       
CONECT   14   12   16                                                       
CONECT   15   13   19                                                       
CONECT   16   14   21                                                       
CONECT   17   18   20                                                       
CONECT   18   17   22                                                       
CONECT   19   15   25                                                       
CONECT   20   17   26                                                       
CONECT   21   16   27                                                       
CONECT   22   18   28                                                       
CONECT   23    9   29                                                       
CONECT   24   10   31                                                       
CONECT   25   19   30                                                       
CONECT   26   20   32                                                       
CONECT   27   21   33                                                       
CONECT   28   22   34                                                       
CONECT   29   23   43                                                       
CONECT   30   25   45                                                       
CONECT   31   24   46                                                       
CONECT   32   26   47                                                       
CONECT   33   27   48                                                       
CONECT   34   28   49                                                       
CONECT   35   36   50                                                       
CONECT   36   35   56                                                       
CONECT   37   40   43                                                       
CONECT   38   44   55                                                       
CONECT   39   44   57                                                       
CONECT   40    3   37   45                                                  
CONECT   41    4   42   46                                                  
CONECT   42    5   41   47                                                  
CONECT   43   29   37   58                                                  
CONECT   44   38   39   59   62                                             
CONECT   45   30   40   58                                                  
CONECT   46   31   41   60                                                  
CONECT   47   32   42   60                                                  
CONECT   48   33   51   55                                                  
CONECT   49   34   52   59                                                  
CONECT   50    6   35                                                       
CONECT   51   48                                                            
CONECT   52   49                                                            
CONECT   53   61                                                            
CONECT   54   61                                                            
CONECT   55   38   48                                                       
CONECT   56   36   61                                                       
CONECT   57   39   61                                                       
CONECT   58   43   45                                                       
CONECT   59   44   49                                                       
CONECT   60   46   47                                                       
CONECT   61   53   54   56   57                                             
CONECT   62   44                                                            
MASTER        0    0    0    0    0    0    0    0   62    0  126    0
END
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3D PDB for HMDB0113808 (PE-NMe(13M5/9D5))

COMPND    HMDB0113808
HETATM    1  C1  UNL     1      -1.438  -7.425  -0.452  1.00  0.00           C  
HETATM    2  C2  UNL     1      -1.345  -6.628  -1.734  1.00  0.00           C  
HETATM    3  C3  UNL     1      -0.025  -5.869  -1.755  1.00  0.00           C  
HETATM    4  C4  UNL     1       0.103  -5.059  -3.008  1.00  0.00           C  
HETATM    5  C5  UNL     1       1.424  -4.286  -3.038  1.00  0.00           C  
HETATM    6  C6  UNL     1       1.505  -3.490  -4.288  1.00  0.00           C  
HETATM    7  C7  UNL     1       0.514  -3.496  -5.255  1.00  0.00           C  
HETATM    8  C8  UNL     1       0.957  -2.647  -6.238  1.00  0.00           C  
HETATM    9  C9  UNL     1       0.258  -2.301  -7.511  1.00  0.00           C  
HETATM   10  C10 UNL     1       2.209  -2.158  -5.817  1.00  0.00           C  
HETATM   11  C11 UNL     1       2.986  -1.214  -6.628  1.00  0.00           C  
HETATM   12  C12 UNL     1       2.410   0.205  -6.523  1.00  0.00           C  
HETATM   13  C13 UNL     1       3.220   1.073  -7.469  1.00  0.00           C  
HETATM   14  C14 UNL     1       2.751   2.482  -7.491  1.00  0.00           C  
HETATM   15  C15 UNL     1       2.923   3.182  -6.190  1.00  0.00           C  
HETATM   16  C16 UNL     1       4.372   3.296  -5.823  1.00  0.00           C  
HETATM   17  C17 UNL     1       4.627   4.050  -4.567  1.00  0.00           C  
HETATM   18  C18 UNL     1       4.048   3.414  -3.355  1.00  0.00           C  
HETATM   19  C19 UNL     1       4.318   4.240  -2.110  1.00  0.00           C  
HETATM   20  C20 UNL     1       3.674   5.596  -2.182  1.00  0.00           C  
HETATM   21  C21 UNL     1       2.160   5.493  -2.235  1.00  0.00           C  
HETATM   22  C22 UNL     1       1.631   4.866  -0.978  1.00  0.00           C  
HETATM   23  C23 UNL     1       0.148   4.720  -1.058  1.00  0.00           C  
HETATM   24  O1  UNL     1      -0.420   4.954  -2.161  1.00  0.00           O  
HETATM   25  O2  UNL     1      -0.605   4.346   0.011  1.00  0.00           O  
HETATM   26  C24 UNL     1      -1.982   4.181  -0.039  1.00  0.00           C  
HETATM   27  C25 UNL     1      -2.531   3.827   1.353  1.00  0.00           C  
HETATM   28  C26 UNL     1      -3.893   3.263   1.196  1.00  0.00           C  
HETATM   29  O3  UNL     1      -3.921   2.255   0.230  1.00  0.00           O  
HETATM   30  P1  UNL     1      -5.507   1.639   0.112  1.00  0.00           P  
HETATM   31  O4  UNL     1      -6.421   2.458   1.016  1.00  0.00           O  
HETATM   32  O5  UNL     1      -6.010   1.764  -1.493  1.00  0.00           O  
HETATM   33  O6  UNL     1      -5.559   0.029   0.623  1.00  0.00           O  
HETATM   34  C27 UNL     1      -6.897  -0.349   0.686  1.00  0.00           C  
HETATM   35  C28 UNL     1      -7.064  -1.773   1.152  1.00  0.00           C  
HETATM   36  N1  UNL     1      -6.509  -1.970   2.478  1.00  0.00           N  
HETATM   37  C29 UNL     1      -6.670  -3.347   2.906  1.00  0.00           C  
HETATM   38  O7  UNL     1      -2.346   4.830   2.267  1.00  0.00           O  
HETATM   39  C30 UNL     1      -1.383   4.853   3.291  1.00  0.00           C  
HETATM   40  O8  UNL     1      -0.656   3.831   3.300  1.00  0.00           O  
HETATM   41  C31 UNL     1      -1.324   5.997   4.188  1.00  0.00           C  
HETATM   42  C32 UNL     1      -2.068   6.025   5.436  1.00  0.00           C  
HETATM   43  C33 UNL     1      -1.783   5.104   6.535  1.00  0.00           C  
HETATM   44  C34 UNL     1      -1.953   3.634   6.367  1.00  0.00           C  
HETATM   45  C35 UNL     1      -1.568   2.965   7.701  1.00  0.00           C  
HETATM   46  C36 UNL     1      -1.688   1.481   7.668  1.00  0.00           C  
HETATM   47  C37 UNL     1      -0.827   0.850   6.598  1.00  0.00           C  
HETATM   48  C38 UNL     1      -0.911  -0.663   6.603  1.00  0.00           C  
HETATM   49  C39 UNL     1      -0.063  -1.218   5.495  1.00  0.00           C  
HETATM   50  O9  UNL     1       1.104  -1.761   5.491  1.00  0.00           O  
HETATM   51  C40 UNL     1       1.457  -2.101   4.249  1.00  0.00           C  
HETATM   52  C41 UNL     1       2.716  -2.748   3.798  1.00  0.00           C  
HETATM   53  C42 UNL     1       2.568  -4.196   3.451  1.00  0.00           C  
HETATM   54  C43 UNL     1       3.913  -4.728   2.997  1.00  0.00           C  
HETATM   55  C44 UNL     1       3.884  -6.173   2.613  1.00  0.00           C  
HETATM   56  C45 UNL     1       2.933  -6.449   1.468  1.00  0.00           C  
HETATM   57  C46 UNL     1       0.430  -1.750   3.377  1.00  0.00           C  
HETATM   58  C47 UNL     1       0.356  -1.932   1.895  1.00  0.00           C  
HETATM   59  C48 UNL     1      -0.533  -1.187   4.186  1.00  0.00           C  
HETATM   60  C49 UNL     1      -1.847  -0.647   3.696  1.00  0.00           C  
HETATM   61  O10 UNL     1       2.471  -2.691  -4.670  1.00  0.00           O  
HETATM   62  H1  UNL     1      -2.301  -8.096  -0.432  1.00  0.00           H  
HETATM   63  H2  UNL     1      -1.523  -6.698   0.387  1.00  0.00           H  
HETATM   64  H3  UNL     1      -0.472  -7.951  -0.301  1.00  0.00           H  
HETATM   65  H4  UNL     1      -2.189  -5.919  -1.765  1.00  0.00           H  
HETATM   66  H5  UNL     1      -1.338  -7.328  -2.595  1.00  0.00           H  
HETATM   67  H6  UNL     1       0.831  -6.558  -1.599  1.00  0.00           H  
HETATM   68  H7  UNL     1      -0.045  -5.178  -0.888  1.00  0.00           H  
HETATM   69  H8  UNL     1      -0.694  -4.300  -3.112  1.00  0.00           H  
HETATM   70  H9  UNL     1       0.022  -5.705  -3.914  1.00  0.00           H  
HETATM   71  H10 UNL     1       2.237  -5.041  -2.958  1.00  0.00           H  
HETATM   72  H11 UNL     1       1.480  -3.638  -2.141  1.00  0.00           H  
HETATM   73  H12 UNL     1      -0.422  -4.070  -5.224  1.00  0.00           H  
HETATM   74  H13 UNL     1      -0.411  -1.421  -7.285  1.00  0.00           H  
HETATM   75  H14 UNL     1       0.943  -2.125  -8.347  1.00  0.00           H  
HETATM   76  H15 UNL     1      -0.363  -3.190  -7.811  1.00  0.00           H  
HETATM   77  H16 UNL     1       4.074  -1.217  -6.419  1.00  0.00           H  
HETATM   78  H17 UNL     1       2.909  -1.457  -7.731  1.00  0.00           H  
HETATM   79  H18 UNL     1       2.488   0.549  -5.462  1.00  0.00           H  
HETATM   80  H19 UNL     1       1.332   0.203  -6.766  1.00  0.00           H  
HETATM   81  H20 UNL     1       3.134   0.572  -8.465  1.00  0.00           H  
HETATM   82  H21 UNL     1       4.283   0.932  -7.180  1.00  0.00           H  
HETATM   83  H22 UNL     1       1.665   2.473  -7.766  1.00  0.00           H  
HETATM   84  H23 UNL     1       3.242   3.049  -8.332  1.00  0.00           H  
HETATM   85  H24 UNL     1       2.313   2.673  -5.431  1.00  0.00           H  
HETATM   86  H25 UNL     1       2.528   4.232  -6.257  1.00  0.00           H  
HETATM   87  H26 UNL     1       4.845   3.913  -6.651  1.00  0.00           H  
HETATM   88  H27 UNL     1       4.899   2.314  -5.857  1.00  0.00           H  
HETATM   89  H28 UNL     1       5.749   4.122  -4.456  1.00  0.00           H  
HETATM   90  H29 UNL     1       4.268   5.087  -4.742  1.00  0.00           H  
HETATM   91  H30 UNL     1       4.541   2.435  -3.202  1.00  0.00           H  
HETATM   92  H31 UNL     1       2.966   3.218  -3.456  1.00  0.00           H  
HETATM   93  H32 UNL     1       5.410   4.392  -2.046  1.00  0.00           H  
HETATM   94  H33 UNL     1       4.007   3.646  -1.241  1.00  0.00           H  
HETATM   95  H34 UNL     1       3.928   6.130  -1.245  1.00  0.00           H  
HETATM   96  H35 UNL     1       4.055   6.152  -3.020  1.00  0.00           H  
HETATM   97  H36 UNL     1       1.776   4.948  -3.104  1.00  0.00           H  
HETATM   98  H37 UNL     1       1.774   6.529  -2.288  1.00  0.00           H  
HETATM   99  H38 UNL     1       1.908   5.456  -0.072  1.00  0.00           H  
HETATM  100  H39 UNL     1       2.013   3.844  -0.806  1.00  0.00           H  
HETATM  101  H40 UNL     1      -2.557   5.012  -0.493  1.00  0.00           H  
HETATM  102  H41 UNL     1      -2.195   3.292  -0.667  1.00  0.00           H  
HETATM  103  H42 UNL     1      -1.829   2.983   1.664  1.00  0.00           H  
HETATM  104  H43 UNL     1      -4.645   4.061   0.955  1.00  0.00           H  
HETATM  105  H44 UNL     1      -4.285   2.792   2.132  1.00  0.00           H  
HETATM  106  H45 UNL     1      -6.372   0.884  -1.762  1.00  0.00           H  
HETATM  107  H46 UNL     1      -7.416   0.364   1.324  1.00  0.00           H  
HETATM  108  H47 UNL     1      -7.288  -0.299  -0.362  1.00  0.00           H  
HETATM  109  H48 UNL     1      -6.591  -2.489   0.467  1.00  0.00           H  
HETATM  110  H49 UNL     1      -8.145  -1.984   1.207  1.00  0.00           H  
HETATM  111  H50 UNL     1      -7.072  -1.390   3.153  1.00  0.00           H  
HETATM  112  H51 UNL     1      -6.347  -3.995   2.043  1.00  0.00           H  
HETATM  113  H52 UNL     1      -6.028  -3.555   3.792  1.00  0.00           H  
HETATM  114  H53 UNL     1      -7.703  -3.615   3.129  1.00  0.00           H  
HETATM  115  H54 UNL     1      -1.589   6.956   3.623  1.00  0.00           H  
HETATM  116  H55 UNL     1      -0.225   6.168   4.435  1.00  0.00           H  
HETATM  117  H56 UNL     1      -3.200   6.019   5.181  1.00  0.00           H  
HETATM  118  H57 UNL     1      -1.994   7.111   5.831  1.00  0.00           H  
HETATM  119  H58 UNL     1      -0.757   5.335   6.977  1.00  0.00           H  
HETATM  120  H59 UNL     1      -2.457   5.391   7.421  1.00  0.00           H  
HETATM  121  H60 UNL     1      -1.377   3.198   5.562  1.00  0.00           H  
HETATM  122  H61 UNL     1      -3.035   3.429   6.168  1.00  0.00           H  
HETATM  123  H62 UNL     1      -2.248   3.388   8.457  1.00  0.00           H  
HETATM  124  H63 UNL     1      -0.541   3.306   7.968  1.00  0.00           H  
HETATM  125  H64 UNL     1      -2.760   1.190   7.566  1.00  0.00           H  
HETATM  126  H65 UNL     1      -1.383   1.049   8.661  1.00  0.00           H  
HETATM  127  H66 UNL     1       0.237   1.119   6.760  1.00  0.00           H  
HETATM  128  H67 UNL     1      -1.130   1.225   5.589  1.00  0.00           H  
HETATM  129  H68 UNL     1      -1.970  -0.942   6.490  1.00  0.00           H  
HETATM  130  H69 UNL     1      -0.559  -1.067   7.569  1.00  0.00           H  
HETATM  131  H70 UNL     1       3.502  -2.690   4.595  1.00  0.00           H  
HETATM  132  H71 UNL     1       3.146  -2.210   2.910  1.00  0.00           H  
HETATM  133  H72 UNL     1       2.231  -4.806   4.328  1.00  0.00           H  
HETATM  134  H73 UNL     1       1.852  -4.342   2.646  1.00  0.00           H  
HETATM  135  H74 UNL     1       4.268  -4.143   2.119  1.00  0.00           H  
HETATM  136  H75 UNL     1       4.699  -4.624   3.800  1.00  0.00           H  
HETATM  137  H76 UNL     1       4.900  -6.457   2.272  1.00  0.00           H  
HETATM  138  H77 UNL     1       3.613  -6.835   3.470  1.00  0.00           H  
HETATM  139  H78 UNL     1       2.974  -7.549   1.283  1.00  0.00           H  
HETATM  140  H79 UNL     1       3.328  -5.972   0.529  1.00  0.00           H  
HETATM  141  H80 UNL     1       1.893  -6.197   1.676  1.00  0.00           H  
HETATM  142  H81 UNL     1      -0.091  -2.911   1.635  1.00  0.00           H  
HETATM  143  H82 UNL     1      -0.315  -1.136   1.498  1.00  0.00           H  
HETATM  144  H83 UNL     1       1.345  -1.749   1.458  1.00  0.00           H  
HETATM  145  H84 UNL     1      -2.577  -0.598   4.540  1.00  0.00           H  
HETATM  146  H85 UNL     1      -1.720   0.370   3.270  1.00  0.00           H  
HETATM  147  H86 UNL     1      -2.253  -1.374   2.981  1.00  0.00           H  
CONECT    1    2   62   63   64
CONECT    2    3   65   66
CONECT    3    4   67   68
CONECT    4    5   69   70
CONECT    5    6   71   72
CONECT    6    7    7   61
CONECT    7    8   73
CONECT    8    9   10   10
CONECT    9   74   75   76
CONECT   10   11   61
CONECT   11   12   77   78
CONECT   12   13   79   80
CONECT   13   14   81   82
CONECT   14   15   83   84
CONECT   15   16   85   86
CONECT   16   17   87   88
CONECT   17   18   89   90
CONECT   18   19   91   92
CONECT   19   20   93   94
CONECT   20   21   95   96
CONECT   21   22   97   98
CONECT   22   23   99  100
CONECT   23   24   24   25
CONECT   25   26
CONECT   26   27  101  102
CONECT   27   28   38  103
CONECT   28   29  104  105
CONECT   29   30
CONECT   30   31   31   32   33
CONECT   32  106
CONECT   33   34
CONECT   34   35  107  108
CONECT   35   36  109  110
CONECT   36   37  111
CONECT   37  112  113  114
CONECT   38   39
CONECT   39   40   40   41
CONECT   41   42  115  116
CONECT   42   43  117  118
CONECT   43   44  119  120
CONECT   44   45  121  122
CONECT   45   46  123  124
CONECT   46   47  125  126
CONECT   47   48  127  128
CONECT   48   49  129  130
CONECT   49   50   59   59
CONECT   50   51
CONECT   51   52   57   57
CONECT   52   53  131  132
CONECT   53   54  133  134
CONECT   54   55  135  136
CONECT   55   56  137  138
CONECT   56  139  140  141
CONECT   57   58   59
CONECT   58  142  143  144
CONECT   59   60
CONECT   60  145  146  147
END
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SMILES for HMDB0113808 (PE-NMe(13M5/9D5))

[H][C@@](COC(=O)CCCCCCCCCCCCC1=C(C)C=C(CCCCC)O1)(COP(O)(=O)OCCNC)OC(=O)CCCCCCCCC1=C(C)C(C)=C(CCCCC)O1
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INCHI for HMDB0113808 (PE-NMe(13M5/9D5))

InChI=1S/C49H86NO10P/c1-7-9-23-29-43-37-40(3)45(58-43)30-25-19-15-13-11-12-14-16-21-27-33-48(51)55-38-44(39-57-61(53,54)56-36-35-50-6)59-49(52)34-28-22-18-17-20-26-32-47-42(5)41(4)46(60-47)31-24-10-8-2/h37,44,50H,7-36,38-39H2,1-6H3,(H,53,54)/t44-/m1/s1
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View in JSmolView Stereo Labels
Synonyms
ValueSource
[(2R)-2-{[9-(3,4-dimethyl-5-pentylfuran-2-yl)nonanoyl]oxy}-3-{[13-(3-methyl-5-pentylfuran-2-yl)tridecanoyl]oxy}propoxy][2-(methylamino)ethoxy]phosphinateGenerator
PE-NMe(MonoMe(13,5)/DiMe(9,5))SMPDB
MMPE(13M5/9D5)SMPDB
MMPE(MonoMe(13,5)/DiMe(9,5))SMPDB
monomethylphosphatidylethanolamineSMPDB
N-monomethylphosphatidylethanolamineSMPDB
phosphatidyl-N-methylethanolamineSMPDB
PE-NMe(13M5/9D5)SMPDB
Chemical FormulaC49H86NO10P
Average Molecular Weight880.198
Monoisotopic Molecular Weight879.598934971
IUPAC Name[(2R)-2-{[9-(3,4-dimethyl-5-pentylfuran-2-yl)nonanoyl]oxy}-3-{[13-(3-methyl-5-pentylfuran-2-yl)tridecanoyl]oxy}propoxy][2-(methylamino)ethoxy]phosphinic acid
Traditional Name(2R)-2-{[9-(3,4-dimethyl-5-pentylfuran-2-yl)nonanoyl]oxy}-3-{[13-(3-methyl-5-pentylfuran-2-yl)tridecanoyl]oxy}propoxy(2-(methylamino)ethoxy)phosphinic acid
CAS Registry NumberNot Available
SMILES
[H][C@@](COC(=O)CCCCCCCCCCCCC1=C(C)C=C(CCCCC)O1)(COP(O)(=O)OCCNC)OC(=O)CCCCCCCCC1=C(C)C(C)=C(CCCCC)O1
InChI Identifier
InChI=1S/C49H86NO10P/c1-7-9-23-29-43-37-40(3)45(58-43)30-25-19-15-13-11-12-14-16-21-27-33-48(51)55-38-44(39-57-61(53,54)56-36-35-50-6)59-49(52)34-28-22-18-17-20-26-32-47-42(5)41(4)46(60-47)31-24-10-8-2/h37,44,50H,7-36,38-39H2,1-6H3,(H,53,54)/t44-/m1/s1
InChI KeyJXJKWUVOPUIDMJ-USYZEHPZSA-N
Chemical Taxonomy
DescriptionThis compound belongs to the class of organic compounds known as monomethylphosphatidylethanolamines. These are lipids with a structure containing a glycerol moiety linked at its terminal C3 atom to a N-methylphosphoethanolamine group, and at its C1 and C2 terminal atoms by an acyl group.
KingdomOrganic compounds
Super ClassLipids and lipid-like molecules
ClassGlycerophospholipids
Sub ClassGlycerophosphoethanolamines
Direct ParentMonomethylphosphatidylethanolamines
Alternative Parents
Substituents
  • Monomethylphosphatidylethanolamine
  • Furanoid fatty acid
  • Phosphoethanolamine
  • Fatty acid ester
  • Dialkyl phosphate
  • Dicarboxylic acid or derivatives
  • Organic phosphoric acid derivative
  • Phosphoric acid ester
  • Alkyl phosphate
  • Fatty acyl
  • Heteroaromatic compound
  • Furan
  • Carboxylic acid ester
  • Amino acid or derivatives
  • Oxacycle
  • Secondary amine
  • Carboxylic acid derivative
  • Organoheterocyclic compound
  • Secondary aliphatic amine
  • Carbonyl group
  • Organic oxygen compound
  • Organic nitrogen compound
  • Amine
  • Organonitrogen compound
  • Organooxygen compound
  • Hydrocarbon derivative
  • Organopnictogen compound
  • Organic oxide
  • Aromatic heteromonocyclic compound
Molecular FrameworkAromatic heteromonocyclic compounds
External DescriptorsNot Available
Ontology
Not AvailableNot Available
Physical Properties
StateSolid
Experimental Molecular Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
PropertyValueSource
logP7.95ALOGPS
logP12.85ChemAxon
logS-5.6ALOGPS
pKa (Strongest Acidic)1.86ChemAxon
pKa (Strongest Basic)10.05ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count5ChemAxon
Hydrogen Donor Count2ChemAxon
Polar Surface Area146.67 ŲChemAxon
Rotatable Bond Count42ChemAxon
Refractivity246.33 m³·mol⁻¹ChemAxon
Polarizability107.63 ųChemAxon
Number of Rings2ChemAxon
BioavailabilityNoChemAxon
Rule of FiveNoChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
Predicted Chromatographic Properties

Predicted Collision Cross Sections

PredictorAdduct TypeCCS Value (Å2)Reference
DarkChem[M+H]+306.2631661259
DarkChem[M-H]-292.64831661259
DeepCCS[M+H]+303.19630932474
DeepCCS[M-H]-301.21130932474
DeepCCS[M-2H]-334.45130932474
DeepCCS[M+Na]+308.93630932474
AllCCS[M+H]+283.232859911
AllCCS[M+H-H2O]+283.132859911
AllCCS[M+NH4]+283.232859911
AllCCS[M+Na]+283.232859911
AllCCS[M-H]-276.032859911
AllCCS[M+Na-2H]-283.432859911
AllCCS[M+HCOO]-291.532859911

Predicted Retention Times

Underivatized

Chromatographic MethodRetention TimeReference
Measured using a Waters Acquity ultraperformance liquid chromatography (UPLC) ethylene-bridged hybrid (BEH) C18 column (100 mm × 2.1 mm; 1.7 μmparticle diameter). Predicted by Afia on May 17, 2022. Predicted by Afia on May 17, 2022.9.36 minutes32390414
Predicted by Siyang on May 30, 202233.8894 minutes33406817
Predicted by Siyang using ReTip algorithm on June 8, 20222.24 minutes32390414
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid4636.2 seconds40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid423.5 seconds40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid395.1 seconds40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid211.5 seconds40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid1041.9 seconds40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid1624.3 seconds40023050
BfG_NTS_RP1 =Agilent Zorbax Eclipse Plus C18 (2.1 mm x 150 mm, 3.5 um) with Water:ACN and 0.1% Formic Acid1526.0 seconds40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)168.6 seconds40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid3458.7 seconds40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid1256.6 seconds40023050
UFZ_Phenomenex = Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex with Water:MeOH and 0.1% Formic Acid3573.4 seconds40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid1207.1 seconds40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid755.8 seconds40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate248.0 seconds40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA432.6 seconds40023050
Meister zic-pHILIC pH9.3 = Merck SeQuant ZIC-pHILIC column with ACN:Water 5mM NH4Ac pH9.3 and 5mM ammonium acetate in water9.9 seconds40023050

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
PE-NMe(13M5/9D5)[H][C@@](COC(=O)CCCCCCCCCCCCC1=C(C)C=C(CCCCC)O1)(COP(O)(=O)OCCNC)OC(=O)CCCCCCCCC1=C(C)C(C)=C(CCCCC)O15508.4Standard polar33892256
PE-NMe(13M5/9D5)[H][C@@](COC(=O)CCCCCCCCCCCCC1=C(C)C=C(CCCCC)O1)(COP(O)(=O)OCCNC)OC(=O)CCCCCCCCC1=C(C)C(C)=C(CCCCC)O15472.0Standard non polar33892256
PE-NMe(13M5/9D5)[H][C@@](COC(=O)CCCCCCCCCCCCC1=C(C)C=C(CCCCC)O1)(COP(O)(=O)OCCNC)OC(=O)CCCCCCCCC1=C(C)C(C)=C(CCCCC)O15834.0Semi standard non polar33892256
Spectra

MS/MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - PE-NMe(13M5/9D5) 10V, Negative-QTOFsplash10-0fb9-4400010090-ea50fabb66834cda8bdc2021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - PE-NMe(13M5/9D5) 20V, Negative-QTOFsplash10-0fb9-9607120020-170c7b8f5ffca0c23b042021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - PE-NMe(13M5/9D5) 40V, Negative-QTOFsplash10-004i-9001000000-c2d9cfeea2aa05d4d18d2021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - PE-NMe(13M5/9D5) 10V, Positive-QTOFsplash10-001i-3200002290-ef394e0d330bab2fb5902021-09-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - PE-NMe(13M5/9D5) 20V, Positive-QTOFsplash10-0a4i-9301004270-d5c5726ba64c3f9d3e302021-09-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - PE-NMe(13M5/9D5) 40V, Positive-QTOFsplash10-0a4i-9111000000-74d223e1499d6811cd162021-09-23Wishart LabView Spectrum
Biological Properties
Cellular LocationsNot Available
Biospecimen LocationsNot Available
Tissue LocationsNot Available
Pathways
Normal Concentrations
Not Available
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDNot Available
KNApSAcK IDNot Available
Chemspider IDNot Available
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem CompoundNot Available
PDB IDNot Available
ChEBI IDNot Available
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDNot Available
Good Scents IDNot Available
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Not Available
General ReferencesNot Available