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Showing metabocard for PGP(i-13:0/a-15:0) (HMDB0116550)

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Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2017-09-09 08:28:01 UTC
Update Date2022-11-30 19:26:39 UTC
HMDB IDHMDB0116550
Secondary Accession NumbersNone
Metabolite Identification
Common NamePGP(i-13:0/a-15:0)
DescriptionPGP(i-13:0/a-15:0) is a phosphatidylglycerophosphate (PGP). It is a glycerophospholipid in which a phosphoglycerol moiety occupies a glycerol substitution site followed by another phosphate moiety. Phosphatidylglycerolphosphate is present at a level of 1-2% in most animal tissues, but it can be the second most abundant phospholipid in lung surfactant (up to 11% of the total). It is well established that the concentration of phosphatidylglycerolphosphate increases during fetal development. Phosphatidylglycerolphosphate may be present in animal tissues merely as a precursor for cardiolipin synthesis. As is the case with diacylglycerols, phosphatidylglycerophosphates can have many different combinations of fatty acids of varying lengths and saturation attached to the C-1 and C-2 positions. Fatty acids containing 16, 18 and 20 carbons are the most common. PGP(i-13:0/a-15:0), in particular, consists of one chain of isotridecanoic acid at the C-1 position and one chain of anteisopentadecanoic acid at the C-2 position. They are synthesized by the addition of glycerol 3-phosphate to a CDP-diacylglycerol. In turn, PGPs are dephosphorylated to phosphatidylglycerols (PGs). While most phospholipids have a saturated fatty acid on C-1 and an unsaturated fatty acid on C-2 of the glycerol backbone, the fatty acid distribution at the C-1 and C-2 positions of glycerol within phospholipids is continually in flux, owing to phospholipid degradation and the continuous phospholipid remodeling that occurs while these molecules are in membranes.
Structure
Data?1563873730
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0116550 (PGP(i-13:0/a-15:0))

PGP(i-13:0/a-15:0)
  Mrv1652309171703162D          

 51 50  0  0  1  0            999 V2000
    2.7850    0.9634    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3818    0.3608    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -3.0920    0.7696    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8022    0.3608    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9714   -0.3495    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7924   -0.3495    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6715    0.7709    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9613    0.3608    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7968    0.3437    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.5071   -0.0665    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2174    0.3437    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.9276   -0.0665    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0493    0.6481    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3125    0.0209    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0493    1.3958    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.8811    0.9262    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.6379    0.3435    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.4301    0.5557    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
    4.4301    1.3759    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.2224    0.3435    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.0200   -0.1546    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5123    0.7696    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5123    1.5410    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.2264    0.3564    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.9405    0.7696    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.6546    0.3564    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.3688    0.7696    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -8.0829    0.3564    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -8.7971    0.7696    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -9.5112    0.3564    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  -10.2254    0.7696    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  -10.9395    0.3564    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  -11.6536    0.7696    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  -12.3677    0.3564    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  -12.3677    1.1814    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5362   -0.7691    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5362   -1.5406    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2504   -0.3560    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9645   -0.7691    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.6787   -0.3560    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.3928   -0.7691    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.1069   -0.3560    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.8210   -0.7691    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -8.5352   -0.3560    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -9.2493   -0.7691    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -9.9635   -0.3560    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  -10.6776   -0.7691    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  -11.3918   -0.3560    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  -12.1059   -0.7691    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  -12.1059    0.0559    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  -12.8200   -0.3573    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  2  3  1  0  0  0  0
  2  6  1  0  0  0  0
  2  5  1  1  0  0  0
  3  4  1  0  0  0  0
  4 22  1  0  0  0  0
  7  2  1  0  0  0  0
  8  7  1  0  0  0  0
 10  9  1  0  0  0  0
 11 10  1  0  0  0  0
 11 16  1  0  0  0  0
 11  1  1  6  0  0  0
 12 11  1  0  0  0  0
 12 17  1  0  0  0  0
 13  9  1  0  0  0  0
 13 14  1  0  0  0  0
 13 15  2  0  0  0  0
 13  8  1  0  0  0  0
 17 18  1  0  0  0  0
 18 19  2  0  0  0  0
 18 20  1  0  0  0  0
 18 21  1  0  0  0  0
 22 23  2  0  0  0  0
 22 24  1  0  0  0  0
 24 25  1  0  0  0  0
 25 26  1  0  0  0  0
 26 27  1  0  0  0  0
 27 28  1  0  0  0  0
 28 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
 33 34  1  0  0  0  0
 33 35  1  0  0  0  0
 36  6  1  0  0  0  0
 36 37  2  0  0  0  0
 36 38  1  0  0  0  0
 38 39  1  0  0  0  0
 39 40  1  0  0  0  0
 40 41  1  0  0  0  0
 41 42  1  0  0  0  0
 42 43  1  0  0  0  0
 43 44  1  0  0  0  0
 44 45  1  0  0  0  0
 45 46  1  0  0  0  0
 46 47  1  0  0  0  0
 47 48  1  0  0  0  0
 48 49  1  0  0  0  0
 48 50  1  0  0  0  0
 50 51  1  0  0  0  0
M  END
Download

3D MOL for HMDB0116550 (PGP(i-13:0/a-15:0))

HMDB0116550
     RDKit          3D
PGP(i-13:0/a-15:0)
117116  0  0  0  0  0  0  0  0999 V2000
   -1.7521    7.1762   -1.3649 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2501    5.9710   -2.0916 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1312    5.5007   -3.2061 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3097    6.5777   -4.2685 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5039    5.0894   -2.7581 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4524    3.9509   -1.7449 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8691    3.5995   -1.3644 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9168    2.4643   -0.3516 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2020    2.8283    0.9148 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2329    1.7423    1.9499 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5831    0.4841    1.4660 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6125   -0.5919    2.5651 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9432   -1.7933    1.9865 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8609   -2.9472    2.9471 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1533   -4.0491    2.2028 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8458   -4.9882    1.7686 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8073   -4.0291    2.0052 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0598   -5.0462    1.3126 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.9094   -5.6099    2.2855 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8094   -4.7939    2.8959 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.8956   -4.0978    2.4979 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2718   -4.1547    1.3246 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.6298   -3.2601    3.4893 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.7921   -2.5502    2.8768 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.5050   -1.6751    3.9158 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.5455   -0.6355    4.4647 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0193    0.2622    3.3786 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0494    1.2681    4.0102 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5024    2.1827    2.9763 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5751    3.2460    3.3237 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8817    4.4557    4.0550 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5147    4.4669    5.3916 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5205    5.9672    5.8518 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0301    4.1908    5.3111 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4613   -4.3963    0.0794 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2460   -5.2036   -0.7081 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.7865   -4.4272   -2.1078 P   0  0  0  0  0  5  0  0  0  0  0  0
    2.1492   -3.0142   -1.7399 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.1683   -5.1793   -2.7066 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.5203   -4.5138   -3.2167 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.6437   -3.6300   -4.2596 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5012   -3.7235   -5.2417 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.2407   -2.7737   -6.2435 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4914   -5.0840   -5.9171 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4439   -5.1800   -6.9062 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3525   -6.7181   -7.5920 P   0  0  0  0  0  5  0  0  0  0  0  0
   -2.3761   -6.8823   -8.7112 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.2009   -7.0117   -8.2015 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7254   -7.8602   -6.4135 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0412    8.0466   -1.4644 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7913    7.4628   -1.6170 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7595    6.9341   -0.2625 H   0  0  0  0  0  0  0  0  0  0  0  0
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   -0.2350    6.2128   -2.4962 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6257    4.6458   -3.6965 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8513    6.1355   -5.1379 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9361    7.3842   -3.8509 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3337    6.9528   -4.6310 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0733    5.9101   -2.3109 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0190    4.6797   -3.6562 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9254    4.3736   -0.8457 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9000    3.1124   -2.1875 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.4516    3.2912   -2.2455 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.3510    4.4692   -0.8767 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.9767    2.2439   -0.1338 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4079    1.5573   -0.7804 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1299    3.0343    0.6537 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5769    3.7927    1.3355 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7233    2.0474    2.8934 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.2952    1.5431    2.2414 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5143    0.6516    1.2361 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0724    0.1053    0.5521 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7013   -0.7966    2.7305 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1755   -0.2153    3.4936 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5099   -2.0874    1.0728 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9190   -1.5617    1.6435 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8198   -3.2775    3.3436 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2264   -2.6325    3.8176 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8235   -5.8467    1.0385 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3574   -6.1662    3.1182 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4637   -6.4961    1.7989 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.0353   -3.9680    4.2561 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.9229   -2.6032    3.9932 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.5740   -1.9439    2.0014 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.5646   -3.2917    2.5510 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.8424   -2.3079    4.7444 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.3602   -1.1946    3.4380 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.1261    0.0102    5.1635 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.7129   -1.0485    5.0258 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.8120    0.8472    2.8610 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.4873   -0.3499    2.6322 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.1755    0.5805    4.3327 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.3864    1.7029    4.9233 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.4043    2.6417    2.4414 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.1019    1.5043    2.1532 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6217    2.7503    3.7688 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1394    3.6177    2.2968 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9343    5.1389    4.1275 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5474    5.1546    3.3991 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0452    3.9136    6.1897 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.9712    5.9614    6.8476 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4772    6.3286    5.9259 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.1413    6.5234    5.1491 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.2791    3.5311    6.1439 H   0  0  0  0  0  0  0  0  0  0  0  0
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M  END
Download

3D SDF for HMDB0116550 (PGP(i-13:0/a-15:0))

PGP(i-13:0/a-15:0)
  Mrv1652309171703162D          

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M  END
> <DATABASE_ID>
HMDB0116550

> <DATABASE_NAME>
hmdb

> <SMILES>
[H][C@](O)(COP(O)(O)=O)COP(O)(=O)OC[C@@]([H])(COC(=O)CCCCCCCCCC(C)C)OC(=O)CCCCCCCCCCC(C)CC

> <INCHI_IDENTIFIER>
InChI=1S/C34H68O13P2/c1-5-30(4)22-18-14-10-6-7-11-16-20-24-34(37)47-32(28-46-49(41,42)45-26-31(35)25-44-48(38,39)40)27-43-33(36)23-19-15-12-8-9-13-17-21-29(2)3/h29-32,35H,5-28H2,1-4H3,(H,41,42)(H2,38,39,40)/t30?,31-,32+/m0/s1

> <INCHI_KEY>
QKEBQNUVJWSQJT-XXWVNBFBSA-N

> <FORMULA>
C34H68O13P2

> <MOLECULAR_WEIGHT>
746.853

> <EXACT_MASS>
746.413516246

> <JCHEM_ACCEPTOR_COUNT>
8

> <JCHEM_ATOM_COUNT>
117

> <JCHEM_AVERAGE_POLARIZABILITY>
83.96895330793025

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
[(2S)-2-hydroxy-3-({hydroxy[(2R)-3-[(11-methyldodecanoyl)oxy]-2-[(12-methyltetradecanoyl)oxy]propoxy]phosphoryl}oxy)propoxy]phosphonic acid

> <ALOGPS_LOGP>
5.06

> <JCHEM_LOGP>
8.720111690666668

> <ALOGPS_LOGS>
-5.57

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-3

> <JCHEM_PKA>
2.0402061436989327

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.354879296415124

> <JCHEM_PKA_STRONGEST_BASIC>
-3.410499386302644

> <JCHEM_POLAR_SURFACE_AREA>
195.34999999999997

> <JCHEM_REFRACTIVITY>
187.673

> <JCHEM_ROTATABLE_BOND_COUNT>
36

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
2.03e-03 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(2S)-2-hydroxy-3-{[hydroxy((2R)-3-[(11-methyldodecanoyl)oxy]-2-[(12-methyltetradecanoyl)oxy]propoxy)phosphoryl]oxy}propoxyphosphonic acid

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for HMDB0116550 (PGP(i-13:0/a-15:0))

HMDB0116550
     RDKit          3D
PGP(i-13:0/a-15:0)
117116  0  0  0  0  0  0  0  0999 V2000
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   -4.0733    5.9101   -2.3109 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0190    4.6797   -3.6562 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9254    4.3736   -0.8457 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9000    3.1124   -2.1875 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.4516    3.2912   -2.2455 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.3510    4.4692   -0.8767 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.9767    2.2439   -0.1338 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4079    1.5573   -0.7804 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1299    3.0343    0.6537 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5769    3.7927    1.3355 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7233    2.0474    2.8934 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.2952    1.5431    2.2414 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5143    0.6516    1.2361 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0724    0.1053    0.5521 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7013   -0.7966    2.7305 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1755   -0.2153    3.4936 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5099   -2.0874    1.0728 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9190   -1.5617    1.6435 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8198   -3.2775    3.3436 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2264   -2.6325    3.8176 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8235   -5.8467    1.0385 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3574   -6.1662    3.1182 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4637   -6.4961    1.7989 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.0353   -3.9680    4.2561 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.9229   -2.6032    3.9932 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.5740   -1.9439    2.0014 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.5646   -3.2917    2.5510 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.8424   -2.3079    4.7444 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.3602   -1.1946    3.4380 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.1261    0.0102    5.1635 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.7129   -1.0485    5.0258 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.8120    0.8472    2.8610 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.4873   -0.3499    2.6322 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.1755    0.5805    4.3327 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.3864    1.7029    4.9233 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.4043    2.6417    2.4414 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.1019    1.5043    2.1532 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6217    2.7503    3.7688 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1394    3.6177    2.2968 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9343    5.1389    4.1275 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5474    5.1546    3.3991 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0452    3.9136    6.1897 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.9712    5.9614    6.8476 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4772    6.3286    5.9259 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.1413    6.5234    5.1491 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.2791    3.5311    6.1439 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.3033    3.8083    4.3191 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.6045    5.1306    5.4446 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4355   -4.0169   -0.5154 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9937   -3.4709    0.3338 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.9799   -4.6544   -2.6242 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7840   -2.5778   -3.9605 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5642   -3.9101   -4.8322 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4699   -3.4784   -4.8047 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1036   -2.5063   -6.6656 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5349   -5.3012   -6.2747 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7087   -5.8737   -5.1491 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1758   -6.7540   -9.1727 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7046   -7.8123   -6.2257 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  1  0
  3  5  1  0
  5  6  1  0
  6  7  1  0
  7  8  1  0
  8  9  1  0
  9 10  1  0
 10 11  1  0
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 49117  1  0
M  END
Download

PDB for HMDB0116550 (PGP(i-13:0/a-15:0))

HEADER    PROTEIN                                 17-SEP-17   NONE
TITLE     NULL                                                        
COMPND    MOLECULE: PGP(i-13:0/a-15:0)                                
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   17-SEP-17         0                                  
HETATM    1  H   UNK     0       5.199   1.798   0.000  0.00  0.00           H+0
HETATM    2  C   UNK     0      -4.446   0.673   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -5.772   1.437   0.000  0.00  0.00           C+0
HETATM    4  O   UNK     0      -7.097   0.673   0.000  0.00  0.00           O+0
HETATM    5  H   UNK     0      -3.680  -0.652   0.000  0.00  0.00           H+0
HETATM    6  O   UNK     0      -5.213  -0.652   0.000  0.00  0.00           O+0
HETATM    7  C   UNK     0      -3.120   1.439   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0      -1.794   0.673   0.000  0.00  0.00           O+0
HETATM    9  O   UNK     0       1.487   0.642   0.000  0.00  0.00           O+0
HETATM   10  C   UNK     0       2.813  -0.124   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       4.139   0.642   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       5.465  -0.124   0.000  0.00  0.00           C+0
HETATM   13  P   UNK     0       0.092   1.210   0.000  0.00  0.00           P+0
HETATM   14  O   UNK     0      -0.583   0.039   0.000  0.00  0.00           O+0
HETATM   15  O   UNK     0       0.092   2.605   0.000  0.00  0.00           O+0
HETATM   16  O   UNK     0       3.511   1.729   0.000  0.00  0.00           O+0
HETATM   17  O   UNK     0       6.791   0.641   0.000  0.00  0.00           O+0
HETATM   18  P   UNK     0       8.270   1.037   0.000  0.00  0.00           P+0
HETATM   19  O   UNK     0       8.270   2.568   0.000  0.00  0.00           O+0
HETATM   20  O   UNK     0       9.748   0.641   0.000  0.00  0.00           O+0
HETATM   21  O   UNK     0       7.504  -0.289   0.000  0.00  0.00           O+0
HETATM   22  C   UNK     0      -8.423   1.437   0.000  0.00  0.00           C+0
HETATM   23  O   UNK     0      -8.423   2.877   0.000  0.00  0.00           O+0
HETATM   24  C   UNK     0      -9.756   0.665   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0     -11.089   1.437   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0     -12.422   0.665   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0     -13.755   1.437   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0     -15.088   0.665   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0     -16.421   1.437   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0     -17.754   0.665   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0     -19.087   1.437   0.000  0.00  0.00           C+0
HETATM   32  C   UNK     0     -20.420   0.665   0.000  0.00  0.00           C+0
HETATM   33  C   UNK     0     -21.753   1.437   0.000  0.00  0.00           C+0
HETATM   34  C   UNK     0     -23.086   0.665   0.000  0.00  0.00           C+0
HETATM   35  C   UNK     0     -23.086   2.205   0.000  0.00  0.00           C+0
HETATM   36  C   UNK     0      -6.601  -1.436   0.000  0.00  0.00           C+0
HETATM   37  O   UNK     0      -6.601  -2.876   0.000  0.00  0.00           O+0
HETATM   38  C   UNK     0      -7.934  -0.665   0.000  0.00  0.00           C+0
HETATM   39  C   UNK     0      -9.267  -1.436   0.000  0.00  0.00           C+0
HETATM   40  C   UNK     0     -10.600  -0.665   0.000  0.00  0.00           C+0
HETATM   41  C   UNK     0     -11.933  -1.436   0.000  0.00  0.00           C+0
HETATM   42  C   UNK     0     -13.266  -0.665   0.000  0.00  0.00           C+0
HETATM   43  C   UNK     0     -14.599  -1.436   0.000  0.00  0.00           C+0
HETATM   44  C   UNK     0     -15.932  -0.665   0.000  0.00  0.00           C+0
HETATM   45  C   UNK     0     -17.265  -1.436   0.000  0.00  0.00           C+0
HETATM   46  C   UNK     0     -18.598  -0.665   0.000  0.00  0.00           C+0
HETATM   47  C   UNK     0     -19.931  -1.436   0.000  0.00  0.00           C+0
HETATM   48  C   UNK     0     -21.265  -0.665   0.000  0.00  0.00           C+0
HETATM   49  C   UNK     0     -22.598  -1.436   0.000  0.00  0.00           C+0
HETATM   50  C   UNK     0     -22.598   0.104   0.000  0.00  0.00           C+0
HETATM   51  C   UNK     0     -23.931  -0.667   0.000  0.00  0.00           C+0
CONECT    1   11                                                            
CONECT    2    3    6    5    7                                             
CONECT    3    2    4                                                       
CONECT    4    3   22                                                       
CONECT    5    2                                                            
CONECT    6    2   36                                                       
CONECT    7    2    8                                                       
CONECT    8    7   13                                                       
CONECT    9   10   13                                                       
CONECT   10    9   11                                                       
CONECT   11   10   16    1   12                                             
CONECT   12   11   17                                                       
CONECT   13    9   14   15    8                                             
CONECT   14   13                                                            
CONECT   15   13                                                            
CONECT   16   11                                                            
CONECT   17   12   18                                                       
CONECT   18   17   19   20   21                                             
CONECT   19   18                                                            
CONECT   20   18                                                            
CONECT   21   18                                                            
CONECT   22    4   23   24                                                  
CONECT   23   22                                                            
CONECT   24   22   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   35                                                  
CONECT   34   33                                                            
CONECT   35   33                                                            
CONECT   36    6   37   38                                                  
CONECT   37   36                                                            
CONECT   38   36   39                                                       
CONECT   39   38   40                                                       
CONECT   40   39   41                                                       
CONECT   41   40   42                                                       
CONECT   42   41   43                                                       
CONECT   43   42   44                                                       
CONECT   44   43   45                                                       
CONECT   45   44   46                                                       
CONECT   46   45   47                                                       
CONECT   47   46   48                                                       
CONECT   48   47   49   50                                                  
CONECT   49   48                                                            
CONECT   50   48   51                                                       
CONECT   51   50                                                            
MASTER        0    0    0    0    0    0    0    0   51    0  100    0
END
Download

3D PDB for HMDB0116550 (PGP(i-13:0/a-15:0))

COMPND    HMDB0116550
HETATM    1  C1  UNL     1      -1.752   7.176  -1.365  1.00  0.00           C  
HETATM    2  C2  UNL     1      -1.250   5.971  -2.092  1.00  0.00           C  
HETATM    3  C3  UNL     1      -2.131   5.501  -3.206  1.00  0.00           C  
HETATM    4  C4  UNL     1      -2.310   6.578  -4.269  1.00  0.00           C  
HETATM    5  C5  UNL     1      -3.504   5.089  -2.758  1.00  0.00           C  
HETATM    6  C6  UNL     1      -3.452   3.951  -1.745  1.00  0.00           C  
HETATM    7  C7  UNL     1      -4.869   3.600  -1.364  1.00  0.00           C  
HETATM    8  C8  UNL     1      -4.917   2.464  -0.352  1.00  0.00           C  
HETATM    9  C9  UNL     1      -4.202   2.828   0.915  1.00  0.00           C  
HETATM   10  C10 UNL     1      -4.233   1.742   1.950  1.00  0.00           C  
HETATM   11  C11 UNL     1      -3.583   0.484   1.466  1.00  0.00           C  
HETATM   12  C12 UNL     1      -3.613  -0.592   2.565  1.00  0.00           C  
HETATM   13  C13 UNL     1      -2.943  -1.793   1.986  1.00  0.00           C  
HETATM   14  C14 UNL     1      -2.861  -2.947   2.947  1.00  0.00           C  
HETATM   15  C15 UNL     1      -2.153  -4.049   2.203  1.00  0.00           C  
HETATM   16  O1  UNL     1      -2.846  -4.988   1.769  1.00  0.00           O  
HETATM   17  O2  UNL     1      -0.807  -4.029   2.005  1.00  0.00           O  
HETATM   18  C16 UNL     1      -0.060  -5.046   1.313  1.00  0.00           C  
HETATM   19  C17 UNL     1       0.909  -5.610   2.285  1.00  0.00           C  
HETATM   20  O3  UNL     1       1.809  -4.794   2.896  1.00  0.00           O  
HETATM   21  C18 UNL     1       2.896  -4.098   2.498  1.00  0.00           C  
HETATM   22  O4  UNL     1       3.272  -4.155   1.325  1.00  0.00           O  
HETATM   23  C19 UNL     1       3.630  -3.260   3.489  1.00  0.00           C  
HETATM   24  C20 UNL     1       4.792  -2.550   2.877  1.00  0.00           C  
HETATM   25  C21 UNL     1       5.505  -1.675   3.916  1.00  0.00           C  
HETATM   26  C22 UNL     1       4.546  -0.636   4.465  1.00  0.00           C  
HETATM   27  C23 UNL     1       4.019   0.262   3.379  1.00  0.00           C  
HETATM   28  C24 UNL     1       3.049   1.268   4.010  1.00  0.00           C  
HETATM   29  C25 UNL     1       2.502   2.183   2.976  1.00  0.00           C  
HETATM   30  C26 UNL     1       1.575   3.246   3.324  1.00  0.00           C  
HETATM   31  C27 UNL     1       1.882   4.456   4.055  1.00  0.00           C  
HETATM   32  C28 UNL     1       2.515   4.467   5.392  1.00  0.00           C  
HETATM   33  C29 UNL     1       2.520   5.967   5.852  1.00  0.00           C  
HETATM   34  C30 UNL     1       4.030   4.191   5.311  1.00  0.00           C  
HETATM   35  C31 UNL     1       0.461  -4.396   0.079  1.00  0.00           C  
HETATM   36  O5  UNL     1       1.246  -5.204  -0.708  1.00  0.00           O  
HETATM   37  P1  UNL     1       1.786  -4.427  -2.108  1.00  0.00           P  
HETATM   38  O6  UNL     1       2.149  -3.014  -1.740  1.00  0.00           O  
HETATM   39  O7  UNL     1       3.168  -5.179  -2.707  1.00  0.00           O  
HETATM   40  O8  UNL     1       0.520  -4.514  -3.217  1.00  0.00           O  
HETATM   41  C32 UNL     1       0.644  -3.630  -4.260  1.00  0.00           C  
HETATM   42  C33 UNL     1      -0.501  -3.723  -5.242  1.00  0.00           C  
HETATM   43  O9  UNL     1      -0.241  -2.774  -6.244  1.00  0.00           O  
HETATM   44  C34 UNL     1      -0.491  -5.084  -5.917  1.00  0.00           C  
HETATM   45  O10 UNL     1      -1.444  -5.180  -6.906  1.00  0.00           O  
HETATM   46  P2  UNL     1      -1.353  -6.718  -7.592  1.00  0.00           P  
HETATM   47  O11 UNL     1      -2.376  -6.882  -8.711  1.00  0.00           O  
HETATM   48  O12 UNL     1       0.201  -7.012  -8.202  1.00  0.00           O  
HETATM   49  O13 UNL     1      -1.725  -7.860  -6.414  1.00  0.00           O  
HETATM   50  H1  UNL     1      -1.041   8.047  -1.464  1.00  0.00           H  
HETATM   51  H2  UNL     1      -2.791   7.463  -1.617  1.00  0.00           H  
HETATM   52  H3  UNL     1      -1.759   6.934  -0.263  1.00  0.00           H  
HETATM   53  H4  UNL     1      -1.081   5.114  -1.400  1.00  0.00           H  
HETATM   54  H5  UNL     1      -0.235   6.213  -2.496  1.00  0.00           H  
HETATM   55  H6  UNL     1      -1.626   4.646  -3.696  1.00  0.00           H  
HETATM   56  H7  UNL     1      -2.851   6.135  -5.138  1.00  0.00           H  
HETATM   57  H8  UNL     1      -2.936   7.384  -3.851  1.00  0.00           H  
HETATM   58  H9  UNL     1      -1.334   6.953  -4.631  1.00  0.00           H  
HETATM   59  H10 UNL     1      -4.073   5.910  -2.311  1.00  0.00           H  
HETATM   60  H11 UNL     1      -4.019   4.680  -3.656  1.00  0.00           H  
HETATM   61  H12 UNL     1      -2.925   4.374  -0.846  1.00  0.00           H  
HETATM   62  H13 UNL     1      -2.900   3.112  -2.188  1.00  0.00           H  
HETATM   63  H14 UNL     1      -5.452   3.291  -2.245  1.00  0.00           H  
HETATM   64  H15 UNL     1      -5.351   4.469  -0.877  1.00  0.00           H  
HETATM   65  H16 UNL     1      -5.977   2.244  -0.134  1.00  0.00           H  
HETATM   66  H17 UNL     1      -4.408   1.557  -0.780  1.00  0.00           H  
HETATM   67  H18 UNL     1      -3.130   3.034   0.654  1.00  0.00           H  
HETATM   68  H19 UNL     1      -4.577   3.793   1.336  1.00  0.00           H  
HETATM   69  H20 UNL     1      -3.723   2.047   2.893  1.00  0.00           H  
HETATM   70  H21 UNL     1      -5.295   1.543   2.241  1.00  0.00           H  
HETATM   71  H22 UNL     1      -2.514   0.652   1.236  1.00  0.00           H  
HETATM   72  H23 UNL     1      -4.072   0.105   0.552  1.00  0.00           H  
HETATM   73  H24 UNL     1      -4.701  -0.797   2.731  1.00  0.00           H  
HETATM   74  H25 UNL     1      -3.176  -0.215   3.494  1.00  0.00           H  
HETATM   75  H26 UNL     1      -3.510  -2.087   1.073  1.00  0.00           H  
HETATM   76  H27 UNL     1      -1.919  -1.562   1.644  1.00  0.00           H  
HETATM   77  H28 UNL     1      -3.820  -3.277   3.344  1.00  0.00           H  
HETATM   78  H29 UNL     1      -2.226  -2.633   3.818  1.00  0.00           H  
HETATM   79  H30 UNL     1      -0.823  -5.847   1.039  1.00  0.00           H  
HETATM   80  H31 UNL     1       0.357  -6.166   3.118  1.00  0.00           H  
HETATM   81  H32 UNL     1       1.464  -6.496   1.799  1.00  0.00           H  
HETATM   82  H33 UNL     1       4.035  -3.968   4.256  1.00  0.00           H  
HETATM   83  H34 UNL     1       2.923  -2.603   3.993  1.00  0.00           H  
HETATM   84  H35 UNL     1       4.574  -1.944   2.001  1.00  0.00           H  
HETATM   85  H36 UNL     1       5.565  -3.292   2.551  1.00  0.00           H  
HETATM   86  H37 UNL     1       5.842  -2.308   4.744  1.00  0.00           H  
HETATM   87  H38 UNL     1       6.360  -1.195   3.438  1.00  0.00           H  
HETATM   88  H39 UNL     1       5.126   0.010   5.164  1.00  0.00           H  
HETATM   89  H40 UNL     1       3.713  -1.048   5.026  1.00  0.00           H  
HETATM   90  H41 UNL     1       4.812   0.847   2.861  1.00  0.00           H  
HETATM   91  H42 UNL     1       3.487  -0.350   2.632  1.00  0.00           H  
HETATM   92  H43 UNL     1       2.176   0.580   4.333  1.00  0.00           H  
HETATM   93  H44 UNL     1       3.386   1.703   4.923  1.00  0.00           H  
HETATM   94  H45 UNL     1       3.404   2.642   2.441  1.00  0.00           H  
HETATM   95  H46 UNL     1       2.102   1.504   2.153  1.00  0.00           H  
HETATM   96  H47 UNL     1       0.622   2.750   3.769  1.00  0.00           H  
HETATM   97  H48 UNL     1       1.139   3.618   2.297  1.00  0.00           H  
HETATM   98  H49 UNL     1       0.934   5.139   4.127  1.00  0.00           H  
HETATM   99  H50 UNL     1       2.547   5.155   3.399  1.00  0.00           H  
HETATM  100  H51 UNL     1       2.045   3.914   6.190  1.00  0.00           H  
HETATM  101  H52 UNL     1       2.971   5.961   6.848  1.00  0.00           H  
HETATM  102  H53 UNL     1       1.477   6.329   5.926  1.00  0.00           H  
HETATM  103  H54 UNL     1       3.141   6.523   5.149  1.00  0.00           H  
HETATM  104  H55 UNL     1       4.279   3.531   6.144  1.00  0.00           H  
HETATM  105  H56 UNL     1       4.303   3.808   4.319  1.00  0.00           H  
HETATM  106  H57 UNL     1       4.604   5.131   5.445  1.00  0.00           H  
HETATM  107  H58 UNL     1      -0.435  -4.017  -0.515  1.00  0.00           H  
HETATM  108  H59 UNL     1       0.994  -3.471   0.334  1.00  0.00           H  
HETATM  109  H60 UNL     1       3.980  -4.654  -2.624  1.00  0.00           H  
HETATM  110  H61 UNL     1       0.784  -2.578  -3.960  1.00  0.00           H  
HETATM  111  H62 UNL     1       1.564  -3.910  -4.832  1.00  0.00           H  
HETATM  112  H63 UNL     1      -1.470  -3.478  -4.805  1.00  0.00           H  
HETATM  113  H64 UNL     1      -1.104  -2.506  -6.666  1.00  0.00           H  
HETATM  114  H65 UNL     1       0.535  -5.301  -6.275  1.00  0.00           H  
HETATM  115  H66 UNL     1      -0.709  -5.874  -5.149  1.00  0.00           H  
HETATM  116  H67 UNL     1       0.176  -6.754  -9.173  1.00  0.00           H  
HETATM  117  H68 UNL     1      -2.705  -7.812  -6.226  1.00  0.00           H  
CONECT    1    2   50   51   52
CONECT    2    3   53   54
CONECT    3    4    5   55
CONECT    4   56   57   58
CONECT    5    6   59   60
CONECT    6    7   61   62
CONECT    7    8   63   64
CONECT    8    9   65   66
CONECT    9   10   67   68
CONECT   10   11   69   70
CONECT   11   12   71   72
CONECT   12   13   73   74
CONECT   13   14   75   76
CONECT   14   15   77   78
CONECT   15   16   16   17
CONECT   17   18
CONECT   18   19   35   79
CONECT   19   20   80   81
CONECT   20   21
CONECT   21   22   22   23
CONECT   23   24   82   83
CONECT   24   25   84   85
CONECT   25   26   86   87
CONECT   26   27   88   89
CONECT   27   28   90   91
CONECT   28   29   92   93
CONECT   29   30   94   95
CONECT   30   31   96   97
CONECT   31   32   98   99
CONECT   32   33   34  100
CONECT   33  101  102  103
CONECT   34  104  105  106
CONECT   35   36  107  108
CONECT   36   37
CONECT   37   38   38   39   40
CONECT   39  109
CONECT   40   41
CONECT   41   42  110  111
CONECT   42   43   44  112
CONECT   43  113
CONECT   44   45  114  115
CONECT   45   46
CONECT   46   47   47   48   49
CONECT   48  116
CONECT   49  117
END
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SMILES for HMDB0116550 (PGP(i-13:0/a-15:0))

[H][C@](O)(COP(O)(O)=O)COP(O)(=O)OC[C@@]([H])(COC(=O)CCCCCCCCCC(C)C)OC(=O)CCCCCCCCCCC(C)CC
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INCHI for HMDB0116550 (PGP(i-13:0/a-15:0))

InChI=1S/C34H68O13P2/c1-5-30(4)22-18-14-10-6-7-11-16-20-24-34(37)47-32(28-46-49(41,42)45-26-31(35)25-44-48(38,39)40)27-43-33(36)23-19-15-12-8-9-13-17-21-29(2)3/h29-32,35H,5-28H2,1-4H3,(H,41,42)(H2,38,39,40)/t30?,31-,32+/m0/s1
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View in JSmolView Stereo Labels
Synonyms
ValueSource
1-Isotridecanoyl-2-anteisopentadecanoyl-sn-glycero-3-phospho-(1'-sn-glycerol-3'-phosphate)HMDB
PGP(28:0)HMDB
3-sn-Phosphatidyl-1'-sn-glycerol 3'-phosphoric acidHMDB
[(2S)-2-Hydroxy-3-({hydroxy[(2R)-3-[(11-methyldodecanoyl)oxy]-2-[(12-methyltetradecanoyl)oxy]propoxy]phosphoryl}oxy)propoxy]phosphonateHMDB
PGP(i-13:0/a-15:0)SMPDB
Chemical FormulaC34H68O13P2
Average Molecular Weight746.853
Monoisotopic Molecular Weight746.413516246
IUPAC Name[(2S)-2-hydroxy-3-({hydroxy[(2R)-3-[(11-methyldodecanoyl)oxy]-2-[(12-methyltetradecanoyl)oxy]propoxy]phosphoryl}oxy)propoxy]phosphonic acid
Traditional Name(2S)-2-hydroxy-3-{[hydroxy((2R)-3-[(11-methyldodecanoyl)oxy]-2-[(12-methyltetradecanoyl)oxy]propoxy)phosphoryl]oxy}propoxyphosphonic acid
CAS Registry NumberNot Available
SMILES
[H][C@](O)(COP(O)(O)=O)COP(O)(=O)OC[C@@]([H])(COC(=O)CCCCCCCCCC(C)C)OC(=O)CCCCCCCCCCC(C)CC
InChI Identifier
InChI=1S/C34H68O13P2/c1-5-30(4)22-18-14-10-6-7-11-16-20-24-34(37)47-32(28-46-49(41,42)45-26-31(35)25-44-48(38,39)40)27-43-33(36)23-19-15-12-8-9-13-17-21-29(2)3/h29-32,35H,5-28H2,1-4H3,(H,41,42)(H2,38,39,40)/t30?,31-,32+/m0/s1
InChI KeyQKEBQNUVJWSQJT-XXWVNBFBSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as phosphatidylglycerophosphates. These are glycerophosphoglycerophosphates in which two fatty acids are bonded to the 1-glycerol moiety through ester linkages.
KingdomOrganic compounds
Super ClassLipids and lipid-like molecules
ClassGlycerophospholipids
Sub ClassGlycerophosphoglycerophosphates
Direct ParentPhosphatidylglycerophosphates
Alternative Parents
Substituents
  • Diacylglycerophosphoglycerophosphate
  • Sn-glycerol-3-phosphate
  • Fatty acid ester
  • Monoalkyl phosphate
  • Dialkyl phosphate
  • Dicarboxylic acid or derivatives
  • Organic phosphoric acid derivative
  • Phosphoric acid ester
  • Alkyl phosphate
  • Fatty acyl
  • Secondary alcohol
  • Carboxylic acid ester
  • Carboxylic acid derivative
  • Organooxygen compound
  • Organic oxide
  • Organic oxygen compound
  • Alcohol
  • Carbonyl group
  • Hydrocarbon derivative
  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic compounds
External DescriptorsNot Available
Ontology
Physiological effectNot Available
Disposition
Source
Process
Naturally occurring process
RoleNot 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
logP5.06ALOGPS
logP8.72ChemAxon
logS-5.6ALOGPS
pKa (Strongest Acidic)1.35ChemAxon
pKa (Strongest Basic)-3.4ChemAxon
Physiological Charge-3ChemAxon
Hydrogen Acceptor Count8ChemAxon
Hydrogen Donor Count4ChemAxon
Polar Surface Area195.35 ŲChemAxon
Rotatable Bond Count36ChemAxon
Refractivity187.67 m³·mol⁻¹ChemAxon
Polarizability83.97 ųChemAxon
Number of Rings0ChemAxon
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]+276.00131661259
DarkChem[M-H]-257.61431661259
DeepCCS[M+H]+258.01930932474
DeepCCS[M-H]-256.12430932474
DeepCCS[M-2H]-289.36430932474
DeepCCS[M+Na]+263.65430932474
AllCCS[M+H]+275.832859911
AllCCS[M+H-H2O]+275.632859911
AllCCS[M+NH4]+275.932859911
AllCCS[M+Na]+275.932859911
AllCCS[M-H]-263.932859911
AllCCS[M+Na-2H]-269.732859911
AllCCS[M+HCOO]-276.132859911

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, 2022.10.58 minutes32390414
Predicted by Siyang on May 30, 202219.5689 minutes33406817
Predicted by Siyang using ReTip algorithm on June 8, 20223.05 minutes32390414
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid3830.0 seconds40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid167.0 seconds40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid273.4 seconds40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid172.0 seconds40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid712.0 seconds40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid1161.0 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 Acid1070.5 seconds40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)257.6 seconds40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid1878.8 seconds40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid919.2 seconds40023050
UFZ_Phenomenex = Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex with Water:MeOH and 0.1% Formic Acid1904.3 seconds40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid767.6 seconds40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid562.7 seconds40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate166.8 seconds40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA201.0 seconds40023050
Meister zic-pHILIC pH9.3 = Merck SeQuant ZIC-pHILIC column with ACN:Water 5mM NH4Ac pH9.3 and 5mM ammonium acetate in water37.2 seconds40023050

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
PGP(i-13:0/a-15:0)[H][C@](O)(COP(O)(O)=O)COP(O)(=O)OC[C@@]([H])(COC(=O)CCCCCCCCCC(C)C)OC(=O)CCCCCCCCCCC(C)CC4619.9Standard polar33892256
PGP(i-13:0/a-15:0)[H][C@](O)(COP(O)(O)=O)COP(O)(=O)OC[C@@]([H])(COC(=O)CCCCCCCCCC(C)C)OC(=O)CCCCCCCCCCC(C)CC4253.0Standard non polar33892256
PGP(i-13:0/a-15:0)[H][C@](O)(COP(O)(O)=O)COP(O)(=O)OC[C@@]([H])(COC(=O)CCCCCCCCCC(C)C)OC(=O)CCCCCCCCCCC(C)CC4963.0Semi standard non polar33892256

Derivatized

Derivative Name / StructureSMILESKovats RI ValueColumn TypeReference
PGP(i-13:0/a-15:0),2TMS,isomer #1CCC(C)CCCCCCCCCCC(=O)O[C@H](COC(=O)CCCCCCCCCC(C)C)COP(=O)(OC[C@H](COP(=O)(O)O)O[Si](C)(C)C)O[Si](C)(C)C5000.3Semi standard non polar33892256
PGP(i-13:0/a-15:0),2TMS,isomer #1CCC(C)CCCCCCCCCCC(=O)O[C@H](COC(=O)CCCCCCCCCC(C)C)COP(=O)(OC[C@H](COP(=O)(O)O)O[Si](C)(C)C)O[Si](C)(C)C4081.7Standard non polar33892256
PGP(i-13:0/a-15:0),2TMS,isomer #1CCC(C)CCCCCCCCCCC(=O)O[C@H](COC(=O)CCCCCCCCCC(C)C)COP(=O)(OC[C@H](COP(=O)(O)O)O[Si](C)(C)C)O[Si](C)(C)C6518.1Standard polar33892256
PGP(i-13:0/a-15:0),2TMS,isomer #2CCC(C)CCCCCCCCCCC(=O)O[C@H](COC(=O)CCCCCCCCCC(C)C)COP(=O)(O)OC[C@H](COP(=O)(O)O[Si](C)(C)C)O[Si](C)(C)C5035.4Semi standard non polar33892256
PGP(i-13:0/a-15:0),2TMS,isomer #2CCC(C)CCCCCCCCCCC(=O)O[C@H](COC(=O)CCCCCCCCCC(C)C)COP(=O)(O)OC[C@H](COP(=O)(O)O[Si](C)(C)C)O[Si](C)(C)C4098.1Standard non polar33892256
PGP(i-13:0/a-15:0),2TMS,isomer #2CCC(C)CCCCCCCCCCC(=O)O[C@H](COC(=O)CCCCCCCCCC(C)C)COP(=O)(O)OC[C@H](COP(=O)(O)O[Si](C)(C)C)O[Si](C)(C)C6611.3Standard polar33892256
PGP(i-13:0/a-15:0),2TMS,isomer #3CCC(C)CCCCCCCCCCC(=O)O[C@H](COC(=O)CCCCCCCCCC(C)C)COP(=O)(OC[C@@H](O)COP(=O)(O)O[Si](C)(C)C)O[Si](C)(C)C5031.1Semi standard non polar33892256
PGP(i-13:0/a-15:0),2TMS,isomer #3CCC(C)CCCCCCCCCCC(=O)O[C@H](COC(=O)CCCCCCCCCC(C)C)COP(=O)(OC[C@@H](O)COP(=O)(O)O[Si](C)(C)C)O[Si](C)(C)C4120.4Standard non polar33892256
PGP(i-13:0/a-15:0),2TMS,isomer #3CCC(C)CCCCCCCCCCC(=O)O[C@H](COC(=O)CCCCCCCCCC(C)C)COP(=O)(OC[C@@H](O)COP(=O)(O)O[Si](C)(C)C)O[Si](C)(C)C6162.6Standard polar33892256
PGP(i-13:0/a-15:0),2TMS,isomer #4CCC(C)CCCCCCCCCCC(=O)O[C@H](COC(=O)CCCCCCCCCC(C)C)COP(=O)(O)OC[C@@H](O)COP(=O)(O[Si](C)(C)C)O[Si](C)(C)C5037.1Semi standard non polar33892256
PGP(i-13:0/a-15:0),2TMS,isomer #4CCC(C)CCCCCCCCCCC(=O)O[C@H](COC(=O)CCCCCCCCCC(C)C)COP(=O)(O)OC[C@@H](O)COP(=O)(O[Si](C)(C)C)O[Si](C)(C)C4120.5Standard non polar33892256
PGP(i-13:0/a-15:0),2TMS,isomer #4CCC(C)CCCCCCCCCCC(=O)O[C@H](COC(=O)CCCCCCCCCC(C)C)COP(=O)(O)OC[C@@H](O)COP(=O)(O[Si](C)(C)C)O[Si](C)(C)C6267.0Standard polar33892256
Spectra

GC-MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted GC-MSPredicted GC-MS Spectrum - PGP(i-13:0/a-15:0) GC-MS (Non-derivatized) - 70eV, PositiveNot Available2021-10-13Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - PGP(i-13:0/a-15:0) GC-MS (TMS_1_1) - 70eV, PositiveNot Available2021-10-18Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - PGP(i-13:0/a-15:0) GC-MS (TMS_1_2) - 70eV, PositiveNot Available2021-10-18Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - PGP(i-13:0/a-15:0) GC-MS (TMS_1_3) - 70eV, PositiveNot Available2021-10-18Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - PGP(i-13:0/a-15:0) GC-MS (TBDMS_1_1) - 70eV, PositiveNot Available2021-10-18Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - PGP(i-13:0/a-15:0) GC-MS (TBDMS_1_2) - 70eV, PositiveNot Available2021-10-18Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - PGP(i-13:0/a-15:0) GC-MS (TBDMS_1_3) - 70eV, PositiveNot Available2021-10-18Wishart LabView Spectrum

MS/MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - PGP(i-13:0/a-15:0) 10V, Positive-QTOFsplash10-054k-1980272800-bf5488b6909a5086398c2019-02-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - PGP(i-13:0/a-15:0) 20V, Positive-QTOFsplash10-054k-4950132200-1540c603f14831e7553d2019-02-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - PGP(i-13:0/a-15:0) 40V, Positive-QTOFsplash10-0a4j-7940401000-801bb4779434f1e6125f2019-02-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - PGP(i-13:0/a-15:0) 10V, Negative-QTOFsplash10-01r2-4490030300-eebcc1ab2cbf00a80cc12019-02-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - PGP(i-13:0/a-15:0) 20V, Negative-QTOFsplash10-004j-9140000000-4a905cbf68a292c424832019-02-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - PGP(i-13:0/a-15:0) 40V, Negative-QTOFsplash10-004i-9010000000-4da368319a5fa498a9f62019-02-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - PGP(i-13:0/a-15:0) 10V, Negative-QTOFsplash10-0002-0010000900-5310ece049448c9238fe2021-09-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - PGP(i-13:0/a-15:0) 20V, Negative-QTOFsplash10-0002-3091040600-3732d4802f28cef599df2021-09-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - PGP(i-13:0/a-15:0) 40V, Negative-QTOFsplash10-0f9e-4092540100-47a3633b16a90b46ceb22021-09-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - PGP(i-13:0/a-15:0) 10V, Positive-QTOFsplash10-0002-5100605900-2beb4e9897d959f2cb7d2021-09-24Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - PGP(i-13:0/a-15:0) 20V, Positive-QTOFsplash10-052b-9500574000-5c85e19999d7b5d7e78d2021-09-24Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - PGP(i-13:0/a-15:0) 40V, Positive-QTOFsplash10-0zfs-9585400000-c7e20dfc9ce91931582d2021-09-24Wishart 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 ID74878262
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound131823205
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 References
  1. Simons K, Toomre D: Lipid rafts and signal transduction. Nat Rev Mol Cell Biol. 2000 Oct;1(1):31-9. [PubMed:11413487 ]
  2. Watson AD: Thematic review series: systems biology approaches to metabolic and cardiovascular disorders. Lipidomics: a global approach to lipid analysis in biological systems. J Lipid Res. 2006 Oct;47(10):2101-11. Epub 2006 Aug 10. [PubMed:16902246 ]
  3. Sethi JK, Vidal-Puig AJ: Thematic review series: adipocyte biology. Adipose tissue function and plasticity orchestrate nutritional adaptation. J Lipid Res. 2007 Jun;48(6):1253-62. Epub 2007 Mar 20. [PubMed:17374880 ]
  4. Lingwood D, Simons K: Lipid rafts as a membrane-organizing principle. Science. 2010 Jan 1;327(5961):46-50. doi: 10.1126/science.1174621. [PubMed:20044567 ]
  5. Divecha N, Irvine RF: Phospholipid signaling. Cell. 1995 Jan 27;80(2):269-78. [PubMed:7834746 ]
  6. Cevc, Gregor (1993). Phospholipids Handbook. Marcel Dekker.
  7. Gunstone, Frank D., John L. Harwood, and Albert J. Dijkstra (2007). The lipid handbook with CD-ROM. CRC Press.