data_P5S
#
_chem_comp.id P5S
_chem_comp.name O-[(R)-{[(2R)-2,3-bis(octadecanoyloxy)propyl]oxy}(hydroxy)phosphoryl]-L-serine
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C42 H82 N O10 P"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms "phosphatidyl serine"
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2012-07-19
_chem_comp.pdbx_modified_date 2021-03-01
_chem_comp.pdbx_ambiguous_flag N
_chem_comp.pdbx_release_status REL
_chem_comp.pdbx_replaced_by ?
_chem_comp.pdbx_replaces ?
_chem_comp.formula_weight 792.075
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code P5S
_chem_comp.pdbx_model_coordinates_details ?
_chem_comp.pdbx_model_coordinates_missing_flag N
_chem_comp.pdbx_ideal_coordinates_details Corina
_chem_comp.pdbx_ideal_coordinates_missing_flag N
_chem_comp.pdbx_model_coordinates_db_code 4B2Z
_chem_comp.pdbx_subcomponent_list ?
_chem_comp.pdbx_processing_site EBI
#
loop_
_chem_comp_atom.comp_id
_chem_comp_atom.atom_id
_chem_comp_atom.alt_atom_id
_chem_comp_atom.type_symbol
_chem_comp_atom.charge
_chem_comp_atom.pdbx_align
_chem_comp_atom.pdbx_aromatic_flag
_chem_comp_atom.pdbx_leaving_atom_flag
_chem_comp_atom.pdbx_stereo_config
_chem_comp_atom.pdbx_backbone_atom_flag
_chem_comp_atom.pdbx_n_terminal_atom_flag
_chem_comp_atom.pdbx_c_terminal_atom_flag
_chem_comp_atom.model_Cartn_x
_chem_comp_atom.model_Cartn_y
_chem_comp_atom.model_Cartn_z
_chem_comp_atom.pdbx_model_Cartn_x_ideal
_chem_comp_atom.pdbx_model_Cartn_y_ideal
_chem_comp_atom.pdbx_model_Cartn_z_ideal
_chem_comp_atom.pdbx_component_atom_id
_chem_comp_atom.pdbx_component_comp_id
_chem_comp_atom.pdbx_ordinal
P5S C C C 0 1 N N N N N N 1.181 -11.291 51.093 -3.306 -3.081 4.930 C P5S 1
P5S N N N 0 1 N N N N N N 3.343 -10.093 50.974 -1.788 -1.551 3.807 N P5S 2
P5S O O O 0 1 N N N N N N 0.571 -12.246 50.570 -2.792 -2.731 5.965 O P5S 3
P5S C1 C1 C 0 1 N N N N N N 1.080 -15.876 45.710 -0.184 -3.075 -3.164 C1 P5S 4
P5S C2 C2 C 0 1 N N R N N N 1.663 -14.419 45.801 1.151 -3.494 -2.546 C2 P5S 5
P5S C3 C3 C 0 1 N N N N N N 2.889 -14.317 46.820 0.895 -4.459 -1.386 C3 P5S 6
P5S CA CA C 0 1 N N S N N N 2.144 -10.420 50.186 -2.681 -2.701 3.612 CA P5S 7
P5S CB CB C 0 1 N N N N N N 2.596 -10.985 48.830 -1.877 -3.885 3.069 CB P5S 8
P5S OG OG O 0 1 N N N N N N 3.611 -12.049 49.105 -1.381 -3.567 1.768 OG P5S 9
P5S P12 P12 P 0 1 N N N N N N 4.300 -12.609 47.890 -0.490 -4.586 0.896 P12 P5S 10
P5S O13 O13 O 0 1 N N N N N N 5.206 -11.500 47.436 0.690 -5.008 1.684 O13 P5S 11
P5S O15 O15 O 0 1 N N N N N N 5.032 -13.664 48.314 -1.371 -5.878 0.514 O15 P5S 12
P5S O16 O16 O 0 1 N N N N N N 3.405 -12.942 46.680 0.000 -3.852 -0.451 O16 P5S 13
P5S C17 C17 C 0 1 N N N N N N -1.191 -15.881 44.728 -2.261 -2.105 -2.512 C17 P5S 14
P5S O18 O18 O 0 1 N N N N N N -1.618 -16.351 45.781 -2.597 -2.196 -3.669 O18 P5S 15
P5S O19 O19 O 0 1 N N N N N N 0.205 -15.664 44.559 -1.043 -2.523 -2.132 O19 P5S 16
P5S C20 C20 C 0 1 N N N N N N -2.071 -15.186 43.677 -3.208 -1.520 -1.495 C20 P5S 17
P5S C21 C21 C 0 1 N N N N N N -2.874 -16.117 42.755 -4.516 -1.126 -2.185 C21 P5S 18
P5S C22 C22 C 0 1 N N N N N N -3.697 -16.892 43.830 -5.477 -0.533 -1.153 C22 P5S 19
P5S C23 C23 C 0 1 N N N N N N -3.457 -18.396 43.538 -6.785 -0.138 -1.842 C23 P5S 20
P5S C24 C24 C 0 1 N N N N N N -3.199 -18.657 42.005 -7.747 0.454 -0.810 C24 P5S 21
P5S C25 C25 C 0 1 N N N N N N -3.102 -20.231 41.932 -9.054 0.849 -1.499 C25 P5S 22
P5S C26 C26 C 0 1 N N N N N N -3.319 -20.888 40.512 -10.016 1.442 -0.467 C26 P5S 23
P5S C27 C27 C 0 1 N N N N N N -2.687 -22.339 40.555 -11.323 1.837 -1.156 C27 P5S 24
P5S C28 C28 C 0 1 N N N N N N -1.117 -22.286 40.747 -12.285 2.430 -0.124 C28 P5S 25
P5S C29 C29 C 0 1 N N N N N N -0.397 -22.383 39.345 -13.593 2.824 -0.813 C29 P5S 26
P5S C30 C30 C 0 1 N N N N N N 0.237 -23.806 39.118 -14.554 3.417 0.219 C30 P5S 27
P5S C31 C31 C 0 1 N N N N N N 0.098 -24.351 37.643 -15.862 3.812 -0.471 C31 P5S 28
P5S C32 C32 C 0 1 N N N N N N 0.169 -25.918 37.732 -16.824 4.405 0.561 C32 P5S 29
P5S C33 C33 C 0 1 N N N N N N 0.087 -26.634 36.354 -18.131 4.799 -0.128 C33 P5S 30
P5S C34 C34 C 0 1 N N N N N N 0.102 -28.161 36.597 -19.093 5.392 0.904 C34 P5S 31
P5S C35 C35 C 0 1 N N N N N N -0.188 -28.939 35.293 -20.401 5.787 0.215 C35 P5S 32
P5S C36 C36 C 0 1 N N N N N N -1.725 -29.054 35.102 -21.362 6.379 1.247 C36 P5S 33
P5S O37 O37 O 0 1 N N N N N N 0.658 -13.392 46.283 1.847 -2.319 -2.054 O37 P5S 34
P5S C38 C38 C 0 1 N N N N N N 0.357 -12.109 45.586 3.189 -2.359 -2.059 C38 P5S 35
P5S C39 C39 C 0 1 N N N N N N -0.555 -10.988 46.112 3.980 -1.176 -1.563 C39 P5S 36
P5S C40 C40 C 0 1 N N N N N N -1.476 -10.341 45.042 5.475 -1.479 -1.676 C40 P5S 37
P5S C41 C41 C 0 1 N N N N N N -2.441 -11.488 44.527 6.278 -0.278 -1.173 C41 P5S 38
P5S C42 C42 C 0 1 N N N N N N -3.476 -10.919 43.479 7.774 -0.581 -1.285 C42 P5S 39
P5S C43 C43 C 0 1 N N N N N N -3.859 -12.030 42.427 8.577 0.620 -0.782 C43 P5S 40
P5S C44 C44 C 0 1 N N N N N N -5.243 -12.658 42.779 10.072 0.317 -0.895 C44 P5S 41
P5S C45 C45 C 0 1 N N N N N N -5.204 -13.002 44.298 10.875 1.518 -0.391 C45 P5S 42
P5S C46 C46 C 0 1 N N N N N N -6.196 -12.166 45.097 12.371 1.215 -0.504 C46 P5S 43
P5S O47 O47 O 0 1 N N N N N N 0.963 -11.959 44.513 3.763 -3.343 -2.462 O47 P5S 44
P5S C48 C48 C 0 1 N N N N N N -6.758 -12.736 46.172 13.174 2.417 -0.000 C48 P5S 45
P5S C49 C49 C 0 1 N N N N N N -6.361 -12.343 47.589 14.669 2.114 -0.113 C49 P5S 46
P5S C50 C50 C 0 1 N N N N N N -5.757 -10.913 47.686 15.472 3.315 0.391 C50 P5S 47
P5S C51 C51 C 0 1 N N N N N N -6.905 -9.858 47.754 16.968 3.012 0.278 C51 P5S 48
P5S C52 C52 C 0 1 N N N N N N -6.435 -8.526 48.422 17.771 4.213 0.782 C52 P5S 49
P5S C53 C53 C 0 1 N N N N N N -5.376 -7.810 47.548 19.266 3.910 0.669 C53 P5S 50
P5S C54 C54 C 0 1 N N N N N N -5.147 -6.343 48.029 20.069 5.111 1.173 C54 P5S 51
P5S C55 C55 C 0 1 N N N N N N -3.928 -5.714 47.313 21.565 4.808 1.060 C55 P5S 52
P5S C56 C56 C 0 1 N N N N N N -3.442 -4.416 48.020 22.368 6.009 1.563 C56 P5S 53
P5S OXT OXT O 0 1 N N N N N N 1.158 -11.080 52.321 -4.431 -3.812 4.953 OXT P5S 54
P5S HN HN H 0 1 N N N N N N 3.967 -9.542 50.420 -2.305 -0.738 4.104 HN P5S 55
P5S HNA HNA H 0 1 N N N N N N 3.076 -9.577 51.788 -1.053 -1.771 4.462 HNA P5S 56
P5S H1 H1 H 0 1 N N N N N N 0.521 -16.160 46.614 -0.008 -2.321 -3.932 H1 P5S 57
P5S H1A H1A H 0 1 N N N N N N 1.859 -16.626 45.510 -0.666 -3.944 -3.612 H1A P5S 58
P5S H2 H2 H 0 1 N N N N N N 2.024 -14.128 44.804 1.762 -3.989 -3.302 H2 P5S 59
P5S H3 H3 H 0 1 N N N N N N 2.548 -14.497 47.850 0.453 -5.378 -1.769 H3 P5S 60
P5S H3A H3A H 0 1 N N N N N N 3.668 -15.048 46.559 1.838 -4.688 -0.890 H3A P5S 61
P5S HA HA H 0 1 N N N N N N 1.612 -9.480 49.980 -3.463 -2.437 2.901 HA P5S 62
P5S HB HB H 0 1 N N N N N N 1.736 -11.415 48.296 -1.040 -4.092 3.737 HB P5S 63
P5S HBA HBA H 0 1 N N N N N N 3.044 -10.186 48.220 -2.520 -4.763 3.009 HBA P5S 64
P5S HO15 HO15 H 0 0 N N N N N N 5.957 -13.463 48.228 -2.162 -5.675 -0.004 HO15 P5S 65
P5S H20 H20 H 0 1 N N N N N N -2.785 -14.540 44.209 -3.414 -2.261 -0.723 H20 P5S 66
P5S H20A H20A H 0 0 N N N N N N -1.417 -14.567 43.045 -2.756 -0.639 -1.042 H20A P5S 67
P5S H21 H21 H 0 1 N N N N N N -3.523 -15.555 42.068 -4.310 -0.385 -2.957 H21 P5S 68
P5S H21A H21A H 0 0 N N N N N N -2.220 -16.786 42.177 -4.968 -2.008 -2.638 H21A P5S 69
P5S H22 H22 H 0 1 N N N N N N -3.345 -16.636 44.840 -5.683 -1.274 -0.380 H22 P5S 70
P5S H22A H22A H 0 0 N N N N N N -4.766 -16.650 43.742 -5.025 0.349 -0.699 H22A P5S 71
P5S H23 H23 H 0 1 N N N N N N -2.581 -18.735 44.110 -6.579 0.602 -2.614 H23 P5S 72
P5S H23A H23A H 0 0 N N N N N N -4.343 -18.966 43.853 -7.237 -1.020 -2.295 H23A P5S 73
P5S H24 H24 H 0 1 N N N N N N -4.033 -18.282 41.393 -7.952 -0.286 -0.037 H24 P5S 74
P5S H24A H24A H 0 0 N N N N N N -2.261 -18.186 41.675 -7.294 1.336 -0.356 H24A P5S 75
P5S H25 H25 H 0 1 N N N N N N -2.101 -20.520 42.284 -8.849 1.590 -2.272 H25 P5S 76
P5S H25A H25A H 0 0 N N N N N N -3.863 -20.644 42.611 -9.507 -0.033 -1.952 H25A P5S 77
P5S H26 H26 H 0 1 N N N N N N -4.394 -20.954 40.289 -10.221 0.701 0.306 H26 P5S 78
P5S H26A H26A H 0 0 N N N N N N -2.821 -20.284 39.739 -9.564 2.324 -0.014 H26A P5S 79
P5S H27 H27 H 0 1 N N N N N N -3.130 -22.897 41.393 -11.118 2.577 -1.929 H27 P5S 80
P5S H27A H27A H 0 0 N N N N N N -2.914 -22.855 39.610 -11.776 0.955 -1.610 H27A P5S 81
P5S H28 H28 H 0 1 N N N N N N -0.841 -21.338 41.233 -12.491 1.689 0.648 H28 P5S 82
P5S H28A H28A H 0 0 N N N N N N -0.799 -23.128 41.379 -11.833 3.312 0.329 H28A P5S 83
P5S H29 H29 H 0 1 N N N N N N -1.133 -22.189 38.551 -13.387 3.565 -1.586 H29 P5S 84
P5S H29A H29A H 0 0 N N N N N N 0.399 -21.626 39.299 -14.045 1.942 -1.267 H29A P5S 85
P5S H30 H30 H 0 1 N N N N N N 1.307 -23.750 39.365 -14.760 2.676 0.991 H30 P5S 86
P5S H30A H30A H 0 0 N N N N N N -0.259 -24.516 39.796 -14.102 4.299 0.672 H30A P5S 87
P5S H31 H31 H 0 1 N N N N N N -0.865 -24.039 37.213 -15.656 4.552 -1.243 H31 P5S 88
P5S H31A H31A H 0 0 N N N N N N 0.919 -23.969 37.019 -16.314 2.930 -0.924 H31A P5S 89
P5S H32 H32 H 0 1 N N N N N N 1.121 -26.195 38.209 -17.029 3.664 1.334 H32 P5S 90
P5S H32A H32A H 0 0 N N N N N N -0.668 -26.267 38.354 -16.371 5.286 1.015 H32A P5S 91
P5S H33 H33 H 0 1 N N N N N N -0.843 -26.348 35.841 -17.926 5.540 -0.900 H33 P5S 92
P5S H33A H33A H 0 0 N N N N N N 0.950 -26.348 35.734 -18.584 3.917 -0.581 H33A P5S 93
P5S H34 H34 H 0 1 N N N N N N 1.092 -28.454 36.977 -19.299 4.651 1.677 H34 P5S 94
P5S H34A H34A H 0 0 N N N N N N -0.666 -28.413 37.343 -18.641 6.274 1.358 H34A P5S 95
P5S H35 H35 H 0 1 N N N N N N 0.250 -28.403 34.439 -20.195 6.528 -0.558 H35 P5S 96
P5S H35A H35A H 0 0 N N N N N N 0.251 -29.945 35.359 -20.853 4.905 -0.238 H35A P5S 97
P5S H36 H36 H 0 1 N N N N N N -1.940 -29.607 34.175 -22.294 6.661 0.756 H36 P5S 98
P5S H36A H36A H 0 0 N N N N N N -2.162 -29.590 35.958 -21.568 5.639 2.020 H36A P5S 99
P5S H36B H36B H 0 0 N N N N N N -2.163 -28.047 35.038 -20.910 7.261 1.700 H36B P5S 100
P5S H39 H39 H 0 1 N N N N N N -1.193 -11.409 46.903 3.740 -0.300 -2.166 H39 P5S 101
P5S H39A H39A H 0 0 N N N N N N 0.083 -10.199 46.537 3.726 -0.980 -0.521 H39A P5S 102
P5S H40 H40 H 0 1 N N N N N N -2.061 -9.524 45.488 5.715 -2.355 -1.073 H40 P5S 103
P5S H40A H40A H 0 0 N N N N N N -0.874 -9.948 44.209 5.729 -1.675 -2.718 H40A P5S 104
P5S H41 H41 H 0 1 N N N N N N -1.841 -12.277 44.050 6.039 0.598 -1.776 H41 P5S 105
P5S H41A H41A H 0 0 N N N N N N -2.989 -11.910 45.383 6.025 -0.082 -0.131 H41A P5S 106
P5S H42 H42 H 0 1 N N N N N N -4.384 -10.591 44.007 8.014 -1.457 -0.682 H42 P5S 107
P5S H42A H42A H 0 0 N N N N N N -3.027 -10.062 42.955 8.028 -0.776 -2.327 H42A P5S 108
P5S H43 H43 H 0 1 N N N N N N -3.910 -11.578 41.425 8.337 1.496 -1.385 H43 P5S 109
P5S H43A H43A H 0 0 N N N N N N -3.091 -12.817 42.436 8.323 0.816 0.260 H43A P5S 110
P5S H44 H44 H 0 1 N N N N N N -6.049 -11.938 42.574 10.312 -0.559 -0.292 H44 P5S 111
P5S H44A H44A H 0 0 N N N N N N -5.407 -13.571 42.187 10.326 0.122 -1.936 H44A P5S 112
P5S H45 H45 H 0 1 N N N N N N -5.450 -14.066 44.428 10.636 2.394 -0.994 H45 P5S 113
P5S H45A H45A H 0 0 N N N N N N -4.190 -12.811 44.680 10.622 1.714 0.651 H45A P5S 114
P5S H46 H46 H 0 1 N N N N N N -5.667 -11.265 45.440 12.611 0.340 0.099 H46 P5S 115
P5S H46A H46A H 0 0 N N N N N N -7.009 -11.876 44.414 12.624 1.020 -1.546 H46A P5S 116
P5S H48 H48 H 0 1 N N N N N N -7.839 -12.549 46.091 12.934 3.292 -0.603 H48 P5S 117
P5S H48A H48A H 0 0 N N N N N N -6.565 -13.815 46.085 12.920 2.612 1.042 H48A P5S 118
P5S H49 H49 H 0 1 N N N N N N -7.256 -12.388 48.227 14.909 1.238 0.490 H49 P5S 119
P5S H49A H49A H 0 0 N N N N N N -5.614 -13.063 47.954 14.923 1.918 -1.155 H49A P5S 120
P5S H50 H50 H 0 1 N N N N N N -5.138 -10.839 48.593 15.233 4.191 -0.212 H50 P5S 121
P5S H50A H50A H 0 0 N N N N N N -5.134 -10.719 46.800 15.219 3.510 1.433 H50A P5S 122
P5S H51 H51 H 0 1 N N N N N N -7.249 -9.641 46.732 17.208 2.136 0.881 H51 P5S 123
P5S H51A H51A H 0 0 N N N N N N -7.737 -10.275 48.340 17.221 2.816 -0.764 H51A P5S 124
P5S H52 H52 H 0 1 N N N N N N -7.303 -7.863 48.551 17.531 5.089 0.179 H52 P5S 125
P5S H52A H52A H 0 0 N N N N N N -5.997 -8.752 49.405 17.517 4.408 1.824 H52A P5S 126
P5S H53 H53 H 0 1 N N N N N N -4.426 -8.361 47.612 19.506 3.034 1.272 H53 P5S 127
P5S H53A H53A H 0 0 N N N N N N -5.722 -7.796 46.504 19.520 3.714 -0.373 H53A P5S 128
P5S H54 H54 H 0 1 N N N N N N -6.044 -5.746 47.806 19.830 5.987 0.570 H54 P5S 129
P5S H54A H54A H 0 0 N N N N N N -4.967 -6.343 49.114 19.816 5.306 2.214 H54A P5S 130
P5S H55 H55 H 0 1 N N N N N N -3.105 -6.444 47.306 21.805 3.932 1.663 H55 P5S 131
P5S H55A H55A H 0 0 N N N N N N -4.211 -5.470 46.278 21.818 4.613 0.018 H55A P5S 132
P5S H56 H56 H 0 1 N N N N N N -2.577 -4.005 47.479 23.433 5.793 1.483 H56 P5S 133
P5S H56A H56A H 0 0 N N N N N N -4.256 -3.676 48.027 22.128 6.885 0.960 H56A P5S 134
P5S H56B H56B H 0 0 N N N N N N -3.150 -4.649 49.054 22.114 6.205 2.605 H56B P5S 135
P5S HXT HXT H 0 1 N N N N N N 0.624 -11.741 52.746 -4.793 -4.034 5.822 HXT P5S 136
#
loop_
_chem_comp_bond.comp_id
_chem_comp_bond.atom_id_1
_chem_comp_bond.atom_id_2
_chem_comp_bond.value_order
_chem_comp_bond.pdbx_aromatic_flag
_chem_comp_bond.pdbx_stereo_config
_chem_comp_bond.pdbx_ordinal
P5S CA C SING N N 1
P5S O C DOUB N N 2
P5S C OXT SING N N 3
P5S CA N SING N N 4
P5S N HN SING N N 5
P5S N HNA SING N N 6
P5S O19 C1 SING N N 7
P5S C1 C2 SING N N 8
P5S C1 H1 SING N N 9
P5S C1 H1A SING N N 10
P5S C2 O37 SING N N 11
P5S C2 C3 SING N N 12
P5S C2 H2 SING N N 13
P5S O16 C3 SING N N 14
P5S C3 H3 SING N N 15
P5S C3 H3A SING N N 16
P5S CB CA SING N N 17
P5S CA HA SING N N 18
P5S CB OG SING N N 19
P5S CB HB SING N N 20
P5S CB HBA SING N N 21
P5S P12 OG SING N N 22
P5S O16 P12 SING N N 23
P5S O13 P12 DOUB N N 24
P5S P12 O15 SING N N 25
P5S O15 HO15 SING N N 26
P5S C20 C17 SING N N 27
P5S O19 C17 SING N N 28
P5S C17 O18 DOUB N N 29
P5S C21 C20 SING N N 30
P5S C20 H20 SING N N 31
P5S C20 H20A SING N N 32
P5S C21 C22 SING N N 33
P5S C21 H21 SING N N 34
P5S C21 H21A SING N N 35
P5S C23 C22 SING N N 36
P5S C22 H22 SING N N 37
P5S C22 H22A SING N N 38
P5S C24 C23 SING N N 39
P5S C23 H23 SING N N 40
P5S C23 H23A SING N N 41
P5S C25 C24 SING N N 42
P5S C24 H24 SING N N 43
P5S C24 H24A SING N N 44
P5S C26 C25 SING N N 45
P5S C25 H25 SING N N 46
P5S C25 H25A SING N N 47
P5S C26 C27 SING N N 48
P5S C26 H26 SING N N 49
P5S C26 H26A SING N N 50
P5S C27 C28 SING N N 51
P5S C27 H27 SING N N 52
P5S C27 H27A SING N N 53
P5S C29 C28 SING N N 54
P5S C28 H28 SING N N 55
P5S C28 H28A SING N N 56
P5S C30 C29 SING N N 57
P5S C29 H29 SING N N 58
P5S C29 H29A SING N N 59
P5S C31 C30 SING N N 60
P5S C30 H30 SING N N 61
P5S C30 H30A SING N N 62
P5S C31 C32 SING N N 63
P5S C31 H31 SING N N 64
P5S C31 H31A SING N N 65
P5S C33 C32 SING N N 66
P5S C32 H32 SING N N 67
P5S C32 H32A SING N N 68
P5S C33 C34 SING N N 69
P5S C33 H33 SING N N 70
P5S C33 H33A SING N N 71
P5S C35 C34 SING N N 72
P5S C34 H34 SING N N 73
P5S C34 H34A SING N N 74
P5S C36 C35 SING N N 75
P5S C35 H35 SING N N 76
P5S C35 H35A SING N N 77
P5S C36 H36 SING N N 78
P5S C36 H36A SING N N 79
P5S C36 H36B SING N N 80
P5S C38 O37 SING N N 81
P5S O47 C38 DOUB N N 82
P5S C38 C39 SING N N 83
P5S C40 C39 SING N N 84
P5S C39 H39 SING N N 85
P5S C39 H39A SING N N 86
P5S C41 C40 SING N N 87
P5S C40 H40 SING N N 88
P5S C40 H40A SING N N 89
P5S C42 C41 SING N N 90
P5S C41 H41 SING N N 91
P5S C41 H41A SING N N 92
P5S C43 C42 SING N N 93
P5S C42 H42 SING N N 94
P5S C42 H42A SING N N 95
P5S C43 C44 SING N N 96
P5S C43 H43 SING N N 97
P5S C43 H43A SING N N 98
P5S C44 C45 SING N N 99
P5S C44 H44 SING N N 100
P5S C44 H44A SING N N 101
P5S C45 C46 SING N N 102
P5S C45 H45 SING N N 103
P5S C45 H45A SING N N 104
P5S C46 C48 SING N N 105
P5S C46 H46 SING N N 106
P5S C46 H46A SING N N 107
P5S C48 C49 SING N N 108
P5S C48 H48 SING N N 109
P5S C48 H48A SING N N 110
P5S C49 C50 SING N N 111
P5S C49 H49 SING N N 112
P5S C49 H49A SING N N 113
P5S C50 C51 SING N N 114
P5S C50 H50 SING N N 115
P5S C50 H50A SING N N 116
P5S C51 C52 SING N N 117
P5S C51 H51 SING N N 118
P5S C51 H51A SING N N 119
P5S C53 C52 SING N N 120
P5S C52 H52 SING N N 121
P5S C52 H52A SING N N 122
P5S C53 C54 SING N N 123
P5S C53 H53 SING N N 124
P5S C53 H53A SING N N 125
P5S C55 C54 SING N N 126
P5S C54 H54 SING N N 127
P5S C54 H54A SING N N 128
P5S C55 C56 SING N N 129
P5S C55 H55 SING N N 130
P5S C55 H55A SING N N 131
P5S C56 H56 SING N N 132
P5S C56 H56A SING N N 133
P5S C56 H56B SING N N 134
P5S OXT HXT SING N N 135
#
loop_
_pdbx_chem_comp_descriptor.comp_id
_pdbx_chem_comp_descriptor.type
_pdbx_chem_comp_descriptor.program
_pdbx_chem_comp_descriptor.program_version
_pdbx_chem_comp_descriptor.descriptor
P5S InChI InChI 1.03 InChI=1S/C42H82NO10P/c1-3-5-7-9-11-13-15-17-19-21-23-25-27-29-31-33-40(44)50-35-38(36-51-54(48,49)52-37-39(43)42(46)47)53-41(45)34-32-30-28-26-24-22-20-18-16-14-12-10-8-6-4-2/h38-39H,3-37,43H2,1-2H3,(H,46,47)(H,48,49)/t38-,39+/m1/s1
P5S InChIKey InChI 1.03 TZCPCKNHXULUIY-RGULYWFUSA-N
P5S SMILES ACDLabs 12.01 O=C(OC(COP(=O)(OCC(C(=O)O)N)O)COC(=O)CCCCCCCCCCCCCCCCC)CCCCCCCCCCCCCCCCC
P5S SMILES_CANONICAL CACTVS 3.370 CCCCCCCCCCCCCCCCCC(=O)OC[C@H](CO[P](O)(=O)OC[C@H](N)C(O)=O)OC(=O)CCCCCCCCCCCCCCCCC
P5S SMILES CACTVS 3.370 CCCCCCCCCCCCCCCCCC(=O)OC[CH](CO[P](O)(=O)OC[CH](N)C(O)=O)OC(=O)CCCCCCCCCCCCCCCCC
P5S SMILES_CANONICAL "OpenEye OEToolkits" 1.7.6 CCCCCCCCCCCCCCCCCC(=O)OC[C@H](COP(=O)(O)OC[C@@H](C(=O)O)N)OC(=O)CCCCCCCCCCCCCCCCC
P5S SMILES "OpenEye OEToolkits" 1.7.6 CCCCCCCCCCCCCCCCCC(=O)OCC(COP(=O)(O)OCC(C(=O)O)N)OC(=O)CCCCCCCCCCCCCCCCC
#
loop_
_pdbx_chem_comp_identifier.comp_id
_pdbx_chem_comp_identifier.type
_pdbx_chem_comp_identifier.program
_pdbx_chem_comp_identifier.program_version
_pdbx_chem_comp_identifier.identifier
P5S "SYSTEMATIC NAME" ACDLabs 12.01 O-[(R)-{[(2R)-2,3-bis(octadecanoyloxy)propyl]oxy}(hydroxy)phosphoryl]-L-serine
P5S "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.7.6 "(2S)-2-azanyl-3-[[(2R)-2,3-di(octadecanoyloxy)propoxy]-oxidanyl-phosphoryl]oxy-propanoic acid"
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
P5S 'Create component' 2012-07-19 EBI
P5S 'Initial release' 2013-06-26 RCSB
P5S 'Modify synonyms' 2021-03-01 PDBE
#
_pdbx_chem_comp_synonyms.ordinal 1
_pdbx_chem_comp_synonyms.comp_id P5S
_pdbx_chem_comp_synonyms.name "phosphatidyl serine"
_pdbx_chem_comp_synonyms.provenance ?
_pdbx_chem_comp_synonyms.type ?
#
_pdbe_chem_comp_drugbank_details.comp_id P5S
_pdbe_chem_comp_drugbank_details.drugbank_id DB00144
_pdbe_chem_comp_drugbank_details.type 'small molecule'
_pdbe_chem_comp_drugbank_details.name 'Phosphatidyl serine'
_pdbe_chem_comp_drugbank_details.description
'Phosphatidyl serine (PS) is a phospholipid nutrient found in fish, green leafy vegetables, soybeans and rice, and is essential for the normal functioning of neuronal cell membranes and activates Protein kinase C (PKC) which has been shown to be involved in memory function. In apoptosis, phosphatidyl serine is transferred to the outer leaflet of the plasma membrane. This is part of the process by which the cell is targeted for phagocytosis. PS has been shown to slow cognitive decline in animal models. PS has been investigated in a small number of double-blind placebo trials and has been shown to increase memory performance in the elderly. Because of the potentail cognitive benefits of phosphatidylserine, the substance is sold as a dietary supplement to people who believe they can benefit from an increased intake.  The dietary supplement was originally processed from bovine sources however Prion disease scares in the 1990s outlawed this process, and a soy-based alternative was adopted.'
_pdbe_chem_comp_drugbank_details.cas_number 1446756-47-3
_pdbe_chem_comp_drugbank_details.mechanism_of_action
"Cholinergic hypofunction is thought to account in part for the cognitive deficits found in Alzheimer's disease. The most commonly used drugs for the treatment of Alzheimer's disease are reversible acetylcholinesterase inhibitors. The rationale of these drugs is to increase acetylcholine levels in the brains of Alzheimer's patients, and they may be somewhat effective in some cases. Phosphatidylserine restores acetylcholine release in aging humans by maintaining an adequate supply of the molecule and is able to increase the availability of endogenous choline for de novo acetylcholine synthesis. The hippocampus of the brain is believed to be important for cognitive processes and is affected in those with Alzheimer's disease. The dendritic spines of pyramidal cells, the post-synaptic target of the excitatory input to the hippocampus, have been proposed as a substrate for information storage. Age-dependent dendritic spine loss in pyramidal neurons has been reported in the human brain, and the extent of synaptic loss appears to correlate with the degree of cognitive impairment. Phosphatidylserine treatment prevents the age-related reduction in dendritic spine density in rat hippocampus. Protein kinase C facilitation of acetylcholine release has been reported in rats. Phosphatidylserine was found to restore protein kinase C activity in aging rats. Stimulation of calcium uptake by brain synaptosomes and activation of protein kinase C are yet other speculative mechanisms of phosphatidylserine's putative cognition-enhancing action."
#
loop_
_pdbe_chem_comp_synonyms.comp_id
_pdbe_chem_comp_synonyms.name
_pdbe_chem_comp_synonyms.provenance
_pdbe_chem_comp_synonyms.type
P5S 'phosphatidyl serine' wwPDB ?
P5S 'Phosphatidyl serine' DrugBank ?
P5S Phosphatidylserine DrugBank ?
P5S PS DrugBank ?
P5S 'LifeExtension PS Caps' DrugBank 'International brand'
#
loop_
_pdbe_chem_comp_drugbank_targets.comp_id
_pdbe_chem_comp_drugbank_targets.drugbank_id
_pdbe_chem_comp_drugbank_targets.name
_pdbe_chem_comp_drugbank_targets.organism
_pdbe_chem_comp_drugbank_targets.uniprot_id
_pdbe_chem_comp_drugbank_targets.pharmacologically_active
_pdbe_chem_comp_drugbank_targets.ordinal
P5S DB00144 'Phosphatidylserine decarboxylase proenzyme, mitochondrial' Humans Q9UG56 unknown 1
P5S DB00144 'Scavenger receptor class B member 1' Humans Q8WTV0 unknown 2
P5S DB00144 'Protein kinase C alpha type' Humans P17252 unknown 3
P5S DB00144 'Phosphatidylserine synthase 1' Humans P48651 unknown 4
P5S DB00144 'Diacylglycerol kinase gamma' Humans P49619 unknown 5
P5S DB00144 'Diacylglycerol kinase delta' Humans Q16760 unknown 6
P5S DB00144 'Phosphatidylserine synthase 2' Humans Q9BVG9 unknown 7
P5S DB00144 'Sphingomyelin phosphodiesterase 4' Humans Q9NXE4 unknown 8
P5S DB00144 'Sphingomyelin phosphodiesterase 3' Humans Q9NY59 unknown 9
P5S DB00144 'Phospholipid-transporting ATPase IA' Humans Q9Y2Q0 unknown 10
#
loop_
_software.name
_software.version
_software.description
rdkit 2023.09.6 'Core functionality.'
pdbeccdutils 0.8.6 'Wrapper to provide 2D templates and molecular fragments.'
#
loop_
_pdbe_chem_comp_atom_depiction.comp_id
_pdbe_chem_comp_atom_depiction.atom_id
_pdbe_chem_comp_atom_depiction.element
_pdbe_chem_comp_atom_depiction.model_Cartn_x
_pdbe_chem_comp_atom_depiction.model_Cartn_y
_pdbe_chem_comp_atom_depiction.pdbx_ordinal
P5S C C 5.104 -12.375 1
P5S N N 3.805 -10.125 2
P5S O O 3.805 -13.125 3
P5S C1 C 12.899 -7.875 4
P5S C2 C 12.899 -9.375 5
P5S C3 C 11.600 -10.125 6
P5S CA C 5.104 -10.875 7
P5S CB C 6.404 -10.125 8
P5S OG O 7.702 -10.875 9
P5S P12 P 9.002 -10.125 10
P5S O13 O 8.252 -8.826 11
P5S O15 O 9.752 -11.424 12
P5S O16 O 10.301 -9.375 13
P5S C17 C 14.198 -5.625 14
P5S O18 O 12.899 -4.875 15
P5S O19 O 14.198 -7.125 16
P5S C20 C 15.497 -4.875 17
P5S C21 C 15.497 -3.375 18
P5S C22 C 16.796 -2.625 19
P5S C23 C 16.796 -1.125 20
P5S C24 C 18.095 -0.375 21
P5S C25 C 18.095 1.125 22
P5S C26 C 19.394 1.875 23
P5S C27 C 19.394 3.375 24
P5S C28 C 20.693 4.125 25
P5S C29 C 20.693 5.625 26
P5S C30 C 21.992 6.375 27
P5S C31 C 21.992 7.875 28
P5S C32 C 23.291 8.625 29
P5S C33 C 23.291 10.125 30
P5S C34 C 24.590 10.875 31
P5S C35 C 24.590 12.375 32
P5S C36 C 25.889 13.125 33
P5S O37 O 14.198 -10.125 34
P5S C38 C 15.497 -9.375 35
P5S C39 C 16.796 -10.125 36
P5S C40 C 18.095 -9.375 37
P5S C41 C 19.394 -10.125 38
P5S C42 C 20.693 -9.375 39
P5S C43 C 21.992 -10.125 40
P5S C44 C 23.291 -9.375 41
P5S C45 C 24.590 -10.125 42
P5S C46 C 25.889 -9.375 43
P5S O47 O 15.497 -7.875 44
P5S C48 C 27.188 -10.125 45
P5S C49 C 28.487 -9.375 46
P5S C50 C 29.786 -10.125 47
P5S C51 C 31.085 -9.375 48
P5S C52 C 32.384 -10.125 49
P5S C53 C 33.683 -9.375 50
P5S C54 C 34.982 -10.125 51
P5S C55 C 36.281 -9.375 52
P5S C56 C 37.580 -10.125 53
P5S OXT O 6.404 -13.125 54
#
loop_
_pdbe_chem_comp_bond_depiction.comp_id
_pdbe_chem_comp_bond_depiction.atom_id_1
_pdbe_chem_comp_bond_depiction.atom_id_2
_pdbe_chem_comp_bond_depiction.value_order
_pdbe_chem_comp_bond_depiction.bond_dir
_pdbe_chem_comp_bond_depiction.pdbx_ordinal
P5S CA C SINGLE NONE 1
P5S O C DOUBLE NONE 2
P5S C OXT SINGLE NONE 3
P5S CA N SINGLE BEGINWEDGE 4
P5S O19 C1 SINGLE NONE 5
P5S C2 C1 SINGLE BEGINWEDGE 6
P5S C2 O37 SINGLE NONE 7
P5S C2 C3 SINGLE NONE 8
P5S O16 C3 SINGLE NONE 9
P5S CB CA SINGLE NONE 10
P5S CB OG SINGLE NONE 11
P5S P12 OG SINGLE NONE 12
P5S O16 P12 SINGLE NONE 13
P5S O13 P12 DOUBLE NONE 14
P5S P12 O15 SINGLE BEGINWEDGE 15
P5S C20 C17 SINGLE NONE 16
P5S O19 C17 SINGLE NONE 17
P5S C17 O18 DOUBLE NONE 18
P5S C21 C20 SINGLE NONE 19
P5S C21 C22 SINGLE NONE 20
P5S C23 C22 SINGLE NONE 21
P5S C24 C23 SINGLE NONE 22
P5S C25 C24 SINGLE NONE 23
P5S C26 C25 SINGLE NONE 24
P5S C26 C27 SINGLE NONE 25
P5S C27 C28 SINGLE NONE 26
P5S C29 C28 SINGLE NONE 27
P5S C30 C29 SINGLE NONE 28
P5S C31 C30 SINGLE NONE 29
P5S C31 C32 SINGLE NONE 30
P5S C33 C32 SINGLE NONE 31
P5S C33 C34 SINGLE NONE 32
P5S C35 C34 SINGLE NONE 33
P5S C36 C35 SINGLE NONE 34
P5S C38 O37 SINGLE NONE 35
P5S O47 C38 DOUBLE NONE 36
P5S C38 C39 SINGLE NONE 37
P5S C40 C39 SINGLE NONE 38
P5S C41 C40 SINGLE NONE 39
P5S C42 C41 SINGLE NONE 40
P5S C43 C42 SINGLE NONE 41
P5S C43 C44 SINGLE NONE 42
P5S C44 C45 SINGLE NONE 43
P5S C45 C46 SINGLE NONE 44
P5S C46 C48 SINGLE NONE 45
P5S C48 C49 SINGLE NONE 46
P5S C49 C50 SINGLE NONE 47
P5S C50 C51 SINGLE NONE 48
P5S C51 C52 SINGLE NONE 49
P5S C53 C52 SINGLE NONE 50
P5S C53 C54 SINGLE NONE 51
P5S C55 C54 SINGLE NONE 52
P5S C55 C56 SINGLE NONE 53
#
loop_
_pdbe_chem_comp_substructure.comp_id
_pdbe_chem_comp_substructure.substructure_name
_pdbe_chem_comp_substructure.id
_pdbe_chem_comp_substructure.substructure_type
_pdbe_chem_comp_substructure.substructure_smiles
_pdbe_chem_comp_substructure.substructure_inchis
_pdbe_chem_comp_substructure.substructure_inchikeys
P5S peptide F1 fragment NCC=O InChI=1S/C2H5NO/c3-1-2-4/h2H,1,3H2 LYIIBVSRGJSHAV-UHFFFAOYSA-N
P5S phosphate F2 fragment O=P(O)(O)O InChI=1S/H3O4P/c1-5(2,3)4/h(H3,1,2,3,4) NBIIXXVUZAFLBC-UHFFFAOYSA-N
#
loop_
_pdbe_chem_comp_substructure_mapping.comp_id
_pdbe_chem_comp_substructure_mapping.atom_id
_pdbe_chem_comp_substructure_mapping.substructure_id
_pdbe_chem_comp_substructure_mapping.substructure_ordinal
P5S O F1 1
P5S C F1 1
P5S CA F1 1
P5S N F1 1
P5S OG F2 1
P5S P12 F2 1
P5S O13 F2 1
P5S O16 F2 1
P5S O15 F2 1
#
_pdbe_chem_comp_rdkit_properties.comp_id P5S
_pdbe_chem_comp_rdkit_properties.exactmw 791.568
_pdbe_chem_comp_rdkit_properties.amw 792.089
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 11
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 4
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 46
_pdbe_chem_comp_rdkit_properties.NumHBD 3
_pdbe_chem_comp_rdkit_properties.NumHBA 11
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 54
_pdbe_chem_comp_rdkit_properties.NumAtoms 136
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 12
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 0
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.929
_pdbe_chem_comp_rdkit_properties.NumRings 0
_pdbe_chem_comp_rdkit_properties.NumAromaticRings 0
_pdbe_chem_comp_rdkit_properties.NumAliphaticRings 0
_pdbe_chem_comp_rdkit_properties.NumSaturatedRings 0
_pdbe_chem_comp_rdkit_properties.NumHeterocycles 0
_pdbe_chem_comp_rdkit_properties.NumAromaticHeterocycles 0
_pdbe_chem_comp_rdkit_properties.NumSaturatedHeterocycles 0
_pdbe_chem_comp_rdkit_properties.NumAliphaticHeterocycles 0
_pdbe_chem_comp_rdkit_properties.NumSpiroAtoms 0
_pdbe_chem_comp_rdkit_properties.NumBridgeheadAtoms 0
_pdbe_chem_comp_rdkit_properties.NumAtomStereoCenters 3
_pdbe_chem_comp_rdkit_properties.NumUnspecifiedAtomStereoCenters 0
_pdbe_chem_comp_rdkit_properties.labuteASA 444.616
_pdbe_chem_comp_rdkit_properties.tpsa 171.680
_pdbe_chem_comp_rdkit_properties.CrippenClogP 11.510
_pdbe_chem_comp_rdkit_properties.CrippenMR 217.271
_pdbe_chem_comp_rdkit_properties.chi0v 26.871
_pdbe_chem_comp_rdkit_properties.chi1v 13.956
_pdbe_chem_comp_rdkit_properties.chi2v 3.838
_pdbe_chem_comp_rdkit_properties.chi3v 3.838
_pdbe_chem_comp_rdkit_properties.chi4v 1.963
_pdbe_chem_comp_rdkit_properties.chi0n 107.977
_pdbe_chem_comp_rdkit_properties.chi1n 53.206
_pdbe_chem_comp_rdkit_properties.chi2n 3.208
_pdbe_chem_comp_rdkit_properties.chi3n 3.208
_pdbe_chem_comp_rdkit_properties.chi4n 1.533
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -1.520
_pdbe_chem_comp_rdkit_properties.kappa1 7.806
_pdbe_chem_comp_rdkit_properties.kappa2 38.359
_pdbe_chem_comp_rdkit_properties.kappa3 37.406
_pdbe_chem_comp_rdkit_properties.Phi 5.545
#
loop_
_pdbe_chem_comp_external_mappings.comp_id
_pdbe_chem_comp_external_mappings.source
_pdbe_chem_comp_external_mappings.resource
_pdbe_chem_comp_external_mappings.resource_id
P5S UniChem ChEMBL CHEMBL4297669
P5S UniChem DrugBank DB00144
P5S UniChem ChEBI 84519
P5S UniChem ZINC ZINC000085588270
P5S UniChem fdasrs 394XK0IH40
P5S UniChem HMDB HMDB0012378
P5S UniChem MetaboLights MTBLC84519
P5S UniChem BRENDA 257311
P5S UniChem ChemicalBook CB1190649
P5S UniChem ChemicalBook CB91236193
P5S UniChem DailyMed 'PHOSPHATIDYL SERINE'
P5S UniChem ClinicalTrials 'PHOSPHATIDYL SERINE'
P5S UniChem rxnorm PHOSPHATIDYLSERINE
P5S UniChem 'Probes And Drugs' PD143917
P5S UniChem Nikkaji J1.757.189C
P5S UniChem SureChEMBL SCHEMBL24649
P5S UniChem PubChem 91746197
P5S UniChem PubChem 9547096
#