data_LPS # _chem_comp.id LPS _chem_comp.name "O-{HYDROXY[((2R)-2-HYDROXY-3-{[(1S)-1-HYDROXYPENTADECYL]OXY}PROPYL)OXY]PHOSPHORYL}-L-SERINE" _chem_comp.type "L-PEPTIDE LINKING" _chem_comp.pdbx_type ATOMP _chem_comp.formula "C21 H44 N O9 P" _chem_comp.mon_nstd_parent_comp_id SER _chem_comp.pdbx_synonyms LYSOPHOSPHOTIDYLSERINE _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2003-02-21 _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 485.549 _chem_comp.one_letter_code S _chem_comp.three_letter_code LPS _chem_comp.pdbx_model_coordinates_details ? _chem_comp.pdbx_model_coordinates_missing_flag N _chem_comp.pdbx_ideal_coordinates_details ? _chem_comp.pdbx_ideal_coordinates_missing_flag N _chem_comp.pdbx_model_coordinates_db_code 1NL2 _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site RCSB # # 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.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 LPS OT2 OT2 O 0 1 N N N 5.676 31.287 131.997 -1.173 -0.921 -12.483 OT2 LPS 1 LPS C C C 0 1 N N N 4.504 31.572 131.622 -0.516 0.135 -11.979 C LPS 2 LPS OT1 OT1 O 0 1 N N N 4.204 32.577 130.930 -0.702 1.237 -12.437 OT1 LPS 3 LPS C12 C12 C 0 1 N N S 3.297 30.690 132.010 0.454 -0.054 -10.842 C12 LPS 4 LPS N N N 0 1 N N N 3.727 29.387 132.606 1.514 0.959 -10.929 N LPS 5 LPS C11 C11 C 0 1 N N N 2.219 31.384 132.905 -0.284 0.094 -9.510 C11 LPS 6 LPS O12 O12 O 0 1 N N N 2.072 32.826 132.722 0.635 -0.084 -8.432 O12 LPS 7 LPS P P P 0 1 N N R 2.650 34.071 133.621 -0.205 0.083 -7.070 P LPS 8 LPS O13 O13 O 0 1 N N N 3.781 33.604 134.462 -0.808 1.434 -7.026 O13 LPS 9 LPS O14 O14 O 0 1 N N N 2.897 35.229 132.745 -1.370 -1.026 -7.017 O14 LPS 10 LPS O11 O11 O 0 1 N N N 1.380 34.424 134.544 0.775 -0.107 -5.807 O11 LPS 11 LPS C1 C1 C 0 1 N N N 0.893 33.903 135.781 -0.025 0.052 -4.634 C1 LPS 12 LPS C2 C2 C 0 1 N N R -0.566 34.345 135.983 0.849 -0.117 -3.391 C2 LPS 13 LPS O21 O21 O 0 1 N N N -0.628 35.600 136.651 1.433 -1.421 -3.395 O21 LPS 14 LPS C3 C3 C 0 1 N N N -1.445 33.338 136.723 -0.007 0.054 -2.136 C3 LPS 15 LPS O31 O31 O 0 1 N N N -1.890 32.339 135.803 0.810 -0.104 -0.975 O31 LPS 16 LPS C31 C31 C 0 1 N N R -3.120 31.840 135.987 -0.043 0.065 0.157 C31 LPS 17 LPS O32 O32 O 0 1 N N N -4.118 32.504 136.204 -1.078 -0.919 0.127 O32 LPS 18 LPS C32 C32 C 0 1 N N N -3.071 30.274 135.816 0.774 -0.092 1.441 C32 LPS 19 LPS C33 C33 C 0 1 N N N -2.606 29.354 136.981 -0.139 0.089 2.654 C33 LPS 20 LPS C34 C34 C 0 1 N N N -3.089 27.885 136.799 0.678 -0.068 3.937 C34 LPS 21 LPS C35 C35 C 0 1 N N N -2.714 26.874 137.903 -0.236 0.113 5.151 C35 LPS 22 LPS C36 C36 C 0 1 N N N -3.491 26.999 139.227 0.581 -0.045 6.434 C36 LPS 23 LPS C37 C37 C 0 1 N N N -4.601 25.956 139.411 -0.332 0.137 7.647 C37 LPS 24 LPS C38 C38 C 0 1 N N N -5.838 26.509 140.147 0.485 -0.021 8.930 C38 LPS 25 LPS C39 C39 C 0 1 N N N -7.205 26.369 139.419 -0.428 0.161 10.144 C39 LPS 26 LPS C40 C40 C 0 1 N N N -7.465 27.221 138.141 0.389 0.002 11.427 C40 LPS 27 LPS C41 C41 C 0 1 N N N -7.683 28.743 138.316 -0.524 0.185 12.640 C41 LPS 28 LPS C42 C42 C 0 1 N N N -6.607 29.610 137.659 0.293 0.026 13.923 C42 LPS 29 LPS C43 C43 C 0 1 N N N -6.515 31.050 138.123 -0.620 0.209 15.137 C43 LPS 30 LPS C44 C44 C 0 1 N N N -5.507 31.272 139.194 0.197 0.050 16.420 C44 LPS 31 LPS C45 C45 C 0 1 N N N -5.173 32.732 139.413 -0.716 0.232 17.633 C45 LPS 32 LPS HT2 HT2 H 0 1 N N N 5.902 30.527 132.520 -1.795 -0.800 -13.213 HT2 LPS 33 LPS H12 H12 H 0 1 N N N 2.784 30.495 131.038 0.896 -1.048 -10.903 H12 LPS 34 LPS HN1 1HN H 0 1 N N N 2.929 28.804 132.862 1.061 1.859 -10.868 HN1 LPS 35 LPS HN2 2HN H 0 1 N N N 4.351 29.530 133.399 2.077 0.862 -10.098 HN2 LPS 36 LPS H111 1H11 H 0 0 N N N 1.232 30.881 132.769 -1.070 -0.657 -9.446 H111 LPS 37 LPS H112 2H11 H 0 0 N N N 2.413 31.155 133.978 -0.726 1.088 -9.449 H112 LPS 38 LPS H14 H14 H 0 1 N N N 3.231 35.949 133.265 -0.935 -1.889 -7.048 H14 LPS 39 LPS H11 1H1 H 0 1 N N N 1.011 32.796 135.848 -0.471 1.047 -4.631 H11 LPS 40 LPS H12A 2H1 H 0 0 N N N 1.542 34.185 136.642 -0.815 -0.698 -4.628 H12A LPS 41 LPS H2 H2 H 0 1 N Y N -0.980 34.426 134.950 1.639 0.634 -3.397 H2 LPS 42 LPS H21 H21 H 0 1 N N N -1.529 35.873 136.775 0.703 -2.054 -3.389 H21 LPS 43 LPS H31A 1H3 H 0 0 N N N -0.931 32.898 137.609 -0.453 1.049 -2.133 H31A LPS 44 LPS H32A 2H3 H 0 0 N N N -2.291 33.827 137.258 -0.797 -0.697 -2.130 H32A LPS 45 LPS H31 H31 H 0 1 N N N -3.996 32.354 136.444 -0.488 1.060 0.131 H31 LPS 46 LPS H32 H32 H 0 1 N N N -4.990 32.150 136.334 -0.642 -1.782 0.152 H32 LPS 47 LPS H321 1H32 H 0 0 N N N -4.078 29.930 135.485 1.219 -1.087 1.467 H321 LPS 48 LPS H322 2H32 H 0 0 N N N -2.445 30.043 134.922 1.563 0.658 1.464 H322 LPS 49 LPS H331 1H33 H 0 0 N N N -1.500 29.401 137.115 -0.584 1.084 2.627 H331 LPS 50 LPS H332 2H33 H 0 0 N N N -2.922 29.763 137.968 -0.928 -0.662 2.631 H332 LPS 51 LPS H341 1H34 H 0 0 N N N -4.193 27.875 136.648 1.123 -1.063 3.964 H341 LPS 52 LPS H342 2H34 H 0 0 N N N -2.740 27.500 135.812 1.467 0.682 3.960 H342 LPS 53 LPS H351 1H35 H 0 0 N N N -2.802 25.834 137.509 -0.680 1.108 5.124 H351 LPS 54 LPS H352 2H35 H 0 0 N N N -1.617 26.920 138.102 -1.025 -0.638 5.127 H352 LPS 55 LPS H361 1H36 H 0 0 N N N -2.789 26.977 140.093 1.026 -1.039 6.460 H361 LPS 56 LPS H362 2H36 H 0 0 N N N -3.902 28.029 139.340 1.370 0.706 6.457 H362 LPS 57 LPS H371 1H37 H 0 0 N N N -4.889 25.506 138.432 -0.777 1.132 7.620 H371 LPS 58 LPS H372 2H37 H 0 0 N N N -4.209 25.045 139.922 -1.121 -0.614 7.624 H372 LPS 59 LPS H381 1H38 H 0 0 N N N -5.905 26.050 141.160 0.930 -1.015 8.957 H381 LPS 60 LPS H382 2H38 H 0 0 N N N -5.665 27.577 140.416 1.274 0.730 8.953 H382 LPS 61 LPS H391 1H39 H 0 0 N N N -7.375 25.294 139.176 -0.873 1.156 10.117 H391 LPS 62 LPS H392 2H39 H 0 0 N N N -8.024 26.558 140.151 -1.217 -0.590 10.120 H392 LPS 63 LPS H401 1H40 H 0 0 N N N -6.637 27.051 137.413 0.834 -0.992 11.453 H401 LPS 64 LPS H402 2H40 H 0 0 N N N -8.328 26.789 137.583 1.178 0.754 11.450 H402 LPS 65 LPS H411 1H41 H 0 0 N N N -8.695 29.036 137.953 -0.969 1.179 12.613 H411 LPS 66 LPS H412 2H41 H 0 0 N N N -7.786 29.000 139.395 -1.313 -0.566 12.617 H412 LPS 67 LPS H421 1H42 H 0 0 N N N -5.612 29.117 137.768 0.738 -0.968 13.950 H421 LPS 68 LPS H422 2H42 H 0 0 N N N -6.729 29.581 136.551 1.082 0.778 13.947 H422 LPS 69 LPS H431 1H43 H 0 0 N N N -6.326 31.729 137.259 -1.065 1.203 15.110 H431 LPS 70 LPS H432 2H43 H 0 0 N N N -7.515 31.424 138.441 -1.409 -0.542 15.113 H432 LPS 71 LPS H441 1H44 H 0 0 N N N -5.831 30.793 140.147 0.642 -0.944 16.446 H441 LPS 72 LPS H442 2H44 H 0 0 N N N -4.582 30.680 138.995 0.986 0.802 16.443 H442 LPS 73 LPS H451 1H45 H 0 0 N N N -4.417 32.898 140.215 -0.134 0.119 18.547 H451 LPS 74 LPS H452 2H45 H 0 0 N N N -4.848 33.210 138.459 -1.161 1.227 17.606 H452 LPS 75 LPS H453 3H45 H 0 0 N N N -6.097 33.323 139.611 -1.505 -0.518 17.610 H453 LPS 76 # # 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 LPS OT2 C SING N N 1 LPS OT2 HT2 SING N N 2 LPS C OT1 DOUB N N 3 LPS C C12 SING N N 4 LPS C12 N SING N N 5 LPS C12 C11 SING N N 6 LPS C12 H12 SING N N 7 LPS N HN1 SING N N 8 LPS N HN2 SING N N 9 LPS C11 O12 SING N N 10 LPS C11 H111 SING N N 11 LPS C11 H112 SING N N 12 LPS O12 P SING N N 13 LPS P O13 DOUB N N 14 LPS P O14 SING N N 15 LPS P O11 SING N N 16 LPS O14 H14 SING N N 17 LPS O11 C1 SING N N 18 LPS C1 C2 SING N N 19 LPS C1 H11 SING N N 20 LPS C1 H12A SING N N 21 LPS C2 O21 SING N N 22 LPS C2 C3 SING N N 23 LPS C2 H2 SING N N 24 LPS O21 H21 SING N N 25 LPS C3 O31 SING N N 26 LPS C3 H31A SING N N 27 LPS C3 H32A SING N N 28 LPS O31 C31 SING N N 29 LPS C31 O32 SING N N 30 LPS C31 C32 SING N N 31 LPS C31 H31 SING N N 32 LPS O32 H32 SING N N 33 LPS C32 C33 SING N N 34 LPS C32 H321 SING N N 35 LPS C32 H322 SING N N 36 LPS C33 C34 SING N N 37 LPS C33 H331 SING N N 38 LPS C33 H332 SING N N 39 LPS C34 C35 SING N N 40 LPS C34 H341 SING N N 41 LPS C34 H342 SING N N 42 LPS C35 C36 SING N N 43 LPS C35 H351 SING N N 44 LPS C35 H352 SING N N 45 LPS C36 C37 SING N N 46 LPS C36 H361 SING N N 47 LPS C36 H362 SING N N 48 LPS C37 C38 SING N N 49 LPS C37 H371 SING N N 50 LPS C37 H372 SING N N 51 LPS C38 C39 SING N N 52 LPS C38 H381 SING N N 53 LPS C38 H382 SING N N 54 LPS C39 C40 SING N N 55 LPS C39 H391 SING N N 56 LPS C39 H392 SING N N 57 LPS C40 C41 SING N N 58 LPS C40 H401 SING N N 59 LPS C40 H402 SING N N 60 LPS C41 C42 SING N N 61 LPS C41 H411 SING N N 62 LPS C41 H412 SING N N 63 LPS C42 C43 SING N N 64 LPS C42 H421 SING N N 65 LPS C42 H422 SING N N 66 LPS C43 C44 SING N N 67 LPS C43 H431 SING N N 68 LPS C43 H432 SING N N 69 LPS C44 C45 SING N N 70 LPS C44 H441 SING N N 71 LPS C44 H442 SING N N 72 LPS C45 H451 SING N N 73 LPS C45 H452 SING N N 74 LPS C45 H453 SING N N 75 # # 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 LPS SMILES ACDLabs 10.04 "O=C(O)C(N)COP(=O)(OCC(O)COC(O)CCCCCCCCCCCCCC)O" LPS SMILES_CANONICAL CACTVS 3.341 "CCCCCCCCCCCCCC[C@H](O)OC[C@@H](O)CO[P@@](O)(=O)OC[C@H](N)C(O)=O" LPS SMILES CACTVS 3.341 "CCCCCCCCCCCCCC[CH](O)OC[CH](O)CO[P](O)(=O)OC[CH](N)C(O)=O" LPS SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "CCCCCCCCCCCCCCC(O)OC[C@H](CO[P@](=O)(O)OC[C@@H](C(=O)O)N)O" LPS SMILES "OpenEye OEToolkits" 1.5.0 "CCCCCCCCCCCCCCC(O)OCC(COP(=O)(O)OCC(C(=O)O)N)O" LPS InChI InChI 1.03 "InChI=1S/C21H44NO9P/c1-2-3-4-5-6-7-8-9-10-11-12-13-14-20(24)29-15-18(23)16-30-32(27,28)31-17-19(22)21(25)26/h18-20,23-24H,2-17,22H2,1H3,(H,25,26)(H,27,28)/t18-,19+,20-/m1/s1" LPS InChIKey InChI 1.03 RPZLJDFLPRHXGM-HSALFYBXSA-N # # 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 LPS "SYSTEMATIC NAME" ACDLabs 10.04 "O-[(R)-hydroxy{[(2R)-2-hydroxy-3-{[(1R)-1-hydroxypentadecyl]oxy}propyl]oxy}phosphoryl]-L-serine" LPS "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "(2S)-2-amino-3-[hydroxy-[(2R)-2-hydroxy-3-(1-hydroxypentadecoxy)propoxy]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 LPS "Create component" 2003-02-21 RCSB LPS "Modify descriptor" 2011-06-04 RCSB LPS "Modify synonyms" 2021-03-01 PDBE # _pdbx_chem_comp_synonyms.ordinal 1 _pdbx_chem_comp_synonyms.comp_id LPS _pdbx_chem_comp_synonyms.name LYSOPHOSPHOTIDYLSERINE _pdbx_chem_comp_synonyms.provenance ? _pdbx_chem_comp_synonyms.type ? ##