data_SPU
#
_chem_comp.id SPU
_chem_comp.name "2-{[(R)-{[(2S,3R,4E)-2-amino-3-hydroxyoctadec-4-en-1-yl]oxy}(hydroxy)phosphoryl]oxy}-N,N,N-trimethylethanaminium"
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C23 H50 N2 O5 P"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms "sphingosylphosphorylcholine, sphingosine phosphorylcholine"
_chem_comp.pdbx_formal_charge 1
_chem_comp.pdbx_initial_date 2009-07-28
_chem_comp.pdbx_modified_date 2020-06-17
_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 465.627
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code SPU
_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 3IF7
_chem_comp.pdbx_subcomponent_list ?
_chem_comp.pdbx_processing_site PDBJ
# #
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
SPU C11 C11 C 0 1 N N N -28.718 7.487 -17.410 11.604 -1.801 -0.565 C11 SPU 1
SPU C14 C14 C 0 1 N N N -27.911 8.466 -18.257 10.711 -0.857 0.241 C14 SPU 2
SPU C17 C17 C 0 1 N N N -28.363 9.910 -18.070 9.331 -0.774 -0.416 C17 SPU 3
SPU C20 C20 C 0 1 N N N -27.333 10.669 -17.262 8.438 0.170 0.390 C20 SPU 4
SPU C23 C23 C 0 1 N N N -26.988 12.047 -17.815 7.059 0.253 -0.267 C23 SPU 5
SPU C26 C26 C 0 1 N N N -26.338 12.897 -16.737 6.165 1.197 0.540 C26 SPU 6
SPU C29 C29 C 0 1 N N N -26.272 14.349 -17.119 4.786 1.280 -0.117 C29 SPU 7
SPU C32 C32 C 0 1 N N N -25.278 15.108 -16.254 3.892 2.224 0.689 C32 SPU 8
SPU C35 C35 C 0 1 N N N -24.714 16.282 -17.017 2.513 2.307 0.032 C35 SPU 9
SPU C38 C38 C 0 1 N N N -23.893 15.744 -18.190 1.620 3.252 0.838 C38 SPU 10
SPU C41 C41 C 0 1 N N N -22.538 16.370 -18.142 0.261 3.333 0.191 C41 SPU 11
SPU C43 C43 C 0 1 N N N -21.926 16.816 -19.233 -0.814 3.066 0.890 C43 SPU 12
SPU C45 C45 C 0 1 N N R -20.567 17.446 -19.070 -2.173 3.148 0.243 C45 SPU 13
SPU O47 O47 O 0 1 N N N -20.236 18.008 -20.321 -2.020 3.418 -1.152 O47 SPU 14
SPU C49 C49 C 0 1 N N S -20.632 18.579 -18.050 -2.906 1.818 0.428 C49 SPU 15
SPU N51 N51 N 0 1 N N N -22.017 19.006 -17.877 -3.063 1.540 1.862 N51 SPU 16
SPU C54 C54 C 0 1 N N N -20.118 18.244 -16.664 -4.285 1.900 -0.230 C54 SPU 17
SPU O57 O57 O 0 1 N N N -20.933 19.008 -15.790 -4.924 0.624 -0.159 O57 SPU 18
SPU P58 P58 P 0 1 N N N -20.797 18.817 -14.223 -6.393 0.344 -0.755 P58 SPU 19
SPU O59 O59 O 0 1 N N N -21.683 17.632 -13.852 -7.478 1.207 0.065 O59 SPU 20
SPU O60 O60 O 0 1 N N N -19.297 18.833 -13.963 -6.430 0.734 -2.182 O60 SPU 21
SPU O61 O61 O 0 1 N N N -21.453 20.131 -13.541 -6.739 -1.222 -0.618 O61 SPU 22
SPU C62 C62 C 0 1 N N N -21.363 20.319 -12.121 -7.930 -1.806 -1.150 C62 SPU 23
SPU C65 C65 C 0 1 N N N -21.298 21.815 -11.776 -7.943 -3.305 -0.844 C65 SPU 24
SPU N68 N68 N 1 1 N N N -19.929 22.352 -11.745 -8.063 -3.508 0.606 N68 SPU 25
SPU C70 C70 C 0 1 N N N -19.186 21.843 -12.893 -9.241 -2.787 1.106 C70 SPU 26
SPU C74 C74 C 0 1 N N N -19.938 23.834 -11.792 -8.210 -4.942 0.889 C74 SPU 27
SPU C78 C78 C 0 1 N N N -19.216 21.876 -10.554 -6.857 -2.999 1.273 C78 SPU 28
SPU C21 C21 C 0 1 N N N -28.206 6.055 -17.651 12.983 -1.884 0.092 C21 SPU 29
SPU C22 C22 C 0 1 N N N -29.539 5.285 -17.651 13.877 -2.828 -0.715 C22 SPU 30
SPU C231 C231 C 0 0 N N N -28.769 3.951 -17.651 15.256 -2.911 -0.058 C231 SPU 31
SPU H11 H11 H 0 1 N N N -28.604 7.743 -16.346 11.154 -2.794 -0.591 H11 SPU 32
SPU H11A H11A H 0 0 N N N -29.780 7.549 -17.691 11.708 -1.423 -1.582 H11A SPU 33
SPU H14 H14 H 0 1 N N N -26.853 8.391 -17.964 10.606 -1.235 1.258 H14 SPU 34
SPU H14A H14A H 0 0 N N N -28.036 8.196 -19.316 11.161 0.136 0.267 H14A SPU 35
SPU H17 H17 H 0 1 N N N -28.478 10.387 -19.055 9.436 -0.396 -1.433 H17 SPU 36
SPU H17A H17A H 0 0 N N N -29.326 9.925 -17.539 8.881 -1.766 -0.442 H17A SPU 37
SPU H20 H20 H 0 1 N N N -27.734 10.804 -16.247 8.334 -0.208 1.407 H20 SPU 38
SPU H20A H20A H 0 0 N N N -26.410 10.071 -17.246 8.888 1.163 0.416 H20A SPU 39
SPU H23 H23 H 0 1 N N N -26.290 11.935 -18.658 7.163 0.631 -1.284 H23 SPU 40
SPU H23A H23A H 0 0 N N N -27.909 12.540 -18.159 6.609 -0.739 -0.293 H23A SPU 41
SPU H26 H26 H 0 1 N N N -26.930 12.804 -15.814 6.061 0.819 1.557 H26 SPU 42
SPU H26A H26A H 0 0 N N N -25.314 12.531 -16.573 6.615 2.190 0.566 H26A SPU 43
SPU H29 H29 H 0 1 N N N -25.958 14.425 -18.170 4.890 1.658 -1.134 H29 SPU 44
SPU H29A H29A H 0 0 N N N -27.269 14.796 -16.989 4.336 0.288 -0.143 H29A SPU 45
SPU H32 H32 H 0 1 N N N -25.789 15.474 -15.351 3.788 1.846 1.706 H32 SPU 46
SPU H32A H32A H 0 0 N N N -24.457 14.434 -15.968 4.343 3.217 0.715 H32A SPU 47
SPU H35 H35 H 0 1 N N N -25.534 16.912 -17.393 2.617 2.685 -0.985 H35 SPU 48
SPU H35A H35A H 0 0 N N N -24.072 16.883 -16.356 2.063 1.315 0.006 H35A SPU 49
SPU H38 H38 H 0 1 N N N -23.802 14.651 -18.112 1.516 2.873 1.855 H38 SPU 50
SPU H38A H38A H 0 0 N N N -24.388 15.997 -19.139 2.070 4.244 0.864 H38A SPU 51
SPU H41 H41 H 0 1 N N N -22.039 16.463 -17.189 0.175 3.611 -0.849 H41 SPU 52
SPU H43 H43 H 0 1 N N N -22.387 16.730 -20.206 -0.727 2.788 1.930 H43 SPU 53
SPU H45 H45 H 0 1 N N N -19.833 16.699 -18.733 -2.749 3.948 0.707 H45 SPU 54
SPU HO47 HO47 H 0 0 N N N -19.381 18.420 -20.268 -1.516 2.745 -1.630 HO47 SPU 55
SPU H49 H49 H 0 1 N N N -19.976 19.355 -18.471 -2.330 1.017 -0.037 H49 SPU 56
SPU HN51 HN51 H 0 0 N N N -22.056 19.748 -17.208 -3.594 2.269 2.315 HN51 SPU 57
SPU HN5A HN5A H 0 0 N N N -22.379 19.327 -18.752 -3.487 0.637 2.011 HN5A SPU 58
SPU H54 H54 H 0 1 N N N -20.211 17.168 -16.455 -4.893 2.640 0.292 H54 SPU 59
SPU H54A H54A H 0 0 N N N -19.057 18.515 -16.557 -4.174 2.194 -1.274 H54A SPU 60
SPU H59 H59 H 0 1 N N N -21.153 16.952 -13.454 -7.509 1.003 1.010 H59 SPU 61
SPU H62 H62 H 0 1 N N N -22.250 19.878 -11.643 -8.800 -1.334 -0.694 H62 SPU 62
SPU H62A H62A H 0 0 N N N -20.453 19.824 -11.750 -7.957 -1.655 -2.229 H62A SPU 63
SPU H65 H65 H 0 1 N N N -21.865 22.367 -12.540 -8.791 -3.771 -1.347 H65 SPU 64
SPU H65A H65A H 0 0 N N N -21.744 21.956 -10.780 -7.017 -3.757 -1.199 H65A SPU 65
SPU H70 H70 H 0 1 N N N -18.161 22.242 -12.874 -10.135 -3.165 0.611 H70 SPU 66
SPU H70A H70A H 0 0 N N N -19.152 20.744 -12.850 -9.330 -2.938 2.182 H70A SPU 67
SPU H70B H70B H 0 0 N N N -19.685 22.158 -13.821 -9.132 -1.723 0.896 H70B SPU 68
SPU H74 H74 H 0 1 N N N -18.904 24.208 -11.768 -7.336 -5.477 0.518 H74 SPU 69
SPU H74A H74A H 0 0 N N N -20.427 24.168 -12.719 -8.299 -5.093 1.965 H74A SPU 70
SPU H74B H74B H 0 0 N N N -20.490 24.225 -10.924 -9.105 -5.320 0.394 H74B SPU 71
SPU H78 H78 H 0 1 N N N -18.196 22.287 -10.548 -6.851 -1.910 1.230 H78 SPU 72
SPU H78A H78A H 0 0 N N N -19.750 22.207 -9.651 -6.854 -3.321 2.314 H78A SPU 73
SPU H78B H78B H 0 0 N N N -19.168 20.777 -10.570 -5.972 -3.387 0.769 H78B SPU 74
SPU H44 H44 H 0 1 N N N -27.658 5.954 -18.599 13.434 -0.891 0.118 H44 SPU 75
SPU H451 H451 H 0 0 N N N -27.518 5.712 -16.864 12.879 -2.262 1.109 H451 SPU 76
SPU H46 H46 H 0 1 N N N -30.211 5.465 -16.799 13.427 -3.821 -0.741 H46 SPU 77
SPU H47 H47 H 0 1 N N N -30.211 5.465 -18.503 13.981 -2.450 -1.732 H47 SPU 78
SPU H48 H48 H 0 1 N N N -29.483 3.115 -17.651 15.706 -1.919 -0.032 H48 SPU 79
SPU H491 H491 H 0 0 N N N -28.137 3.893 -18.549 15.152 -3.289 0.959 H491 SPU 80
SPU H50 H50 H 0 1 N N N -28.137 3.893 -16.753 15.892 -3.584 -0.632 H50 SPU 81
# #
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
SPU C11 C14 SING N N 1
SPU C11 C21 SING N N 2
SPU C14 C17 SING N N 3
SPU C17 C20 SING N N 4
SPU C20 C23 SING N N 5
SPU C23 C26 SING N N 6
SPU C26 C29 SING N N 7
SPU C29 C32 SING N N 8
SPU C32 C35 SING N N 9
SPU C35 C38 SING N N 10
SPU C38 C41 SING N N 11
SPU C41 C43 DOUB N N 12
SPU C43 C45 SING N N 13
SPU C45 O47 SING N N 14
SPU C45 C49 SING N N 15
SPU C49 N51 SING N N 16
SPU C49 C54 SING N N 17
SPU C54 O57 SING N N 18
SPU O57 P58 SING N N 19
SPU P58 O59 SING N N 20
SPU P58 O60 DOUB N N 21
SPU P58 O61 SING N N 22
SPU O61 C62 SING N N 23
SPU C62 C65 SING N N 24
SPU C65 N68 SING N N 25
SPU N68 C70 SING N N 26
SPU N68 C74 SING N N 27
SPU N68 C78 SING N N 28
SPU C21 C22 SING N N 29
SPU C22 C231 SING N N 30
SPU C11 H11 SING N N 31
SPU C11 H11A SING N E 32
SPU C14 H14 SING N N 33
SPU C14 H14A SING N N 34
SPU C17 H17 SING N N 35
SPU C17 H17A SING N N 36
SPU C20 H20 SING N N 37
SPU C20 H20A SING N N 38
SPU C23 H23 SING N N 39
SPU C23 H23A SING N N 40
SPU C26 H26 SING N N 41
SPU C26 H26A SING N N 42
SPU C29 H29 SING N N 43
SPU C29 H29A SING N N 44
SPU C32 H32 SING N N 45
SPU C32 H32A SING N N 46
SPU C35 H35 SING N N 47
SPU C35 H35A SING N N 48
SPU C38 H38 SING N N 49
SPU C38 H38A SING N N 50
SPU C41 H41 SING N N 51
SPU C43 H43 SING N N 52
SPU C45 H45 SING N N 53
SPU O47 HO47 SING N N 54
SPU C49 H49 SING N N 55
SPU N51 HN51 SING N N 56
SPU N51 HN5A SING N N 57
SPU C54 H54 SING N N 58
SPU C54 H54A SING N N 59
SPU O59 H59 SING N N 60
SPU C62 H62 SING N N 61
SPU C62 H62A SING N N 62
SPU C65 H65 SING N N 63
SPU C65 H65A SING N N 64
SPU C70 H70 SING N N 65
SPU C70 H70A SING N N 66
SPU C70 H70B SING N N 67
SPU C74 H74 SING N N 68
SPU C74 H74A SING N N 69
SPU C74 H74B SING N N 70
SPU C78 H78 SING N N 71
SPU C78 H78A SING N N 72
SPU C78 H78B SING N N 73
SPU C21 H44 SING N N 74
SPU C21 H451 SING N N 75
SPU C22 H46 SING N N 76
SPU C22 H47 SING N N 77
SPU C231 H48 SING N N 78
SPU C231 H491 SING N N 79
SPU C231 H50 SING N N 80
# #
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
SPU SMILES ACDLabs 11.02 "O=P(OCC(N)C(O)/C=C/CCCCCCCCCCCCC)(OCC[N+](C)(C)C)O"
SPU SMILES_CANONICAL CACTVS 3.352 "CCCCCCCCCCCCC\C=C\[C@@H](O)[C@@H](N)CO[P](O)(=O)OCC[N+](C)(C)C"
SPU SMILES CACTVS 3.352 "CCCCCCCCCCCCCC=C[CH](O)[CH](N)CO[P](O)(=O)OCC[N+](C)(C)C"
SPU SMILES_CANONICAL "OpenEye OEToolkits" 1.7.0 "CCCCCCCCCCCCC/C=C/[C@H]([C@H](CO[P@](=O)(O)OCC[N+](C)(C)C)N)O"
SPU SMILES "OpenEye OEToolkits" 1.7.0 "CCCCCCCCCCCCCC=CC(C(COP(=O)(O)OCC[N+](C)(C)C)N)O"
SPU InChI InChI 1.03 "InChI=1S/C23H49N2O5P/c1-5-6-7-8-9-10-11-12-13-14-15-16-17-18-23(26)22(24)21-30-31(27,28)29-20-19-25(2,3)4/h17-18,22-23,26H,5-16,19-21,24H2,1-4H3/p+1/b18-17+/t22-,23+/m0/s1"
SPU InChIKey InChI 1.03 JLVSPVFPBBFMBE-HXSWCURESA-O
# #
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
SPU "SYSTEMATIC NAME" ACDLabs 11.02 "2-{[(R)-{[(2S,3R,4E)-2-amino-3-hydroxyoctadec-4-en-1-yl]oxy}(hydroxy)phosphoryl]oxy}-N,N,N-trimethylethanaminium"
SPU "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.6.1 "2-[[(E,2S,3R)-2-azanyl-3-hydroxy-octadec-4-enoxy]-hydroxy-phosphoryl]oxyethyl-trimethyl-azanium"
# #
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
SPU "Create component" 2009-07-28 PDBJ
SPU "Modify descriptor" 2011-06-04 RCSB
SPU "Modify synonyms" 2020-06-05 PDBE
#
_pdbx_chem_comp_synonyms.ordinal 1
_pdbx_chem_comp_synonyms.comp_id SPU
_pdbx_chem_comp_synonyms.name "sphingosylphosphorylcholine, sphingosine phosphorylcholine"
_pdbx_chem_comp_synonyms.provenance ?
_pdbx_chem_comp_synonyms.type ?
##