data_S1P
#

_chem_comp.id                                   S1P
_chem_comp.name                                 "(2S,3R,4E)-2-amino-3-hydroxyoctadec-4-en-1-yl dihydrogen phosphate"
_chem_comp.type                                 NON-POLYMER
_chem_comp.pdbx_type                            HETAIN
_chem_comp.formula                              "C18 H38 N O5 P"
_chem_comp.mon_nstd_parent_comp_id              ?
_chem_comp.pdbx_synonyms                        "sphingosine 1-phosphate"
_chem_comp.pdbx_formal_charge                   0
_chem_comp.pdbx_initial_date                    2009-07-14
_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                       379.472
_chem_comp.one_letter_code                      ?
_chem_comp.three_letter_code                    S1P
_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       3I9G
_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
S1P  C1    C1    C  0  1  N  N  N   1.176  14.756  38.557  -6.232   0.235  -0.103  C1    S1P   1  
S1P  O1    O1    O  0  1  N  N  N   2.576  15.024  38.468  -6.676  -1.041   0.364  O1    S1P   2  
S1P  C2    C2    C  0  1  N  N  S   0.688  14.320  37.182  -4.845   0.533   0.470  C2    S1P   3  
S1P  N2    N2    N  0  1  N  N  N   1.387  13.099  36.758  -4.935   0.664   1.930  N2    S1P   4  
S1P  C3    C3    C  0  1  N  N  R   0.926  15.438  36.154  -4.317   1.839  -0.127  C3    S1P   5  
S1P  O3    O3    O  0  1  N  N  N   0.042  16.520  36.452  -4.228   1.712  -1.548  O3    S1P   6  
S1P  C4    C4    C  0  1  N  N  N   0.619  14.958  34.749  -2.950   2.133   0.437  C4    S1P   7  
S1P  C5    C5    C  0  1  N  N  N   1.576  15.002  33.828  -1.937   2.329  -0.370  C5    S1P   8  
S1P  C6    C6    C  0  1  N  N  N   1.297  14.528  32.422  -0.571   2.622   0.194  C6    S1P   9  
S1P  C7    C7    C  0  1  N  N  N   1.727  15.648  31.470   0.438   1.615  -0.362  C7    S1P  10  
S1P  C8    C8    C  0  1  N  N  N   0.517  16.100  30.691   1.825   1.913   0.210  C8    S1P  11  
S1P  C9    C9    C  0  1  N  N  N  -0.211  17.316  31.203   2.833   0.905  -0.345  C9    S1P  12  
S1P  C10   C10   C  0  1  N  N  N  -0.685  18.029  29.949   4.221   1.204   0.227  C10   S1P  13  
S1P  C11   C11   C  0  1  N  N  N  -2.190  17.987  29.693   5.229   0.196  -0.329  C11   S1P  14  
S1P  C12   C12   C  0  1  N  N  N  -2.461  18.528  28.287   6.616   0.494   0.244  C12   S1P  15  
S1P  C13   C13   C  0  1  N  N  N  -3.474  19.662  28.391   7.625  -0.513  -0.312  C13   S1P  16  
S1P  C14   C14   C  0  1  N  N  N  -3.533  20.629  27.190   9.012  -0.215   0.260  C14   S1P  17  
S1P  C15   C15   C  0  1  N  N  N  -2.735  21.920  27.414  10.020  -1.223  -0.295  C15   S1P  18  
S1P  C16   C16   C  0  1  N  N  N  -3.160  22.741  28.632  11.407  -0.924   0.277  C16   S1P  19  
S1P  C17   C17   C  0  1  N  N  N  -2.258  23.951  28.796  12.416  -1.932  -0.279  C17   S1P  20  
S1P  C18   C18   C  0  1  N  N  N  -2.816  24.962  29.780  13.803  -1.634   0.294  C18   S1P  21  
S1P  P22   P22   P  0  1  N  N  N   3.627  14.289  39.455  -8.098  -1.677  -0.041  P22   S1P  22  
S1P  O23   O23   O  0  1  N  N  N   3.053  14.337  40.809  -8.123  -1.972  -1.624  O23   S1P  23  
S1P  O24   O24   O  0  1  N  N  N   4.897  15.019  39.186  -8.320  -3.052   0.765  O24   S1P  24  
S1P  O25   O25   O  0  1  N  N  N   3.775  12.880  38.888  -9.179  -0.725   0.300  O25   S1P  25  
S1P  H1    H1    H  0  1  N  N  N   0.640  15.663  38.874  -6.181   0.226  -1.191  H1    S1P  26  
S1P  H1A   H1A   H  0  1  N  N  N   0.993  13.957  39.290  -6.932   1.004   0.222  H1A   S1P  27  
S1P  H2    H2    H  0  1  N  N  N  -0.391  14.113  37.244  -4.165  -0.282   0.219  H2    S1P  28  
S1P  HN2   HN2   H  0  1  N  N  N   1.058  12.823  35.855  -4.022   0.797   2.339  HN2   S1P  29  
S1P  HN2A  HN2A  H  0  0  N  N  N   2.370  13.276  36.715  -5.560   1.413   2.188  HN2A  S1P  30  
S1P  H3    H3    H  0  1  N  N  N   1.980  15.747  36.207  -4.996   2.654   0.123  H3    S1P  31  
S1P  HO3   HO3   H  0  1  N  N  N   0.176  17.221  35.825  -3.639   1.004  -1.844  HO3   S1P  32  
S1P  H4    H4    H  0  1  N  N  N  -0.364  14.586  34.500  -2.806   2.182   1.506  H4    S1P  33  
S1P  H5    H5    H  0  1  N  N  N   2.555  15.378  34.086  -2.081   2.280  -1.439  H5    S1P  34  
S1P  H6    H6    H  0  1  N  N  N   1.866  13.611  32.211  -0.270   3.631  -0.089  H6    S1P  35  
S1P  H6A   H6A   H  0  1  N  N  N   0.225  14.315  32.299  -0.601   2.544   1.280  H6A   S1P  36  
S1P  H7    H7    H  0  1  N  N  N   2.137  16.491  32.046   0.137   0.606  -0.079  H7    S1P  37  
S1P  H7A   H7A   H  0  1  N  N  N   2.498  15.276  30.779   0.469   1.693  -1.449  H7A   S1P  38  
S1P  H8    H8    H  0  1  N  N  N   0.859  16.334  29.672   2.126   2.922  -0.073  H8    S1P  39  
S1P  H8A   H8A   H  0  1  N  N  N  -0.201  15.267  30.699   1.794   1.834   1.297  H8A   S1P  40  
S1P  H9    H9    H  0  1  N  N  N  -1.059  17.031  31.843   2.533  -0.103  -0.062  H9    S1P  41  
S1P  H9A   H9A   H  0  1  N  N  N   0.456  17.958  31.797   2.864   0.984  -1.432  H9A   S1P  42  
S1P  H10   H10   H  0  1  N  N  N  -0.395  19.086  30.041   4.521   2.212  -0.056  H10   S1P  43  
S1P  H10A  H10A  H  0  0  N  N  N  -0.191  17.551  29.091   4.190   1.125   1.314  H10A  S1P  44  
S1P  H11   H11   H  0  1  N  N  N  -2.552  16.951  29.769   4.928  -0.813  -0.046  H11   S1P  45  
S1P  H11A  H11A  H  0  0  N  N  N  -2.711  18.607  30.437   5.260   0.275  -1.416  H11A  S1P  46  
S1P  H12   H12   H  0  1  N  N  N  -1.526  18.903  27.846   6.917   1.503  -0.039  H12   S1P  47  
S1P  H12A  H12A  H  0  0  N  N  N  -2.864  17.726  27.651   6.585   0.416   1.330  H12A  S1P  48  
S1P  H13   H13   H  0  1  N  N  N  -4.469  19.204  28.493   7.324  -1.522  -0.029  H13   S1P  49  
S1P  H13A  H13A  H  0  0  N  N  N  -3.211  20.257  29.278   7.655  -0.435  -1.399  H13A  S1P  50  
S1P  H14   H14   H  0  1  N  N  N  -3.116  20.114  26.312   9.312   0.794  -0.023  H14   S1P  51  
S1P  H14A  H14A  H  0  0  N  N  N  -4.585  20.900  27.017   8.981  -0.294   1.347  H14A  S1P  52  
S1P  H15   H15   H  0  1  N  N  N  -1.680  21.640  27.552   9.720  -2.231  -0.012  H15   S1P  53  
S1P  H15A  H15A  H  0  0  N  N  N  -2.866  22.552  26.523  10.051  -1.144  -1.382  H15A  S1P  54  
S1P  H16   H16   H  0  1  N  N  N  -4.197  23.080  28.495  11.708   0.084  -0.006  H16   S1P  55  
S1P  H16A  H16A  H  0  0  N  N  N  -3.090  22.114  29.533  11.377  -1.003   1.364  H16A  S1P  56  
S1P  H17   H17   H  0  1  N  N  N  -1.280  23.609  29.165  12.115  -2.941   0.004  H17   S1P  57  
S1P  H17A  H17A  H  0  0  N  N  N  -2.150  24.441  27.817  12.447  -1.854  -1.365  H17A  S1P  58  
S1P  H18   H18   H  0  1  N  N  N  -2.126  25.815  29.861  14.104  -0.625   0.011  H18   S1P  59  
S1P  H18A  H18A  H  0  0  N  N  N  -3.796  25.315  29.426  13.772  -1.712   1.380  H18A  S1P  60  
S1P  H18B  H18B  H  0  0  N  N  N  -2.931  24.489  30.766  14.521  -2.352  -0.102  H18B  S1P  61  
S1P  HO23  HO23  H  0  0  N  N  N   2.868  13.454  41.106  -7.440  -2.589  -1.919  HO23  S1P  62  
S1P  HO24  HO24  H  0  0  N  N  N   5.501  14.446  38.728  -9.159  -3.492   0.569  HO24  S1P  63  
#   #
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
S1P  C2   C1    SING  N  N   1  
S1P  O1   C1    SING  N  N   2  
S1P  C1   H1    SING  N  N   3  
S1P  C1   H1A   SING  N  N   4  
S1P  O1   P22   SING  N  N   5  
S1P  C3   C2    SING  N  N   6  
S1P  N2   C2    SING  N  N   7  
S1P  C2   H2    SING  N  N   8  
S1P  N2   HN2   SING  N  N   9  
S1P  N2   HN2A  SING  N  N  10  
S1P  C4   C3    SING  N  N  11  
S1P  C3   O3    SING  N  N  12  
S1P  C3   H3    SING  N  N  13  
S1P  O3   HO3   SING  N  N  14  
S1P  C5   C4    DOUB  N  N  15  
S1P  C4   H4    SING  N  E  16  
S1P  C6   C5    SING  N  N  17  
S1P  C5   H5    SING  N  N  18  
S1P  C7   C6    SING  N  N  19  
S1P  C6   H6    SING  N  N  20  
S1P  C6   H6A   SING  N  N  21  
S1P  C8   C7    SING  N  N  22  
S1P  C7   H7    SING  N  N  23  
S1P  C7   H7A   SING  N  N  24  
S1P  C8   C9    SING  N  N  25  
S1P  C8   H8    SING  N  N  26  
S1P  C8   H8A   SING  N  N  27  
S1P  C10  C9    SING  N  N  28  
S1P  C9   H9    SING  N  N  29  
S1P  C9   H9A   SING  N  N  30  
S1P  C11  C10   SING  N  N  31  
S1P  C10  H10   SING  N  N  32  
S1P  C10  H10A  SING  N  N  33  
S1P  C12  C11   SING  N  N  34  
S1P  C11  H11   SING  N  N  35  
S1P  C11  H11A  SING  N  N  36  
S1P  C12  C13   SING  N  N  37  
S1P  C12  H12   SING  N  N  38  
S1P  C12  H12A  SING  N  N  39  
S1P  C14  C13   SING  N  N  40  
S1P  C13  H13   SING  N  N  41  
S1P  C13  H13A  SING  N  N  42  
S1P  C14  C15   SING  N  N  43  
S1P  C14  H14   SING  N  N  44  
S1P  C14  H14A  SING  N  N  45  
S1P  C15  C16   SING  N  N  46  
S1P  C15  H15   SING  N  N  47  
S1P  C15  H15A  SING  N  N  48  
S1P  C16  C17   SING  N  N  49  
S1P  C16  H16   SING  N  N  50  
S1P  C16  H16A  SING  N  N  51  
S1P  C17  C18   SING  N  N  52  
S1P  C17  H17   SING  N  N  53  
S1P  C17  H17A  SING  N  N  54  
S1P  C18  H18   SING  N  N  55  
S1P  C18  H18A  SING  N  N  56  
S1P  C18  H18B  SING  N  N  57  
S1P  O25  P22   DOUB  N  N  58  
S1P  O24  P22   SING  N  N  59  
S1P  P22  O23   SING  N  N  60  
S1P  O23  HO23  SING  N  N  61  
S1P  O24  HO24  SING  N  N  62  
#   #
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
S1P  SMILES            ACDLabs               11.02  "O=P(OCC(N)C(O)/C=C/CCCCCCCCCCCCC)(O)O"  
S1P  SMILES_CANONICAL  CACTVS                3.352  "CCCCCCCCCCCCC\C=C\[C@@H](O)[C@@H](N)CO[P](O)(O)=O"  
S1P  SMILES            CACTVS                3.352  "CCCCCCCCCCCCCC=C[CH](O)[CH](N)CO[P](O)(O)=O"  
S1P  SMILES_CANONICAL  "OpenEye OEToolkits"  1.7.0  "CCCCCCCCCCCCC/C=C/[C@H]([C@H](COP(=O)(O)O)N)O"  
S1P  SMILES            "OpenEye OEToolkits"  1.7.0  "CCCCCCCCCCCCCC=CC(C(COP(=O)(O)O)N)O"  
S1P  InChI             InChI                 1.03   "InChI=1S/C18H38NO5P/c1-2-3-4-5-6-7-8-9-10-11-12-13-14-15-18(20)17(19)16-24-25(21,22)23/h14-15,17-18,20H,2-13,16,19H2,1H3,(H2,21,22,23)/b15-14+/t17-,18+/m0/s1"  
S1P  InChIKey          InChI                 1.03   DUYSYHSSBDVJSM-KRWOKUGFSA-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
S1P  "SYSTEMATIC NAME"  ACDLabs               11.02  "(2S,3R,4E)-2-amino-3-hydroxyoctadec-4-en-1-yl dihydrogen phosphate"  
S1P  "SYSTEMATIC NAME"  "OpenEye OEToolkits"  1.6.1  "[(E,2S,3R)-2-azanyl-3-hydroxy-octadec-4-enyl] dihydrogen phosphate"  
#   #
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
S1P  "Create component"   2009-07-14  RCSB  
S1P  "Modify descriptor"  2011-06-04  RCSB  
S1P  "Modify synonyms"    2020-06-05  PDBE  
#
_pdbx_chem_comp_synonyms.ordinal     1
_pdbx_chem_comp_synonyms.comp_id     S1P
_pdbx_chem_comp_synonyms.name        "sphingosine 1-phosphate"
_pdbx_chem_comp_synonyms.provenance  ?
_pdbx_chem_comp_synonyms.type        ?
##
