data_VSD
#

_chem_comp.id                                   VSD
_chem_comp.name                                 3-Dehydrosphinganine
_chem_comp.type                                 non-polymer
_chem_comp.pdbx_type                            HETAIN
_chem_comp.formula                              "C18 H37 N O2"
_chem_comp.mon_nstd_parent_comp_id              ?
_chem_comp.pdbx_synonyms                        "(2S,6E)-2-amino-1-hydroxyoctadec-6-en-3-one"
_chem_comp.pdbx_formal_charge                   0
_chem_comp.pdbx_initial_date                    2020-09-11
_chem_comp.pdbx_modified_date                   2021-03-13
_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                       299.492
_chem_comp.one_letter_code                      ?
_chem_comp.three_letter_code                    VSD
_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       7K0K
_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
VSD  C15  C1   C  0  1  N  N  N  203.072  210.135  214.391  -5.416  -0.292   0.414  C15  VSD   1  
VSD  C16  C2   C  0  1  N  N  N  202.374  209.394  215.519  -6.646   0.511   0.078  C16  VSD   2  
VSD  C10  C3   C  0  1  N  N  N  207.312  208.112  209.718   0.829   0.449  -0.088  C10  VSD   3  
VSD  C11  C4   C  0  1  N  N  N  206.864  208.544  211.152  -0.420  -0.342   0.307  C11  VSD   4  
VSD  C12  C5   C  0  1  N  N  N  205.329  208.642  211.414  -1.669   0.474  -0.035  C12  VSD   5  
VSD  C13  C6   C  0  1  N  N  N  204.926  209.031  212.869  -2.918  -0.317   0.361  C13  VSD   6  
VSD  C14  C7   C  0  1  N  N  N  203.420  209.301  213.125  -4.167   0.499   0.019  C14  VSD   7  
VSD  C01  C8   C  0  1  N  N  N  208.820  210.910  198.365  12.069  -0.466   0.039  C01  VSD   8  
VSD  C02  C9   C  0  1  N  N  N  208.820  209.975  199.570  10.820   0.349  -0.303  C02  VSD   9  
VSD  C03  C10  C  0  1  N  N  N  208.218  210.587  200.843   9.571  -0.441   0.092  C03  VSD  10  
VSD  C04  C11  C  0  1  N  N  N  208.629  209.867  202.148   8.322   0.374  -0.249  C04  VSD  11  
VSD  C05  C12  C  0  1  N  N  N  207.663  210.066  203.348   7.073  -0.416   0.146  C05  VSD  12  
VSD  C06  C13  C  0  1  N  N  N  207.933  209.179  204.594   5.824   0.399  -0.196  C06  VSD  13  
VSD  C07  C14  C  0  1  N  N  N  207.341  209.671  205.957   4.575  -0.391   0.199  C07  VSD  14  
VSD  C08  C15  C  0  1  N  N  N  207.762  208.836  207.209   3.327   0.424  -0.142  C08  VSD  15  
VSD  C09  C16  C  0  1  N  N  N  206.953  209.068  208.527   2.078  -0.366   0.253  C09  VSD  16  
VSD  C18  C17  C  0  1  N  N  S  202.353  209.926  216.978  -8.014  -0.048   0.370  C18  VSD  17  
VSD  C19  C18  C  0  1  N  N  N  203.193  209.046  217.940  -8.354  -1.128  -0.659  C19  VSD  18  
VSD  N21  N1   N  0  1  N  N  N  200.954  209.941  217.449  -9.010   1.029   0.296  N21  VSD  19  
VSD  O17  O1   O  0  1  N  N  N  201.806  208.333  215.296  -6.535   1.603  -0.426  O17  VSD  20  
VSD  O20  O2   O  0  1  N  N  N  203.623  209.880  218.967  -9.599  -1.739  -0.314  O20  VSD  21  
VSD  H1   H1   H  0  1  N  N  N  204.012  210.544  214.791  -5.395  -0.493   1.485  H1   VSD  22  
VSD  H2   H2   H  0  1  N  N  N  202.417  210.961  214.078  -5.437  -1.235  -0.132  H2   VSD  23  
VSD  H3   H3   H  0  1  N  N  N  206.849  207.137  209.508   0.808   0.650  -1.160  H3   VSD  24  
VSD  H4   H4   H  0  1  N  N  N  208.406  208.003  209.734   0.850   1.392   0.458  H4   VSD  25  
VSD  H5   H5   H  0  1  N  N  N  207.276  207.813  211.863  -0.441  -1.285  -0.239  H5   VSD  26  
VSD  H6   H6   H  0  1  N  N  N  207.299  209.535  211.351  -0.399  -0.542   1.378  H6   VSD  27  
VSD  H7   H7   H  0  1  N  N  N  204.915  209.400  210.732  -1.648   1.417   0.511  H7   VSD  28  
VSD  H8   H8   H  0  1  N  N  N  205.235  208.209  213.532  -2.939  -1.260  -0.186  H8   VSD  29  
VSD  H9   H9   H  0  1  N  N  N  203.023  209.838  212.251  -4.188   0.700  -1.052  H9   VSD  30  
VSD  H10  H10  H  0  1  N  N  N  202.916  208.327  213.217  -4.146   1.442   0.565  H10  VSD  31  
VSD  H11  H11  H  0  1  N  N  N  209.266  210.395  197.501  12.959   0.097  -0.243  H11  VSD  32  
VSD  H12  H12  H  0  1  N  N  N  207.786  211.199  198.126  12.090  -0.667   1.110  H12  VSD  33  
VSD  H13  H13  H  0  1  N  N  N  209.408  211.810  198.599  12.048  -1.409  -0.508  H13  VSD  34  
VSD  H14  H14  H  0  1  N  N  N  208.239  209.078  199.310  10.841   1.292   0.243  H14  VSD  35  
VSD  H15  H15  H  0  1  N  N  N  209.860  209.688  199.784  10.799   0.550  -1.374  H15  VSD  36  
VSD  H16  H16  H  0  1  N  N  N  208.545  211.635  200.910   9.550  -1.384  -0.454  H16  VSD  37  
VSD  H17  H17  H  0  1  N  N  N  207.122  210.549  200.759   9.592  -0.642   1.163  H17  VSD  38  
VSD  H18  H18  H  0  1  N  N  N  208.691  208.789  201.937   8.343   1.317   0.297  H18  VSD  39  
VSD  H19  H19  H  0  1  N  N  N  207.730  211.118  203.663   7.052  -1.359  -0.400  H19  VSD  40  
VSD  H20  H20  H  0  1  N  N  N  207.513  208.183  204.390   5.846   1.342   0.350  H20  VSD  41  
VSD  H21  H21  H  0  1  N  N  N  207.669  210.709  206.115   4.554  -1.334  -0.347  H21  VSD  42  
VSD  H22  H22  H  0  1  N  N  N  207.667  207.772  206.945   3.348   1.367   0.404  H22  VSD  43  
VSD  H23  H23  H  0  1  N  N  N  207.132  210.102  208.857   2.099  -0.567   1.324  H23  VSD  44  
VSD  H24  H24  H  0  1  N  N  N  202.759  210.948  216.987  -8.023  -0.483   1.370  H24  VSD  45  
VSD  H25  H25  H  0  1  N  N  N  202.576  208.231  218.346  -8.433  -0.676  -1.648  H25  VSD  46  
VSD  H26  H26  H  0  1  N  N  N  204.057  208.621  217.409  -7.568  -1.883  -0.666  H26  VSD  47  
VSD  H27  H27  H  0  1  N  N  N  200.922  210.282  218.389  -8.845   1.724   1.009  H27  VSD  48  
VSD  H28  H28  H  0  1  N  N  N  200.410  210.538  216.859  -9.021   1.449  -0.622  H28  VSD  49  
VSD  H30  H30  H  0  1  N  N  N  204.145  209.380  219.584  -9.878  -2.435  -0.925  H30  VSD  50  
VSD  H29  H29  H  0  1  N  N  N  209.620  210.240  202.444   8.301   0.575  -1.321  H29  VSD  51  
VSD  H31  H31  H  0  1  N  N  N  206.642  209.852  202.998   7.094  -0.617   1.217  H31  VSD  52  
VSD  H32  H32  H  0  1  N  N  N  209.023  209.099  204.715   5.803   0.600  -1.267  H32  VSD  53  
VSD  H33  H33  H  0  1  N  N  N  206.244  209.641  205.882   4.596  -0.592   1.271  H33  VSD  54  
VSD  H34  H34  H  0  1  N  N  N  208.816  209.068  207.422   3.306   0.625  -1.213  H34  VSD  55  
VSD  H35  H35  H  0  1  N  N  N  205.885  208.936  208.297   2.056  -1.309  -0.293  H35  VSD  56  
VSD  H36  H36  H  0  1  N  N  N  204.882  207.663  211.188  -1.690   0.675  -1.106  H36  VSD  57  
VSD  H37  H37  H  0  1  N  N  N  205.479  209.944  213.135  -2.897  -0.517   1.432  H37  VSD  58  
#   #
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
VSD  C01  C02  SING  N  N   1  
VSD  C02  C03  SING  N  N   2  
VSD  C03  C04  SING  N  N   3  
VSD  C04  C05  SING  N  N   4  
VSD  C05  C06  SING  N  N   5  
VSD  C06  C07  SING  N  N   6  
VSD  C07  C08  SING  N  N   7  
VSD  C08  C09  SING  N  N   8  
VSD  C09  C10  SING  N  N   9  
VSD  C10  C11  SING  N  N  10  
VSD  C11  C12  SING  N  N  11  
VSD  C12  C13  SING  N  N  12  
VSD  C13  C14  SING  N  N  13  
VSD  C14  C15  SING  N  N  14  
VSD  C15  C16  SING  N  N  15  
VSD  O17  C16  DOUB  N  N  16  
VSD  C16  C18  SING  N  N  17  
VSD  C18  N21  SING  N  N  18  
VSD  C18  C19  SING  N  N  19  
VSD  C19  O20  SING  N  N  20  
VSD  C15  H1   SING  N  N  21  
VSD  C15  H2   SING  N  N  22  
VSD  C10  H3   SING  N  N  23  
VSD  C10  H4   SING  N  N  24  
VSD  C11  H5   SING  N  N  25  
VSD  C11  H6   SING  N  N  26  
VSD  C12  H7   SING  N  N  27  
VSD  C13  H8   SING  N  N  28  
VSD  C14  H9   SING  N  N  29  
VSD  C14  H10  SING  N  N  30  
VSD  C01  H11  SING  N  N  31  
VSD  C01  H12  SING  N  N  32  
VSD  C01  H13  SING  N  N  33  
VSD  C02  H14  SING  N  N  34  
VSD  C02  H15  SING  N  N  35  
VSD  C03  H16  SING  N  N  36  
VSD  C03  H17  SING  N  N  37  
VSD  C04  H18  SING  N  N  38  
VSD  C05  H19  SING  N  N  39  
VSD  C06  H20  SING  N  N  40  
VSD  C07  H21  SING  N  N  41  
VSD  C08  H22  SING  N  N  42  
VSD  C09  H23  SING  N  N  43  
VSD  C18  H24  SING  N  N  44  
VSD  C19  H25  SING  N  N  45  
VSD  C19  H26  SING  N  N  46  
VSD  N21  H27  SING  N  N  47  
VSD  N21  H28  SING  N  N  48  
VSD  O20  H30  SING  N  N  49  
VSD  C04  H29  SING  N  N  50  
VSD  C05  H31  SING  N  N  51  
VSD  C06  H32  SING  N  N  52  
VSD  C07  H33  SING  N  N  53  
VSD  C08  H34  SING  N  N  54  
VSD  C09  H35  SING  N  N  55  
VSD  C12  H36  SING  N  N  56  
VSD  C13  H37  SING  N  N  57  
#   #
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
VSD  SMILES            ACDLabs               12.01  "C(C(C(N)CO)=O)CCCCCCCCCCCCCC"  
VSD  InChI             InChI                 1.03   "InChI=1S/C18H37NO2/c1-2-3-4-5-6-7-8-9-10-11-12-13-14-15-18(21)17(19)16-20/h17,20H,2-16,19H2,1H3/t17-/m0/s1"  
VSD  InChIKey          InChI                 1.03   KBUNOSOGGAARKZ-KRWDZBQOSA-N  
VSD  SMILES_CANONICAL  CACTVS                3.385  "CCCCCCCCCCCCCCCC(=O)[C@@H](N)CO"  
VSD  SMILES            CACTVS                3.385  "CCCCCCCCCCCCCCCC(=O)[CH](N)CO"  
VSD  SMILES_CANONICAL  "OpenEye OEToolkits"  2.0.7  "CCCCCCCCCCCCCCCC(=O)[C@H](CO)N"  
VSD  SMILES            "OpenEye OEToolkits"  2.0.7  "CCCCCCCCCCCCCCCC(=O)C(CO)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
VSD  "SYSTEMATIC NAME"  ACDLabs               12.01  "(2S)-2-amino-1-hydroxyoctadecan-3-one"  
VSD  "SYSTEMATIC NAME"  "OpenEye OEToolkits"  2.0.7  "(2~{S})-2-azanyl-1-oxidanyl-octadecan-3-one"  
#   #
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
VSD  "Create component"  2020-09-11  RCSB  
VSD  "Initial release"   2021-02-24  RCSB  
VSD  "Modify synonyms"   2021-03-13  RCSB  
#
_pdbx_chem_comp_synonyms.ordinal     1
_pdbx_chem_comp_synonyms.comp_id     VSD
_pdbx_chem_comp_synonyms.name        "(2S,6E)-2-amino-1-hydroxyoctadec-6-en-3-one"
_pdbx_chem_comp_synonyms.provenance  PDB
_pdbx_chem_comp_synonyms.type        ?
##
