data_Y3D
#

_chem_comp.id                                   Y3D
_chem_comp.name                                 "(1R,3S)-3-[(E)-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene)amino]-4-oxocyclopentane-1-carboxylic acid"
_chem_comp.type                                 non-polymer
_chem_comp.pdbx_type                            HETAIN
_chem_comp.formula                              "C14 H17 N2 O8 P"
_chem_comp.mon_nstd_parent_comp_id              ?
_chem_comp.pdbx_synonyms                        ?
_chem_comp.pdbx_formal_charge                   0
_chem_comp.pdbx_initial_date                    2021-02-01
_chem_comp.pdbx_modified_date                   2022-02-11
_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                       372.267
_chem_comp.one_letter_code                      ?
_chem_comp.three_letter_code                    Y3D
_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       7LK0
_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
Y3D  C15  C1   C  0  1  N  N  N  65.872  -49.997   -5.016  -0.329   0.040   0.144  C15  Y3D   1  
Y3D  C17  C2   C  0  1  N  N  S  64.427  -51.493   -6.172  -2.505   1.011   0.327  C17  Y3D   2  
Y3D  C18  C3   C  0  1  N  N  N  64.267  -50.617   -7.391  -3.502   0.995  -0.850  C18  Y3D   3  
Y3D  C19  C4   C  0  1  N  N  R  63.980  -51.501   -8.589  -4.825   1.500  -0.219  C19  Y3D   4  
Y3D  C20  C5   C  0  1  N  N  N  63.688  -52.918   -8.066  -4.785   0.858   1.190  C20  Y3D   5  
Y3D  C21  C6   C  0  1  N  N  N  64.131  -52.925   -6.593  -3.324   0.932   1.598  C21  Y3D   6  
Y3D  C01  C7   C  0  1  Y  N  N  67.242  -50.453   -1.717   0.967  -3.492  -0.016  C01  Y3D   7  
Y3D  C03  C8   C  0  1  Y  N  N  68.470  -48.821   -2.808   2.774  -2.062  -0.125  C03  Y3D   8  
Y3D  C04  C9   C  0  1  Y  N  N  67.674  -48.953   -3.936   1.963  -0.948  -0.043  C04  Y3D   9  
Y3D  C05  C10  C  0  1  Y  N  N  66.634  -49.863   -3.940   0.577  -1.121   0.053  C05  Y3D  10  
Y3D  C06  C11  C  0  1  Y  N  N  66.408  -50.633   -2.815   0.075  -2.433   0.066  C06  Y3D  11  
Y3D  C07  C12  C  0  1  N  N  N  66.997  -51.286   -0.461   0.446  -4.906  -0.003  C07  Y3D  12  
Y3D  C09  C13  C  0  1  N  N  N  67.951  -48.111   -5.181   2.561   0.435  -0.062  C09  Y3D  13  
Y3D  C23  C14  C  0  1  N  N  N  64.536  -51.209   -9.978  -6.014   1.004  -1.000  C23  Y3D  14  
Y3D  N02  N1   N  0  1  Y  N  N  68.240  -49.578   -1.734   2.263  -3.277  -0.109  N02  Y3D  15  
Y3D  N16  N2   N  0  1  N  N  N  65.023  -51.177   -5.109  -1.605  -0.141   0.237  N16  Y3D  16  
Y3D  O08  O1   O  0  1  N  N  N  65.372  -51.577   -2.767  -1.260  -2.659   0.157  O08  Y3D  17  
Y3D  O10  O2   O  0  1  N  N  N  67.104  -46.998   -5.253   3.982   0.339  -0.170  O10  Y3D  18  
Y3D  O12  O3   O  0  1  N  N  N  66.193  -47.245   -7.635   4.520   2.523  -1.316  O12  Y3D  19  
Y3D  O13  O4   O  0  1  N  N  N  68.401  -46.007   -7.352   4.861   2.414   1.183  O13  Y3D  20  
Y3D  O14  O5   O  0  1  N  N  N  66.068  -45.138   -6.652   6.464   1.151  -0.474  O14  Y3D  21  
Y3D  O22  O6   O  0  1  N  N  N  64.233  -53.881   -5.900  -2.895   0.926   2.727  O22  Y3D  22  
Y3D  O24  O7   O  0  1  N  N  N  65.745  -50.873  -10.099  -7.257   1.237  -0.551  O24  Y3D  23  
Y3D  O25  O8   O  0  1  N  N  N  63.794  -51.309  -10.985  -5.849   0.396  -2.032  O25  Y3D  24  
Y3D  P11  P1   P  0  1  N  N  N  66.924  -46.326   -6.746   4.948   1.626  -0.218  P11  Y3D  25  
Y3D  H1   H1   H  0  1  N  N  N  65.880  -49.254   -5.800   0.075   1.042   0.136  H1   Y3D  26  
Y3D  H2   H2   H  0  1  N  N  N  63.414  -51.301   -5.789  -1.928   1.936   0.313  H2   Y3D  27  
Y3D  H3   H3   H  0  1  N  N  N  65.193  -50.049   -7.563  -3.173   1.669  -1.641  H3   Y3D  28  
Y3D  H4   H4   H  0  1  N  N  N  63.431  -49.918   -7.238  -3.622  -0.017  -1.237  H4   Y3D  29  
Y3D  H5   H5   H  0  1  N  N  N  62.941  -51.187   -8.769  -4.831   2.588  -0.150  H5   Y3D  30  
Y3D  H6   H6   H  0  1  N  N  N  62.613  -53.140   -8.143  -5.403   1.427   1.885  H6   Y3D  31  
Y3D  H7   H7   H  0  1  N  N  N  64.259  -53.663   -8.640  -5.117  -0.179   1.146  H7   Y3D  32  
Y3D  H8   H8   H  0  1  N  N  N  69.278  -48.104   -2.799   3.843  -1.935  -0.204  H8   Y3D  33  
Y3D  H9   H9   H  0  1  N  N  N  67.739  -51.020    0.306   0.247  -5.229  -1.025  H9   Y3D  34  
Y3D  H10  H10  H  0  1  N  N  N  65.986  -51.084   -0.078   1.189  -5.564   0.448  H10  Y3D  35  
Y3D  H11  H11  H  0  1  N  N  N  67.089  -52.354   -0.706  -0.476  -4.949   0.577  H11  Y3D  36  
Y3D  H12  H12  H  0  1  N  N  N  67.797  -48.734   -6.074   2.168   0.989  -0.914  H12  Y3D  37  
Y3D  H13  H13  H  0  1  N  N  N  68.994  -47.764   -5.151   2.301   0.956   0.860  H13  Y3D  38  
Y3D  H14  H14  H  0  1  N  N  N  65.373  -52.006   -1.919  -1.710  -2.710  -0.698  H14  Y3D  39  
Y3D  H15  H15  H  0  1  N  N  N  68.516  -46.476   -8.170   5.128   1.886   1.948  H15  Y3D  40  
Y3D  H16  H16  H  0  1  N  N  N  65.286  -45.268   -7.176   7.103   1.876  -0.515  H16  Y3D  41  
Y3D  H17  H17  H  0  1  N  N  N  65.944  -50.730  -11.017  -7.989   0.900  -1.086  H17  Y3D  42  
#   #
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
Y3D  O25  C23  DOUB  N  N   1  
Y3D  O24  C23  SING  N  N   2  
Y3D  C23  C19  SING  N  N   3  
Y3D  C19  C20  SING  N  N   4  
Y3D  C19  C18  SING  N  N   5  
Y3D  C20  C21  SING  N  N   6  
Y3D  O12  P11  DOUB  N  N   7  
Y3D  C18  C17  SING  N  N   8  
Y3D  O13  P11  SING  N  N   9  
Y3D  P11  O14  SING  N  N  10  
Y3D  P11  O10  SING  N  N  11  
Y3D  C21  C17  SING  N  N  12  
Y3D  C21  O22  DOUB  N  N  13  
Y3D  C17  N16  SING  N  N  14  
Y3D  O10  C09  SING  N  N  15  
Y3D  C09  C04  SING  N  N  16  
Y3D  N16  C15  DOUB  N  N  17  
Y3D  C15  C05  SING  N  N  18  
Y3D  C05  C04  DOUB  Y  N  19  
Y3D  C05  C06  SING  Y  N  20  
Y3D  C04  C03  SING  Y  N  21  
Y3D  C06  O08  SING  N  N  22  
Y3D  C06  C01  DOUB  Y  N  23  
Y3D  C03  N02  DOUB  Y  N  24  
Y3D  N02  C01  SING  Y  N  25  
Y3D  C01  C07  SING  N  N  26  
Y3D  C15  H1   SING  N  N  27  
Y3D  C17  H2   SING  N  N  28  
Y3D  C18  H3   SING  N  N  29  
Y3D  C18  H4   SING  N  N  30  
Y3D  C19  H5   SING  N  N  31  
Y3D  C20  H6   SING  N  N  32  
Y3D  C20  H7   SING  N  N  33  
Y3D  C03  H8   SING  N  N  34  
Y3D  C07  H9   SING  N  N  35  
Y3D  C07  H10  SING  N  N  36  
Y3D  C07  H11  SING  N  N  37  
Y3D  C09  H12  SING  N  N  38  
Y3D  C09  H13  SING  N  N  39  
Y3D  O08  H14  SING  N  N  40  
Y3D  O13  H15  SING  N  N  41  
Y3D  O14  H16  SING  N  N  42  
Y3D  O24  H17  SING  N  N  43  
#   #
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
Y3D  SMILES            ACDLabs               12.01  "[C@H](c1c(cnc(C)c1O)COP(=O)(O)O)=NC2CC(CC2=O)C(O)=O"  
Y3D  InChI             InChI                 1.03   "InChI=1S/C14H17N2O8P/c1-7-13(18)10(9(4-15-7)6-24-25(21,22)23)5-16-11-2-8(14(19)20)3-12(11)17/h4-5,8,11,18H,2-3,6H2,1H3,(H,19,20)(H2,21,22,23)/b16-5+/t8-,11+/m1/s1"  
Y3D  InChIKey          InChI                 1.03   XLGFWCHBZWEILL-SNTOBFBISA-N  
Y3D  SMILES_CANONICAL  CACTVS                3.385  "Cc1ncc(CO[P](O)(O)=O)c(C=N[C@H]2C[C@H](CC2=O)C(O)=O)c1O"  
Y3D  SMILES            CACTVS                3.385  "Cc1ncc(CO[P](O)(O)=O)c(C=N[CH]2C[CH](CC2=O)C(O)=O)c1O"  
Y3D  SMILES_CANONICAL  "OpenEye OEToolkits"  2.0.7  "Cc1c(c(c(cn1)COP(=O)(O)O)/C=N/[C@H]2C[C@H](CC2=O)C(=O)O)O"  
Y3D  SMILES            "OpenEye OEToolkits"  2.0.7  "Cc1c(c(c(cn1)COP(=O)(O)O)C=NC2CC(CC2=O)C(=O)O)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
Y3D  "SYSTEMATIC NAME"  ACDLabs               12.01  "(1R,3S)-3-[(E)-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene)amino]-4-oxocyclopentane-1-carboxylic acid"  
Y3D  "SYSTEMATIC NAME"  "OpenEye OEToolkits"  2.0.7  "(1~{R},3~{S})-3-[(~{E})-[2-methyl-3-oxidanyl-5-(phosphonooxymethyl)pyridin-4-yl]methylideneamino]-4-oxidanylidene-cyclopentane-1-carboxylic 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
Y3D  "Create component"  2021-02-01  RCSB  
Y3D  "Initial release"   2022-02-16  RCSB  
##
