data_Y7S
#

_chem_comp.id                                   Y7S
_chem_comp.name                                 "(1~{R},3~{S},4~{R})-3-methyl-4-[[2-methyl-3-oxidanyl-5-(phosphonooxymethyl)pyridin-4-yl]methylamino]cyclopentane-1-carboxylic acid"
_chem_comp.type                                 non-polymer
_chem_comp.pdbx_type                            HETAIN
_chem_comp.formula                              "C15 H21 N2 O7 P"
_chem_comp.mon_nstd_parent_comp_id              ?
_chem_comp.pdbx_synonyms                        ?
_chem_comp.pdbx_formal_charge                   0
_chem_comp.pdbx_initial_date                    2021-02-09
_chem_comp.pdbx_modified_date                   2021-08-20
_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                       372.310
_chem_comp.one_letter_code                      ?
_chem_comp.three_letter_code                    ?
_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       7LNM
_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
Y7S  C11  C1   C  0  1  Y  N  N  -4.610   3.640  -6.328   2.965  -1.852  -0.014  C11  Y7S   1  
Y7S  C12  C2   C  0  1  Y  N  N  -4.773   2.636  -5.357   1.868  -1.043   0.216  C12  Y7S   2  
Y7S  C13  C3   C  0  1  Y  N  N  -5.732   1.634  -5.546   0.627  -1.626   0.416  C13  Y7S   3  
Y7S  C14  C4   C  0  1  N  N  N  -3.882   2.618  -4.089   2.019   0.456   0.248  C14  Y7S   4  
Y7S  C16  C5   C  0  1  N  N  N  -7.153   2.843  -8.944   1.597  -5.263   0.093  C16  Y7S   5  
Y7S  C17  C6   C  0  1  N  N  N  -4.434  -2.666  -4.088  -3.270  -0.475  -2.820  C17  Y7S   6  
Y7S  C18  C7   C  0  1  N  N  N  -7.404  -2.982  -0.358  -5.351   1.267   0.975  C18  Y7S   7  
Y7S  C01  C8   C  0  1  N  N  S  -5.908  -2.862  -3.637  -3.126   0.726  -1.882  C01  Y7S   8  
Y7S  C02  C9   C  0  1  N  N  N  -6.280  -3.651  -2.448  -4.514   1.192  -1.388  C02  Y7S   9  
Y7S  C03  C10  C  0  1  N  N  N  -6.766  -1.776  -3.760  -2.384   0.327  -0.628  C03  Y7S  10  
Y7S  C05  C11  C  0  1  N  N  N  -7.461  -1.580  -2.465  -2.973   0.815   0.442  C05  Y7S  11  
Y7S  C06  C12  C  0  1  N  N  N  -5.907   0.473  -4.420  -0.593  -0.779   0.669  C06  Y7S  12  
Y7S  C07  C13  C  0  1  N  N  R  -7.560  -3.001  -1.743  -4.199   1.614   0.066  C07  Y7S  13  
Y7S  C08  C14  C  0  1  Y  N  N  -6.506   1.718  -6.721   0.535  -3.014   0.379  C08  Y7S  14  
Y7S  C09  C15  C  0  1  Y  N  N  -6.301   2.762  -7.652   1.682  -3.759   0.142  C09  Y7S  15  
Y7S  N04  N1   N  0  1  N  N  N  -6.621  -0.755  -4.863  -1.233  -0.451  -0.607  N04  Y7S  16  
Y7S  N10  N2   N  0  1  Y  N  N  -5.373   3.677  -7.428   2.842  -3.164  -0.049  N10  Y7S  17  
Y7S  O15  O1   O  0  1  N  N  N  -7.487   0.771  -6.972  -0.661  -3.631   0.570  O15  Y7S  18  
Y7S  O19  O2   O  0  1  N  N  N  -6.308  -3.305   0.157  -6.337   0.734   0.523  O19  Y7S  19  
Y7S  O20  O3   O  0  1  N  N  N  -8.355  -2.663   0.389  -5.281   1.550   2.285  O20  Y7S  20  
Y7S  O39  O4   O  0  1  N  N  N  -2.952   1.543  -4.261   3.386   0.802   0.015  O39  Y7S  21  
Y7S  O41  O5   O  0  1  N  N  N  -3.120   0.044  -2.115   3.736   2.985   1.437  O41  Y7S  22  
Y7S  O42  O6   O  0  1  N  N  N  -1.703   2.077  -2.055   5.468   2.343  -0.433  O42  Y7S  23  
Y7S  O43  O7   O  0  1  N  N  N  -0.990   0.098  -3.426   3.128   3.094  -1.010  O43  Y7S  24  
Y7S  P40  P1   P  0  1  N  N  N  -2.166   0.921  -2.922   3.912   2.323  -0.020  P40  Y7S  25  
Y7S  H1   H1   H  0  1  N  N  N  -3.854   4.397  -6.184   3.934  -1.403  -0.171  H1   Y7S  26  
Y7S  H2   H2   H  0  1  N  N  N  -3.345   3.573  -3.988   1.395   0.901  -0.527  H2   Y7S  27  
Y7S  H3   H3   H  0  1  N  N  N  -4.498   2.448  -3.194   1.710   0.832   1.223  H3   Y7S  28  
Y7S  H4   H4   H  0  1  N  N  N  -6.841   3.716  -9.536   1.765  -5.669   1.090  H4   Y7S  29  
Y7S  H5   H5   H  0  1  N  N  N  -7.008   1.928  -9.537   0.608  -5.559  -0.259  H5   Y7S  30  
Y7S  H6   H6   H  0  1  N  N  N  -8.215   2.942  -8.677   2.355  -5.647  -0.590  H6   Y7S  31  
Y7S  H7   H7   H  0  1  N  N  N  -3.876  -3.601  -3.935  -3.878  -0.193  -3.680  H7   Y7S  32  
Y7S  H8   H8   H  0  1  N  N  N  -4.410  -2.395  -5.154  -2.284  -0.791  -3.159  H8   Y7S  33  
Y7S  H9   H9   H  0  1  N  N  N  -3.973  -1.862  -3.495  -3.752  -1.295  -2.288  H9   Y7S  34  
Y7S  H10  H10  H  0  1  N  N  N  -6.272  -3.519  -4.441  -2.609   1.541  -2.388  H10  Y7S  35  
Y7S  H11  H11  H  0  1  N  N  N  -6.515  -4.681  -2.753  -4.872   2.040  -1.971  H11  Y7S  36  
Y7S  H12  H12  H  0  1  N  N  N  -5.439  -3.661  -1.739  -5.233   0.373  -1.410  H12  Y7S  37  
Y7S  H14  H14  H  0  1  N  N  N  -7.834  -0.643  -2.079  -2.628   0.664   1.454  H14  Y7S  38  
Y7S  H16  H16  H  0  1  N  N  N  -4.903   0.177  -4.082  -1.294  -1.329   1.297  H16  Y7S  39  
Y7S  H17  H17  H  0  1  N  N  N  -6.466   0.903  -3.576  -0.298   0.141   1.174  H17  Y7S  40  
Y7S  H18  H18  H  0  1  N  N  N  -8.472  -3.524  -2.066  -3.986   2.682   0.114  H18  Y7S  41  
Y7S  H19  H19  H  0  1  N  N  N  -7.533  -0.497  -5.182  -0.853  -0.777  -1.438  H19  Y7S  42  
Y7S  H21  H21  H  0  1  N  N  N  -7.506   0.139  -6.263  -1.164  -3.775  -0.243  H21  Y7S  43  
Y7S  H22  H22  H  0  1  N  N  N  -8.078  -2.719   1.296  -6.044   1.309   2.827  H22  Y7S  44  
Y7S  H23  H23  H  0  1  N  N  N  -2.787  -0.845  -2.088   4.224   2.530   2.138  H23  Y7S  45  
Y7S  H24  H24  H  0  1  N  N  N  -0.755   2.066  -1.992   5.853   3.230  -0.474  H24  Y7S  46  
#   #
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
Y7S  C16  C09  SING  N  N   1  
Y7S  C09  N10  DOUB  Y  N   2  
Y7S  C09  C08  SING  Y  N   3  
Y7S  N10  C11  SING  Y  N   4  
Y7S  O15  C08  SING  N  N   5  
Y7S  C08  C13  DOUB  Y  N   6  
Y7S  C11  C12  DOUB  Y  N   7  
Y7S  C13  C12  SING  Y  N   8  
Y7S  C13  C06  SING  N  N   9  
Y7S  C12  C14  SING  N  N  10  
Y7S  N04  C06  SING  N  N  11  
Y7S  N04  C03  SING  N  N  12  
Y7S  O39  C14  SING  N  N  13  
Y7S  O39  P40  SING  N  N  14  
Y7S  C17  C01  SING  N  N  15  
Y7S  C03  C01  SING  N  N  16  
Y7S  C03  C05  DOUB  N  N  17  
Y7S  C01  C02  SING  N  N  18  
Y7S  O43  P40  DOUB  N  N  19  
Y7S  P40  O41  SING  N  N  20  
Y7S  P40  O42  SING  N  N  21  
Y7S  C05  C07  SING  N  N  22  
Y7S  C02  C07  SING  N  N  23  
Y7S  C07  C18  SING  N  N  24  
Y7S  C18  O19  DOUB  N  N  25  
Y7S  C18  O20  SING  N  N  26  
Y7S  C11  H1   SING  N  N  27  
Y7S  C14  H2   SING  N  N  28  
Y7S  C14  H3   SING  N  N  29  
Y7S  C16  H4   SING  N  N  30  
Y7S  C16  H5   SING  N  N  31  
Y7S  C16  H6   SING  N  N  32  
Y7S  C17  H7   SING  N  N  33  
Y7S  C17  H8   SING  N  N  34  
Y7S  C17  H9   SING  N  N  35  
Y7S  C01  H10  SING  N  N  36  
Y7S  C02  H11  SING  N  N  37  
Y7S  C02  H12  SING  N  N  38  
Y7S  C05  H14  SING  N  N  39  
Y7S  C06  H16  SING  N  N  40  
Y7S  C06  H17  SING  N  N  41  
Y7S  C07  H18  SING  N  N  42  
Y7S  N04  H19  SING  N  N  43  
Y7S  O15  H21  SING  N  N  44  
Y7S  O20  H22  SING  N  N  45  
Y7S  O41  H23  SING  N  N  46  
Y7S  O42  H24  SING  N  N  47  
#   #
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
Y7S  SMILES            ACDLabs               12.01  "Oc1c(CNC2=CC(CC2C)C(=O)O)c(cnc1C)COP(=O)(O)O"  
Y7S  InChI             InChI                 1.03   "InChI=1S/C15H21N2O7P/c1-8-3-10(15(19)20)4-13(8)17-6-12-11(7-24-25(21,22)23)5-16-9(2)14(12)18/h4-5,8,10,17-18H,3,6-7H2,1-2H3,(H,19,20)(H2,21,22,23)/t8-,10+/m0/s1"  
Y7S  InChIKey          InChI                 1.03   LZIGREAGJMTTOE-WCBMZHEXSA-N  
Y7S  SMILES_CANONICAL  CACTVS                3.385  "C[C@H]1C[C@H](C=C1NCc2c(O)c(C)ncc2CO[P](O)(O)=O)C(O)=O"  
Y7S  SMILES            CACTVS                3.385  "C[CH]1C[CH](C=C1NCc2c(O)c(C)ncc2CO[P](O)(O)=O)C(O)=O"  
Y7S  SMILES_CANONICAL  "OpenEye OEToolkits"  2.0.7  "Cc1c(c(c(cn1)COP(=O)(O)O)CNC2=C[C@@H](C[C@@H]2C)C(=O)O)O"  
Y7S  SMILES            "OpenEye OEToolkits"  2.0.7  "Cc1c(c(c(cn1)COP(=O)(O)O)CNC2=CC(CC2C)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
Y7S  "SYSTEMATIC NAME"  ACDLabs               12.01  "(1R,4S)-3-[({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl)amino]-4-methylcyclopent-2-ene-1-carboxylic acid"  
Y7S  "SYSTEMATIC NAME"  "OpenEye OEToolkits"  2.0.7  "(1~{R},4~{S})-4-methyl-3-[[2-methyl-3-oxidanyl-5-(phosphonooxymethyl)pyridin-4-yl]methylamino]cyclopent-2-ene-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
Y7S  "Create component"    2021-02-09  RCSB  
Y7S  "Modify value order"  2021-08-17  RCSB  
Y7S  "Initial release"     2021-08-25  RCSB  
##
