data_YAD
#

_chem_comp.id                                   YAD
_chem_comp.name                                 "(phenylmethyl) (2~{S})-2-[5-oxidanyl-6-oxidanylidene-4-(2-pyridin-4-ylethylcarbamoyl)-1~{H}-pyrimidin-2-yl]pyrrolidine-1-carboxylate"
_chem_comp.type                                 non-polymer
_chem_comp.pdbx_type                            HETAIN
_chem_comp.formula                              "C24 H25 N5 O5"
_chem_comp.mon_nstd_parent_comp_id              ?
_chem_comp.pdbx_synonyms                        ?
_chem_comp.pdbx_formal_charge                   0
_chem_comp.pdbx_initial_date                    2021-02-15
_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                       463.486
_chem_comp.one_letter_code                      ?
_chem_comp.three_letter_code                    YAD
_chem_comp.pdbx_model_coordinates_details       ?
_chem_comp.pdbx_model_coordinates_missing_flag  Y
_chem_comp.pdbx_ideal_coordinates_details       Corina
_chem_comp.pdbx_ideal_coordinates_missing_flag  N
_chem_comp.pdbx_model_coordinates_db_code       7LP7
_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
YAD  O15  O1   O  0  1  N  N  N  -32.330  6.971  12.894   2.625  -1.732   1.038  O15  YAD   1  
YAD  O16  O2   O  0  1  N  N  N  -30.622  7.369  14.303   1.020  -2.823  -0.038  O16  YAD   2  
YAD  C02  C1   C  0  1  N  N  N  -29.147  4.616  17.641   2.707   3.007   1.105  C02  YAD   3  
YAD  C03  C2   C  0  1  N  N  N  -30.138  4.034  16.707   1.713   2.284   0.465  C03  YAD   4  
YAD  C05  C3   C  0  1  N  N  N  -31.462  6.173  16.822   3.280   0.820  -0.410  C05  YAD   5  
YAD  C07  C4   C  0  1  N  N  N  -29.324  6.003  18.169   4.095   2.558   0.936  C07  YAD   6  
YAD  C09  C5   C  0  1  N  N  S  -32.674  6.918  16.370   3.565  -0.395  -1.255  C09  YAD   7  
YAD  C10  C6   C  0  1  N  N  N  -33.993  6.319  17.212   3.671   0.012  -2.740  C10  YAD   8  
YAD  C11  C7   C  0  1  N  N  N  -34.462  5.310  16.530   2.982  -1.168  -3.474  C11  YAD   9  
YAD  C12  C8   C  0  1  N  N  N  -34.005  5.544  15.030   1.855  -1.539  -2.478  C12  YAD  10  
YAD  C14  C9   C  0  1  N  N  N  -31.950  7.001  14.018   2.054  -1.961  -0.010  C14  YAD  11  
YAD  C24  C10  C  0  1  N  N  N  -29.959  2.622  16.169   0.296   2.691   0.592  C24  YAD  12  
YAD  C27  C11  C  0  1  N  N  N  -30.443  0.935  14.367  -2.070   2.386   0.093  C27  YAD  13  
YAD  C28  C12  C  0  1  N  N  N  -29.953  0.989  12.916  -2.950   1.423  -0.707  C28  YAD  14  
YAD  C29  C13  C  0  1  Y  N  N  -30.574  2.094  12.056  -4.393   1.837  -0.577  C29  YAD  15  
YAD  C30  C14  C  0  1  Y  N  N  -31.943  2.305  12.005  -4.960   2.727  -1.477  C30  YAD  16  
YAD  C31  C15  C  0  1  Y  N  N  -32.463  3.309  11.196  -6.287   3.083  -1.327  C31  YAD  17  
YAD  C33  C16  C  0  1  Y  N  N  -30.359  3.908  10.478  -6.507   1.735   0.527  C33  YAD  18  
YAD  C34  C17  C  0  1  Y  N  N  -29.786  2.920  11.267  -5.188   1.333   0.441  C34  YAD  19  
YAD  N04  N1   N  0  1  N  N  N  -31.281  4.802  16.299   2.047   1.210  -0.273  N04  YAD  20  
YAD  N06  N2   N  0  1  N  N  N  -30.480  6.783  17.758   4.318   1.466   0.173  N06  YAD  21  
YAD  N13  N3   N  0  1  N  N  N  -32.867  6.653  15.091   2.455  -1.353  -1.144  N13  YAD  22  
YAD  N26  N4   N  0  1  N  N  N  -30.592  2.272  14.917  -0.667   1.983  -0.032  N26  YAD  23  
YAD  N32  N5   N  0  1  Y  N  N  -31.671  4.076  10.464  -7.011   2.587  -0.344  N32  YAD  24  
YAD  O01  O3   O  0  1  N  N  N  -28.054  3.826  18.003   2.409   4.096   1.857  O01  YAD  25  
YAD  O08  O4   O  0  1  N  N  N  -28.527  6.469  18.919   5.017   3.152   1.468  O08  YAD  26  
YAD  O25  O5   O  0  1  N  N  N  -29.309  1.833  16.765  -0.001   3.662   1.260  O25  YAD  27  
YAD  H2   H2   H  0  1  N  N  N  -32.578  7.992  16.590   4.495  -0.862  -0.931  H2   YAD  28  
YAD  H3   H3   H  0  1  N  N  N  -33.681  5.985  18.212   3.138   0.945  -2.924  H3   YAD  29  
YAD  H4   H4   H  0  1  N  N  N  -34.763  7.098  17.309   4.715   0.101  -3.042  H4   YAD  30  
YAD  H5   H5   H  0  1  N  N  N  -35.560  5.282  16.595   2.568  -0.846  -4.430  H5   YAD  31  
YAD  H6   H6   H  0  1  N  N  N  -34.048  4.365  16.912   3.673  -2.000  -3.611  H6   YAD  32  
YAD  H7   H7   H  0  1  N  N  N  -34.851  5.897  14.422   1.002  -0.874  -2.606  H7   YAD  33  
YAD  H8   H8   H  0  1  N  N  N  -33.609  4.612  14.601   1.553  -2.577  -2.616  H8   YAD  34  
YAD  H9   H9   H  0  1  N  N  N  -31.416  0.422  14.399  -2.194   3.398  -0.293  H9   YAD  35  
YAD  H10  H10  H  0  1  N  N  N  -29.714  0.376  14.972  -2.363   2.359   1.143  H10  YAD  36  
YAD  H11  H11  H  0  1  N  N  N  -30.182  0.022  12.444  -2.657   1.450  -1.756  H11  YAD  37  
YAD  H12  H12  H  0  1  N  N  N  -28.864  1.141  12.931  -2.826   0.412  -0.320  H12  YAD  38  
YAD  H13  H13  H  0  1  N  N  N  -32.606  1.689  12.594  -4.372   3.137  -2.285  H13  YAD  39  
YAD  H14  H14  H  0  1  N  N  N  -33.531  3.466  11.164  -6.735   3.776  -2.024  H14  YAD  40  
YAD  H15  H15  H  0  1  N  N  N  -29.730  4.543   9.872  -7.133   1.346   1.317  H15  YAD  41  
YAD  H16  H16  H  0  1  N  N  N  -28.714  2.793  11.267  -4.781   0.635   1.157  H16  YAD  42  
YAD  H17  H17  H  0  1  N  N  N  -30.613  7.714  18.099   5.224   1.141   0.045  H17  YAD  43  
YAD  H18  H18  H  0  1  N  N  N  -31.135  2.954  14.427  -0.431   1.208  -0.565  H18  YAD  44  
YAD  H19  H19  H  0  1  N  N  N  -28.183  2.941  17.683   3.180   4.524   2.253  H19  YAD  45  
YAD  C35  C35  C  0  1  N  N  N        ?      ?       ?   0.641  -3.441   1.220  C35  YAD  46  
YAD  C36  C36  C  0  1  Y  N  N        ?      ?       ?  -0.526  -4.367   0.994  C36  YAD  47  
YAD  C37  C37  C  0  1  Y  N  N        ?      ?       ?  -0.304  -5.694   0.675  C37  YAD  48  
YAD  C38  C38  C  0  1  Y  N  N        ?      ?       ?  -1.374  -6.543   0.468  C38  YAD  49  
YAD  C39  C39  C  0  1  Y  N  N        ?      ?       ?  -2.667  -6.066   0.581  C39  YAD  50  
YAD  C40  C40  C  0  1  Y  N  N        ?      ?       ?  -2.889  -4.740   0.900  C40  YAD  51  
YAD  C41  C41  C  0  1  Y  N  N        ?      ?       ?  -1.818  -3.891   1.112  C41  YAD  52  
YAD  H1   H1   H  0  1  N  N  N        ?      ?       ?   1.485  -4.008   1.614  H1   YAD  53  
YAD  H20  H20  H  0  1  N  N  N        ?      ?       ?   0.359  -2.667   1.934  H20  YAD  54  
YAD  H21  H21  H  0  1  N  N  N        ?      ?       ?   0.706  -6.066   0.588  H21  YAD  55  
YAD  H22  H22  H  0  1  N  N  N        ?      ?       ?  -1.201  -7.580   0.219  H22  YAD  56  
YAD  H23  H23  H  0  1  N  N  N        ?      ?       ?  -3.503  -6.730   0.418  H23  YAD  57  
YAD  H24  H24  H  0  1  N  N  N        ?      ?       ?  -3.899  -4.367   0.988  H24  YAD  58  
YAD  H25  H25  H  0  1  N  N  N        ?      ?       ?  -1.992  -2.855   1.362  H25  YAD  59  
#   #
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
YAD  N32  C33  DOUB  Y  N   1  
YAD  N32  C31  SING  Y  N   2  
YAD  C33  C34  SING  Y  N   3  
YAD  C31  C30  DOUB  Y  N   4  
YAD  C34  C29  DOUB  Y  N   5  
YAD  C30  C29  SING  Y  N   6  
YAD  C29  C28  SING  N  N   7  
YAD  O15  C14  DOUB  N  N   8  
YAD  C28  C27  SING  N  N   9  
YAD  C14  O16  SING  N  N  10  
YAD  C14  N13  SING  N  N  11  
YAD  C27  N26  SING  N  N  12  
YAD  N26  C24  SING  N  N  13  
YAD  C12  N13  SING  N  N  14  
YAD  C12  C11  SING  N  N  15  
YAD  N13  C09  SING  N  N  16  
YAD  C24  C03  SING  N  N  17  
YAD  C24  O25  DOUB  N  N  18  
YAD  N04  C03  SING  N  N  19  
YAD  N04  C05  DOUB  N  N  20  
YAD  C09  C05  SING  N  N  21  
YAD  C09  C10  SING  N  N  22  
YAD  C11  C10  SING  N  N  23  
YAD  C03  C02  DOUB  N  N  24  
YAD  C05  N06  SING  N  N  25  
YAD  C02  O01  SING  N  N  26  
YAD  C02  C07  SING  N  N  27  
YAD  N06  C07  SING  N  N  28  
YAD  C07  O08  DOUB  N  N  29  
YAD  C09  H2   SING  N  N  30  
YAD  C10  H3   SING  N  N  31  
YAD  C10  H4   SING  N  N  32  
YAD  C11  H5   SING  N  N  33  
YAD  C11  H6   SING  N  N  34  
YAD  C12  H7   SING  N  N  35  
YAD  C12  H8   SING  N  N  36  
YAD  C27  H9   SING  N  N  37  
YAD  C27  H10  SING  N  N  38  
YAD  C28  H11  SING  N  N  39  
YAD  C28  H12  SING  N  N  40  
YAD  C30  H13  SING  N  N  41  
YAD  C31  H14  SING  N  N  42  
YAD  C33  H15  SING  N  N  43  
YAD  C34  H16  SING  N  N  44  
YAD  N06  H17  SING  N  N  45  
YAD  N26  H18  SING  N  N  46  
YAD  O01  H19  SING  N  N  47  
YAD  O16  C35  SING  N  N  48  
YAD  C35  C36  SING  N  N  49  
YAD  C36  C37  SING  Y  N  50  
YAD  C37  C38  DOUB  Y  N  51  
YAD  C38  C39  SING  Y  N  52  
YAD  C39  C40  DOUB  Y  N  53  
YAD  C40  C41  SING  Y  N  54  
YAD  C41  C36  DOUB  Y  N  55  
YAD  C35  H1   SING  N  N  56  
YAD  C35  H20  SING  N  N  57  
YAD  C37  H21  SING  N  N  58  
YAD  C38  H22  SING  N  N  59  
YAD  C39  H23  SING  N  N  60  
YAD  C40  H24  SING  N  N  61  
YAD  C41  H25  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
YAD  InChI             InChI                 1.03   "InChI=1S/C24H25N5O5/c30-20-19(22(31)26-13-10-16-8-11-25-12-9-16)27-21(28-23(20)32)18-7-4-14-29(18)24(33)34-15-17-5-2-1-3-6-17/h1-3,5-6,8-9,11-12,18,30H,4,7,10,13-15H2,(H,26,31)(H,27,28,32)/t18-/m0/s1"  
YAD  InChIKey          InChI                 1.03   PLCSROHBVUGSBJ-SFHVURJKSA-N  
YAD  SMILES_CANONICAL  CACTVS                3.385  "OC1=C(N=C(NC1=O)[C@@H]2CCCN2C(=O)OCc3ccccc3)C(=O)NCCc4ccncc4"  
YAD  SMILES            CACTVS                3.385  "OC1=C(N=C(NC1=O)[CH]2CCCN2C(=O)OCc3ccccc3)C(=O)NCCc4ccncc4"  
YAD  SMILES_CANONICAL  "OpenEye OEToolkits"  2.0.7  "c1ccc(cc1)COC(=O)N2CCC[C@H]2C3=NC(=C(C(=O)N3)O)C(=O)NCCc4ccncc4"  
YAD  SMILES            "OpenEye OEToolkits"  2.0.7  "c1ccc(cc1)COC(=O)N2CCCC2C3=NC(=C(C(=O)N3)O)C(=O)NCCc4ccncc4"  
#
_pdbx_chem_comp_identifier.comp_id          YAD
_pdbx_chem_comp_identifier.type             "SYSTEMATIC NAME"
_pdbx_chem_comp_identifier.program          "OpenEye OEToolkits"
_pdbx_chem_comp_identifier.program_version  2.0.7
_pdbx_chem_comp_identifier.identifier       "(phenylmethyl) (2~{S})-2-[5-oxidanyl-6-oxidanylidene-4-(2-pyridin-4-ylethylcarbamoyl)-1~{H}-pyrimidin-2-yl]pyrrolidine-1-carboxylate"
#   #
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
YAD  "Create component"  2021-02-15  RCSB  
YAD  "Initial release"   2022-02-16  RCSB  
##
