data_5YY
#

_chem_comp.id                                   5YY
_chem_comp.name                                 "ethyl 2-(2-(4-azido-N-((2-(1,5-dimethyl-6-oxo-1,6-dihydropyridin-3-yl)-1-((tetrahydro-2H-pyran-4-yl)methyl)-1H-benzo[d]imidazol-6-yl)methyl)benzamido)acetamido)acetate"
_chem_comp.type                                 non-polymer
_chem_comp.pdbx_type                            HETAIN
_chem_comp.formula                              "C34 H39 N8 O6"
_chem_comp.mon_nstd_parent_comp_id              ?
_chem_comp.pdbx_synonyms                        ?
_chem_comp.pdbx_formal_charge                   1
_chem_comp.pdbx_initial_date                    2021-07-20
_chem_comp.pdbx_modified_date                   2021-10-01
_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                       655.723
_chem_comp.one_letter_code                      ?
_chem_comp.three_letter_code                    5YY
_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       7P6W
_chem_comp.pdbx_subcomponent_list               ?
_chem_comp.pdbx_processing_site                 PDBE
#   #
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
5YY  N1   N1   N  0  1  N  N  N  22.124   -6.809   -4.819  -1.957  -1.614   1.464  N1   5YY   1  
5YY  N3   N2   N  0  1  N  N  N  14.749  -12.669   -8.972   7.530  -0.375  -1.508  N3   5YY   2  
5YY  C4   C1   C  0  1  N  N  N  24.209   -6.932   -6.139  -3.378   0.351   1.369  C4   5YY   3  
5YY  C5   C2   C  0  1  N  N  N  22.964   -7.651   -5.650  -2.270  -0.411   0.689  C5   5YY   4  
5YY  C6   C3   C  0  1  N  N  N  21.016   -6.136   -5.505  -1.057  -1.530   2.617  C6   5YY   5  
5YY  C7   C4   C  0  1  Y  N  N  20.144   -7.016   -6.375   0.361  -1.766   2.165  C7   5YY   6  
5YY  C8   C5   C  0  1  Y  N  N  19.497   -6.464   -7.481   0.872  -3.056   2.145  C8   5YY   7  
5YY  C10  C6   C  0  1  Y  N  N  18.244   -8.486   -7.821   2.970  -2.219   1.335  C10  5YY   8  
5YY  C13  C7   C  0  1  N  N  N  17.114  -13.033   -7.660   6.617   0.509   0.941  C13  5YY   9  
5YY  C15  C8   C  0  1  N  N  N  16.992  -15.522   -7.917   8.653   1.900   1.273  C15  5YY  10  
5YY  C17  C9   C  0  1  N  N  N  13.450  -12.485   -9.619   8.027  -0.843  -2.804  C17  5YY  11  
5YY  C20  C10  C  0  1  N  N  N  17.998  -10.777   -4.179   3.049   1.717  -0.684  C20  5YY  12  
5YY  C21  C11  C  0  1  N  N  N  18.081  -11.878   -3.132   3.111   3.236  -0.877  C21  5YY  13  
5YY  C22  C12  C  0  1  N  N  N  17.382  -11.446   -1.868   2.694   3.578  -2.310  C22  5YY  14  
5YY  C24  C13  C  0  1  N  N  N  16.538  -10.379   -4.358   1.634   1.230  -1.010  C24  5YY  15  
5YY  C26  C14  C  0  1  Y  N  N  19.862   -8.337   -6.027   1.140  -0.699   1.769  C26  5YY  16  
5YY  C28  C15  C  0  1  Y  N  N  21.646   -5.728   -2.661  -3.504  -2.862   0.036  C28  5YY  17  
5YY  N7   N3   N  0  1  N  N  N  20.189   -2.395    1.976  -8.054  -1.648  -2.971  N7   5YY  18  
5YY  N6   N4   N  1  1  N  N  N  19.900   -2.936    1.016  -7.177  -2.351  -2.974  N6   5YY  19  
5YY  N5   N5   N  0  1  N  N  N  19.298   -3.444    0.005  -6.300  -3.053  -2.976  N5   5YY  20  
5YY  C31  C16  C  0  1  Y  N  N  20.178   -4.148   -0.875  -5.401  -2.992  -2.008  C31  5YY  21  
5YY  C30  C17  C  0  1  Y  N  N  21.462   -3.773   -1.257  -4.251  -3.900  -1.995  C30  5YY  22  
5YY  C29  C18  C  0  1  Y  N  N  22.185   -4.551   -2.146  -3.346  -3.809  -0.983  C29  5YY  23  
5YY  C32  C19  C  0  1  Y  N  N  19.634   -5.315   -1.399  -5.533  -2.014  -0.924  C32  5YY  24  
5YY  C33  C20  C  0  1  Y  N  N  20.359   -6.094   -2.282  -4.589  -1.979   0.055  C33  5YY  25  
5YY  C27  C21  C  0  1  N  N  N  22.485   -6.609   -3.532  -2.503  -2.798   1.120  C27  5YY  26  
5YY  O5   O1   O  0  1  N  N  N  23.494   -7.107   -3.060  -2.171  -3.812   1.702  O5   5YY  27  
5YY  O2   O2   O  0  1  N  N  N  24.297   -5.708   -6.084  -3.860  -0.070   2.399  O2   5YY  28  
5YY  N    N6   N  0  1  N  N  N  25.171   -7.713   -6.622  -3.834   1.500   0.832  N    5YY  29  
5YY  C3   C22  C  0  1  N  N  N  26.479   -7.769   -6.007  -4.911   2.241   1.493  C3   5YY  30  
5YY  C2   C23  C  0  1  N  N  N  26.944   -9.185   -5.799  -5.232   3.479   0.695  C2   5YY  31  
5YY  O1   O3   O  0  1  N  N  N  26.306  -10.174   -6.047  -4.623   3.718  -0.321  O1   5YY  32  
5YY  O    O4   O  0  1  N  N  N  28.185   -9.199   -5.312  -6.194   4.316   1.114  O    5YY  33  
5YY  C1   C24  C  0  1  N  N  N  29.195   -9.832   -6.151  -6.450   5.488   0.296  C1   5YY  34  
5YY  C    C25  C  0  1  N  N  N  30.510   -9.428   -5.684  -7.570   6.316   0.928  C    5YY  35  
5YY  C25  C26  C  0  1  Y  N  N  18.919   -9.058   -6.753   2.445  -0.915   1.352  C25  5YY  36  
5YY  C9   C27  C  0  1  Y  N  N  18.548   -7.179   -8.201   2.163  -3.290   1.730  C9   5YY  37  
5YY  N4   N7   N  0  1  Y  N  N  18.366  -10.331   -6.600   3.461  -0.084   0.917  N4   5YY  38  
5YY  C19  C28  C  0  1  N  N  N  18.651  -11.226   -5.470   3.390   1.371   0.766  C19  5YY  39  
5YY  C23  C29  C  0  1  N  N  N  15.905  -10.046   -3.028   1.273   1.650  -2.438  C23  5YY  40  
5YY  O4   O5   O  0  1  N  N  N  16.012  -11.133   -2.109   1.382   3.070  -2.557  O4   5YY  41  
5YY  C11  C30  C  0  1  Y  N  N  17.380  -10.443   -7.558   4.547  -0.877   0.653  C11  5YY  42  
5YY  N2   N8   N  0  1  Y  N  N  17.273   -9.364   -8.313   4.252  -2.130   0.901  N2   5YY  43  
5YY  C12  C31  C  0  1  N  N  N  16.651  -11.704   -7.910   5.854  -0.392   0.163  C12  5YY  44  
5YY  C18  C32  C  0  1  N  N  N  15.507  -11.581   -8.632   6.338  -0.814  -1.056  C18  5YY  45  
5YY  C16  C33  C  0  1  N  N  N  15.145  -13.983   -8.693   8.272   0.482  -0.783  C16  5YY  46  
5YY  O3   O6   O  0  1  N  N  N  14.386  -14.920   -8.936   9.348   0.865  -1.214  O3   5YY  47  
5YY  C14  C34  C  0  1  N  N  N  16.427  -14.136   -8.048   7.817   0.940   0.467  C14  5YY  48  
5YY  H1   H1   H  0  1  N  N  N  22.381   -7.979   -6.523  -1.383   0.219   0.623  H1   5YY  49  
5YY  H2   H2   H  0  1  N  N  N  23.272   -8.530   -5.064  -2.587  -0.697  -0.314  H2   5YY  50  
5YY  H3   H3   H  0  1  N  N  N  21.443   -5.349   -6.143  -1.135  -0.540   3.067  H3   5YY  51  
5YY  H4   H4   H  0  1  N  N  N  20.374   -5.678   -4.738  -1.336  -2.286   3.351  H4   5YY  52  
5YY  H5   H5   H  0  1  N  N  N  19.740   -5.456   -7.785   0.251  -3.883   2.458  H5   5YY  53  
5YY  H6   H6   H  0  1  N  N  N  18.051  -13.164   -7.140   6.252   0.851   1.899  H6   5YY  54  
5YY  H7   H7   H  0  1  N  N  N  17.966  -15.475   -7.408   9.571   2.126   0.732  H7   5YY  55  
5YY  H8   H8   H  0  1  N  N  N  16.301  -16.145   -7.330   8.092   2.820   1.438  H8   5YY  56  
5YY  H9   H9   H  0  1  N  N  N  17.122  -15.961   -8.917   8.899   1.448   2.234  H9   5YY  57  
5YY  H10  H10  H  0  1  N  N  N  13.268  -11.412   -9.778   8.999  -0.392  -3.004  H10  5YY  58  
5YY  H11  H11  H  0  1  N  N  N  13.446  -13.005  -10.588   8.127  -1.928  -2.785  H11  5YY  59  
5YY  H12  H12  H  0  1  N  N  N  12.659  -12.900   -8.977   7.326  -0.556  -3.587  H12  5YY  60  
5YY  H13  H13  H  0  1  N  N  N  18.548   -9.902   -3.801   3.763   1.235  -1.352  H13  5YY  61  
5YY  H14  H14  H  0  1  N  N  N  17.599  -12.787   -3.521   2.433   3.720  -0.175  H14  5YY  62  
5YY  H15  H15  H  0  1  N  N  N  19.137  -12.089   -2.909   4.129   3.584  -0.701  H15  5YY  63  
5YY  H16  H16  H  0  1  N  N  N  17.438  -12.262   -1.132   2.696   4.660  -2.440  H16  5YY  64  
5YY  H17  H17  H  0  1  N  N  N  17.887  -10.555   -1.467   3.397   3.127  -3.011  H17  5YY  65  
5YY  H18  H18  H  0  1  N  N  N  16.482   -9.498   -5.014   1.595   0.144  -0.929  H18  5YY  66  
5YY  H19  H19  H  0  1  N  N  N  15.991  -11.214   -4.819   0.926   1.674  -0.310  H19  5YY  67  
5YY  H20  H20  H  0  1  N  N  N  20.374   -8.799   -5.196   0.734   0.302   1.783  H20  5YY  68  
5YY  H21  H21  H  0  1  N  N  N  19.402   -1.959    2.412  -8.877  -1.901  -2.523  H21  5YY  69  
5YY  H22  H22  H  0  1  N  N  N  21.898   -2.869   -0.858  -4.124  -4.632  -2.778  H22  5YY  70  
5YY  H23  H23  H  0  1  N  N  N  23.176   -4.242   -2.443  -2.496  -4.474  -0.966  H23  5YY  71  
5YY  H24  H24  H  0  1  N  N  N  18.637   -5.616   -1.114  -6.368  -1.330  -0.904  H24  5YY  72  
5YY  H25  H25  H  0  1  N  N  N  19.921   -6.997   -2.682  -4.679  -1.262   0.858  H25  5YY  73  
5YY  H26  H26  H  0  1  N  N  N  24.986   -8.274   -7.429  -3.448   1.837   0.008  H26  5YY  74  
5YY  H27  H27  H  0  1  N  N  N  27.199   -7.250   -6.657  -5.798   1.611   1.558  H27  5YY  75  
5YY  H28  H28  H  0  1  N  N  N  26.435   -7.263   -5.031  -4.593   2.527   2.495  H28  5YY  76  
5YY  H29  H29  H  0  1  N  N  N  29.060   -9.515   -7.196  -5.544   6.091   0.233  H29  5YY  77  
5YY  H30  H30  H  0  1  N  N  N  29.099  -10.926   -6.084  -6.748   5.175  -0.704  H30  5YY  78  
5YY  H31  H31  H  0  1  N  N  N  31.283   -9.899   -6.309  -7.762   7.196   0.314  H31  5YY  79  
5YY  H32  H32  H  0  1  N  N  N  30.602   -8.334   -5.750  -8.476   5.713   0.991  H32  5YY  80  
5YY  H33  H33  H  0  1  N  N  N  30.641   -9.745   -4.639  -7.272   6.629   1.928  H33  5YY  81  
5YY  H34  H34  H  0  1  N  N  N  18.051   -6.727   -9.047   2.555  -4.296   1.722  H34  5YY  82  
5YY  H35  H35  H  0  1  N  N  N  18.282  -12.232   -5.718   4.353   1.811   1.028  H35  5YY  83  
5YY  H36  H36  H  0  1  N  N  N  19.740  -11.262   -5.318   2.618   1.767   1.426  H36  5YY  84  
5YY  H37  H37  H  0  1  N  N  N  16.411   -9.167   -2.602   1.957   1.173  -3.140  H37  5YY  85  
5YY  H38  H38  H  0  1  N  N  N  14.841   -9.816   -3.187   0.251   1.343  -2.660  H38  5YY  86  
5YY  H39  H39  H  0  1  N  N  N  15.187  -10.599   -8.946   5.758  -1.502  -1.654  H39  5YY  87  
#   #
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
5YY  C17  N3   SING  N  N   1  
5YY  N3   C16  SING  N  N   2  
5YY  N3   C18  SING  N  N   3  
5YY  O3   C16  DOUB  N  N   4  
5YY  C16  C14  SING  N  N   5  
5YY  C18  C12  DOUB  N  N   6  
5YY  N2   C10  SING  Y  N   7  
5YY  N2   C11  DOUB  Y  N   8  
5YY  C9   C10  DOUB  Y  N   9  
5YY  C9   C8   SING  Y  N  10  
5YY  C14  C15  SING  N  N  11  
5YY  C14  C13  DOUB  N  N  12  
5YY  C12  C13  SING  N  N  13  
5YY  C12  C11  SING  N  N  14  
5YY  C10  C25  SING  Y  N  15  
5YY  C11  N4   SING  Y  N  16  
5YY  C8   C7   DOUB  Y  N  17  
5YY  C25  N4   SING  Y  N  18  
5YY  C25  C26  DOUB  Y  N  19  
5YY  N    C4   SING  N  N  20  
5YY  N    C3   SING  N  N  21  
5YY  N4   C19  SING  N  N  22  
5YY  C7   C26  SING  Y  N  23  
5YY  C7   C6   SING  N  N  24  
5YY  C1   C    SING  N  N  25  
5YY  C1   O    SING  N  N  26  
5YY  C4   O2   DOUB  N  N  27  
5YY  C4   C5   SING  N  N  28  
5YY  O1   C2   DOUB  N  N  29  
5YY  C3   C2   SING  N  N  30  
5YY  C2   O    SING  N  N  31  
5YY  C5   N1   SING  N  N  32  
5YY  C6   N1   SING  N  N  33  
5YY  C19  C20  SING  N  N  34  
5YY  N1   C27  SING  N  N  35  
5YY  C24  C20  SING  N  N  36  
5YY  C24  C23  SING  N  N  37  
5YY  C20  C21  SING  N  N  38  
5YY  C27  O5   DOUB  N  N  39  
5YY  C27  C28  SING  N  N  40  
5YY  C21  C22  SING  N  N  41  
5YY  C23  O4   SING  N  N  42  
5YY  C28  C33  DOUB  Y  N  43  
5YY  C28  C29  SING  Y  N  44  
5YY  C33  C32  SING  Y  N  45  
5YY  C29  C30  DOUB  Y  N  46  
5YY  O4   C22  SING  N  N  47  
5YY  C32  C31  DOUB  Y  N  48  
5YY  C30  C31  SING  Y  N  49  
5YY  C31  N5   SING  N  N  50  
5YY  N5   N6   DOUB  N  N  51  
5YY  N6   N7   DOUB  N  N  52  
5YY  C5   H1   SING  N  N  53  
5YY  C5   H2   SING  N  N  54  
5YY  C6   H3   SING  N  N  55  
5YY  C6   H4   SING  N  N  56  
5YY  C8   H5   SING  N  N  57  
5YY  C13  H6   SING  N  N  58  
5YY  C15  H7   SING  N  N  59  
5YY  C15  H8   SING  N  N  60  
5YY  C15  H9   SING  N  N  61  
5YY  C17  H10  SING  N  N  62  
5YY  C17  H11  SING  N  N  63  
5YY  C17  H12  SING  N  N  64  
5YY  C20  H13  SING  N  N  65  
5YY  C21  H14  SING  N  N  66  
5YY  C21  H15  SING  N  N  67  
5YY  C22  H16  SING  N  N  68  
5YY  C22  H17  SING  N  N  69  
5YY  C24  H18  SING  N  N  70  
5YY  C24  H19  SING  N  N  71  
5YY  C26  H20  SING  N  N  72  
5YY  N7   H21  SING  N  N  73  
5YY  C30  H22  SING  N  N  74  
5YY  C29  H23  SING  N  N  75  
5YY  C32  H24  SING  N  N  76  
5YY  C33  H25  SING  N  N  77  
5YY  N    H26  SING  N  N  78  
5YY  C3   H27  SING  N  N  79  
5YY  C3   H28  SING  N  N  80  
5YY  C1   H29  SING  N  N  81  
5YY  C1   H30  SING  N  N  82  
5YY  C    H31  SING  N  N  83  
5YY  C    H32  SING  N  N  84  
5YY  C    H33  SING  N  N  85  
5YY  C9   H34  SING  N  N  86  
5YY  C19  H35  SING  N  N  87  
5YY  C19  H36  SING  N  N  88  
5YY  C23  H37  SING  N  N  89  
5YY  C23  H38  SING  N  N  90  
5YY  C18  H39  SING  N  N  91  
#   #
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
5YY  InChI             InChI                 1.03   "InChI=1S/C34H38N8O6/c1-4-48-31(44)17-36-30(43)21-41(34(46)25-6-8-27(9-7-25)38-39-35)18-24-5-10-28-29(16-24)42(19-23-11-13-47-14-12-23)32(37-28)26-15-22(2)33(45)40(3)20-26/h5-10,15-16,20,23,35H,4,11-14,17-19,21H2,1-3H3/p+1"  
5YY  InChIKey          InChI                 1.03   GHCAGGKSFJHAIR-UHFFFAOYSA-O  
5YY  SMILES_CANONICAL  CACTVS                3.385  "CCOC(=O)CNC(=O)CN(Cc1ccc2nc(n(CC3CCOCC3)c2c1)C4=CN(C)C(=O)C(=C4)C)C(=O)c5ccc(cc5)N=[N+]=N"  
5YY  SMILES            CACTVS                3.385  "CCOC(=O)CNC(=O)CN(Cc1ccc2nc(n(CC3CCOCC3)c2c1)C4=CN(C)C(=O)C(=C4)C)C(=O)c5ccc(cc5)N=[N+]=N"  
5YY  SMILES_CANONICAL  "OpenEye OEToolkits"  2.0.7  "CCOC(=O)CNC(=O)CN(Cc1ccc2c(c1)n(c(n2)C3=CN(C(=O)C(=C3)C)C)CC4CCOCC4)C(=O)c5ccc(cc5)N=[N+]=N"  
5YY  SMILES            "OpenEye OEToolkits"  2.0.7  "CCOC(=O)CNC(=O)CN(Cc1ccc2c(c1)n(c(n2)C3=CN(C(=O)C(=C3)C)C)CC4CCOCC4)C(=O)c5ccc(cc5)N=[N+]=N"  
#
_pdbx_chem_comp_identifier.comp_id          5YY
_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       "azanylidene-[4-[[2-(1,5-dimethyl-6-oxidanylidene-pyridin-3-yl)-3-(oxan-4-ylmethyl)benzimidazol-5-yl]methyl-[2-[(2-ethoxy-2-oxidanylidene-ethyl)amino]-2-oxidanylidene-ethyl]carbamoyl]phenyl]imino-azanium"
#   #
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
5YY  "Create component"  2021-07-20  PDBE  
5YY  "Initial release"   2021-10-06  RCSB  
##
