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 ##