data_Y4O # _chem_comp.id Y4O _chem_comp.name "3-[4-(dimethylamino)butanoylamino]-~{N}-[3-methyl-4-[(4-pyridin-3-ylpyrimidin-2-yl)amino]phenyl]benzamide" _chem_comp.type non-polymer _chem_comp.pdbx_type HETAIN _chem_comp.formula "C29 H31 N7 O2" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2023-11-20 _chem_comp.pdbx_modified_date 2023-12-22 _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 509.602 _chem_comp.one_letter_code ? _chem_comp.three_letter_code Y4O _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 8X5M _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site PDBJ # 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.pdbx_n_terminal_atom_flag _chem_comp_atom.pdbx_backbone_atom_flag _chem_comp_atom.pdbx_c_terminal_atom_flag _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 Y4O C1 C1 C 0 1 N N N N N N -19.035 -30.764 16.976 1.636 2.106 0.739 C1 Y4O 1 Y4O C2 C2 C 0 1 Y N N N N N -17.770 -31.530 16.697 1.636 0.645 0.371 C2 Y4O 2 Y4O N3 N1 N 0 1 N N N N N N -8.504 -42.474 17.537 -9.564 3.749 0.022 N3 Y4O 3 Y4O C4 C3 C 0 1 Y N N N N N -15.926 -32.142 15.243 2.820 -1.325 -0.340 C4 Y4O 4 Y4O N5 N2 N 0 1 Y N N N N N -17.718 -29.353 12.506 5.237 -1.194 0.390 N5 Y4O 5 Y4O C6 C4 C 0 1 Y N N N N N -16.060 -33.062 17.452 0.457 -1.421 0.059 C6 Y4O 6 Y4O C7 C5 C 0 1 Y N N N N N -17.233 -32.348 17.668 0.457 -0.074 0.398 C7 Y4O 7 Y4O C10 C6 C 0 1 Y N N N N N -13.135 -36.298 19.551 -4.385 -1.658 -0.389 C10 Y4O 8 Y4O C11 C7 C 0 1 Y N N N N N -12.949 -37.349 20.449 -5.575 -2.357 -0.259 C11 Y4O 9 Y4O C15 C8 C 0 1 N N N N N N -10.979 -38.443 19.362 -6.975 -0.433 -0.288 C15 Y4O 10 Y4O C16 C9 C 0 1 N N N N N N -9.974 -39.536 19.640 -8.316 0.209 -0.530 C16 Y4O 11 Y4O C17 C10 C 0 1 N N N N N N -9.813 -40.522 18.478 -8.258 1.683 -0.123 C17 Y4O 12 Y4O C18 C11 C 0 1 N N N N N N -8.660 -41.518 18.640 -9.620 2.334 -0.368 C18 Y4O 13 Y4O C19 C12 C 0 1 N N N N N N -7.918 -41.834 16.362 -10.770 4.465 -0.415 C19 Y4O 14 Y4O C20 C13 C 0 1 N N N N N N -7.691 -43.615 17.942 -9.367 3.888 1.472 C20 Y4O 15 Y4O C21 C14 C 0 1 Y N N N N N -16.970 -29.894 13.496 5.228 0.101 0.108 C21 Y4O 16 Y4O C22 C15 C 0 1 Y N N N N N -17.035 -28.682 11.580 6.377 -1.852 0.533 C22 Y4O 17 Y4O C23 C16 C 0 1 Y N N N N N -15.664 -28.527 11.595 7.573 -1.174 0.385 C23 Y4O 18 Y4O C24 C17 C 0 1 Y N N N N N -14.978 -29.096 12.656 7.533 0.191 0.088 C24 Y4O 19 Y4O C25 C18 C 0 1 Y N N N N N -13.494 -29.047 12.797 8.788 0.963 -0.080 C25 Y4O 20 Y4O C29 C19 C 0 1 Y N N N N N -12.826 -29.769 13.775 8.751 2.348 -0.268 C29 Y4O 21 Y4O C3 C20 C 0 1 Y N N N N N -17.101 -31.431 15.474 2.820 0.022 -0.000 C3 Y4O 22 Y4O C5 C21 C 0 1 Y N N N N N -15.412 -32.959 16.224 1.643 -2.045 -0.308 C5 Y4O 23 Y4O N1 N3 N 0 1 N N N N N N -15.595 -33.901 18.494 -0.738 -2.149 0.087 N1 Y4O 24 Y4O C8 C22 C 0 1 N N N N N N -14.319 -34.256 18.773 -1.904 -1.543 -0.214 C8 Y4O 25 Y4O O1 O1 O 0 1 N N N N N N -13.337 -33.703 18.284 -1.909 -0.389 -0.596 O1 Y4O 26 Y4O C9 C23 C 0 1 Y N N N N N -14.155 -35.377 19.756 -3.178 -2.282 -0.079 C9 Y4O 27 Y4O C12 C24 C 0 1 Y N N N N N -13.792 -37.462 21.556 -5.563 -3.673 0.184 C12 Y4O 28 Y4O C13 C25 C 0 1 Y N N N N N -14.797 -36.542 21.759 -4.366 -4.291 0.497 C13 Y4O 29 Y4O C14 C26 C 0 1 Y N N N N N -14.983 -35.501 20.867 -3.175 -3.608 0.360 C14 Y4O 30 Y4O N2 N4 N 0 1 N N N N N N -11.931 -38.322 20.308 -6.789 -1.736 -0.575 N2 Y4O 31 Y4O O2 O2 O 0 1 N N N N N N -10.916 -37.722 18.372 -6.061 0.224 0.166 O2 Y4O 32 Y4O N4 N5 N 0 1 N N N N N N -17.632 -30.596 14.463 4.014 0.752 -0.034 N4 Y4O 33 Y4O N6 N6 N 0 1 Y N N N N N -15.633 -29.781 13.603 6.350 0.788 -0.041 N6 Y4O 34 Y4O C26 C27 C 0 1 Y N N N N N -12.705 -28.326 11.908 10.024 0.320 -0.049 C26 Y4O 35 Y4O N7 N7 N 0 1 Y N N N N N -11.372 -28.262 11.958 11.139 1.005 -0.198 N7 Y4O 36 Y4O C27 C28 C 0 1 Y N N N N N -10.770 -28.960 12.928 11.135 2.311 -0.382 C27 Y4O 37 Y4O C28 C29 C 0 1 Y N N N N N -11.452 -29.717 13.847 9.950 3.022 -0.420 C28 Y4O 38 Y4O H1 H1 H 0 1 N N N N N N -19.904 -31.370 16.679 1.458 2.705 -0.154 H1 Y4O 39 Y4O H2 H2 H 0 1 N N N N N N -19.096 -30.537 18.050 0.849 2.297 1.468 H2 Y4O 40 Y4O H3 H3 H 0 1 N N N N N N -19.029 -29.825 16.402 2.602 2.372 1.169 H3 Y4O 41 Y4O H4 H5 H 0 1 N N N N N N -15.418 -32.052 14.294 3.742 -1.810 -0.625 H4 Y4O 42 Y4O H6 H6 H 0 1 N N N N N N -17.736 -32.436 18.620 -0.465 0.411 0.684 H6 Y4O 43 Y4O H8 H7 H 0 1 N N N N N N -12.485 -36.200 18.694 -4.393 -0.634 -0.733 H8 Y4O 44 Y4O H31 H8 H 0 1 N N N N N N -8.998 -39.070 19.840 -8.570 0.134 -1.587 H31 Y4O 45 Y4O H13 H9 H 0 1 N N N N N N -10.303 -40.095 20.529 -9.076 -0.301 0.063 H13 Y4O 46 Y4O H14 H10 H 0 1 N N N N N N -10.748 -41.093 18.381 -8.005 1.758 0.935 H14 Y4O 47 Y4O H32 H11 H 0 1 N N N N N N -9.640 -39.943 17.559 -7.499 2.194 -0.715 H32 Y4O 48 Y4O H16 H12 H 0 1 N N N N N N -7.725 -40.945 18.730 -10.379 1.824 0.224 H16 Y4O 49 Y4O H15 H13 H 0 1 N N N N N N -8.830 -42.089 19.565 -9.873 2.259 -1.426 H15 Y4O 50 Y4O H18 H14 H 0 1 N N N N N N -7.814 -42.574 15.555 -10.702 5.510 -0.113 H18 Y4O 51 Y4O H17 H15 H 0 1 N N N N N N -8.571 -41.015 16.027 -10.854 4.405 -1.501 H17 Y4O 52 Y4O H19 H16 H 0 1 N N N N N N -6.927 -41.431 16.620 -11.649 4.010 0.043 H19 Y4O 53 Y4O H20 H17 H 0 1 N N N N N N -7.591 -44.313 17.098 -10.228 3.475 1.997 H20 Y4O 54 Y4O H21 H18 H 0 1 N N N N N N -6.694 -43.265 18.248 -8.467 3.349 1.769 H21 Y4O 55 Y4O H22 H19 H 0 1 N N N N N N -8.174 -44.128 18.787 -9.259 4.943 1.724 H22 Y4O 56 Y4O H24 H20 H 0 1 N N N N N N -17.588 -28.232 10.768 6.372 -2.908 0.762 H24 Y4O 57 Y4O H25 H21 H 0 1 N N N N N N -15.149 -27.986 10.815 8.517 -1.687 0.497 H25 Y4O 58 Y4O H29 H22 H 0 1 N N N N N N -13.382 -30.371 14.478 7.810 2.878 -0.293 H29 Y4O 59 Y4O H5 H23 H 0 1 N N N N N N -14.507 -33.520 16.042 1.643 -3.093 -0.568 H5 Y4O 60 Y4O H7 H24 H 0 1 N N N N N N -16.297 -34.278 19.099 -0.727 -3.090 0.322 H7 Y4O 61 Y4O H9 H25 H 0 1 N N N N N N -13.656 -38.273 22.256 -6.491 -4.216 0.285 H9 Y4O 62 Y4O H10 H26 H 0 1 N N N N N N -15.443 -36.634 22.619 -4.363 -5.315 0.842 H10 Y4O 63 Y4O H11 H27 H 0 1 N N N N N N -15.773 -34.783 21.033 -2.242 -4.095 0.601 H11 Y4O 64 Y4O H12 H28 H 0 1 N N N N N N -11.916 -39.026 21.018 -7.497 -2.244 -1.001 H12 Y4O 65 Y4O H23 H29 H 0 1 N N N N N N -18.628 -30.508 14.455 3.991 1.714 -0.155 H23 Y4O 66 Y4O H26 H30 H 0 1 N N N N N N -13.205 -27.779 11.122 10.068 -0.749 0.100 H26 Y4O 67 Y4O H27 H31 H 0 1 N N N N N N -9.692 -28.926 12.991 12.073 2.834 -0.500 H27 Y4O 68 Y4O H28 H32 H 0 1 N N N N N N -10.921 -30.262 14.613 9.959 4.091 -0.572 H28 Y4O 69 # 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 Y4O C1 C2 SING N N 1 Y4O C2 C3 DOUB Y N 2 Y4O C2 C7 SING Y N 3 Y4O C3 C4 SING Y N 4 Y4O C3 N4 SING N N 5 Y4O C4 C5 DOUB Y N 6 Y4O C5 C6 SING Y N 7 Y4O C6 C7 DOUB Y N 8 Y4O C6 N1 SING N N 9 Y4O N1 C8 SING N N 10 Y4O C8 O1 DOUB N N 11 Y4O C8 C9 SING N N 12 Y4O C9 C10 DOUB Y N 13 Y4O C9 C14 SING Y N 14 Y4O C10 C11 SING Y N 15 Y4O C11 C12 DOUB Y N 16 Y4O C11 N2 SING N N 17 Y4O C12 C13 SING Y N 18 Y4O C13 C14 DOUB Y N 19 Y4O N2 C15 SING N N 20 Y4O C15 O2 DOUB N N 21 Y4O C15 C16 SING N N 22 Y4O C16 C17 SING N N 23 Y4O C17 C18 SING N N 24 Y4O C18 N3 SING N N 25 Y4O N3 C19 SING N N 26 Y4O N3 C20 SING N N 27 Y4O N4 C21 SING N N 28 Y4O C21 N5 DOUB Y N 29 Y4O C21 N6 SING Y N 30 Y4O N5 C22 SING Y N 31 Y4O C22 C23 DOUB Y N 32 Y4O C23 C24 SING Y N 33 Y4O C24 N6 DOUB Y N 34 Y4O C24 C25 SING N N 35 Y4O C25 C26 DOUB Y N 36 Y4O C25 C29 SING Y N 37 Y4O C26 N7 SING Y N 38 Y4O N7 C27 DOUB Y N 39 Y4O C27 C28 SING Y N 40 Y4O C28 C29 DOUB Y N 41 Y4O C1 H1 SING N N 42 Y4O C1 H2 SING N N 43 Y4O C1 H3 SING N N 44 Y4O C4 H4 SING N N 45 Y4O C7 H6 SING N N 46 Y4O C10 H8 SING N N 47 Y4O C16 H31 SING N N 48 Y4O C16 H13 SING N N 49 Y4O C17 H14 SING N N 50 Y4O C17 H32 SING N N 51 Y4O C18 H16 SING N N 52 Y4O C18 H15 SING N N 53 Y4O C19 H18 SING N N 54 Y4O C19 H17 SING N N 55 Y4O C19 H19 SING N N 56 Y4O C20 H20 SING N N 57 Y4O C20 H21 SING N N 58 Y4O C20 H22 SING N N 59 Y4O C22 H24 SING N N 60 Y4O C23 H25 SING N N 61 Y4O C29 H29 SING N N 62 Y4O C5 H5 SING N N 63 Y4O N1 H7 SING N N 64 Y4O C12 H9 SING N N 65 Y4O C13 H10 SING N N 66 Y4O C14 H11 SING N N 67 Y4O N2 H12 SING N N 68 Y4O N4 H23 SING N N 69 Y4O C26 H26 SING N N 70 Y4O C27 H27 SING N N 71 Y4O C28 H28 SING N N 72 # 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 Y4O InChI InChI 1.06 "InChI=1S/C29H31N7O2/c1-20-17-24(11-12-25(20)34-29-31-15-13-26(35-29)22-8-5-14-30-19-22)33-28(38)21-7-4-9-23(18-21)32-27(37)10-6-16-36(2)3/h4-5,7-9,11-15,17-19H,6,10,16H2,1-3H3,(H,32,37)(H,33,38)(H,31,34,35)" Y4O InChIKey InChI 1.06 JCQSXSKNIVAALC-UHFFFAOYSA-N Y4O SMILES_CANONICAL CACTVS 3.385 "CN(C)CCCC(=O)Nc1cccc(c1)C(=O)Nc2ccc(Nc3nccc(n3)c4cccnc4)c(C)c2" Y4O SMILES CACTVS 3.385 "CN(C)CCCC(=O)Nc1cccc(c1)C(=O)Nc2ccc(Nc3nccc(n3)c4cccnc4)c(C)c2" Y4O SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "Cc1cc(ccc1Nc2nccc(n2)c3cccnc3)NC(=O)c4cccc(c4)NC(=O)CCCN(C)C" Y4O SMILES "OpenEye OEToolkits" 2.0.7 "Cc1cc(ccc1Nc2nccc(n2)c3cccnc3)NC(=O)c4cccc(c4)NC(=O)CCCN(C)C" # _pdbx_chem_comp_identifier.comp_id Y4O _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 "3-[4-(dimethylamino)butanoylamino]-~{N}-[3-methyl-4-[(4-pyridin-3-ylpyrimidin-2-yl)amino]phenyl]benzamide" # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site Y4O "Create component" 2023-11-20 PDBJ Y4O "Initial release" 2023-12-27 RCSB #