data_5YZ # _chem_comp.id 5YZ _chem_comp.name "6-[(5-cyclopropyl-1~{H}-pyrazol-3-yl)amino]-2-[4-[(3-methyl-4-oxidanyl-phenyl)methyl]piperazin-1-yl]-~{N}-prop-2-ynyl-pyrimidine-4-carboxamide" _chem_comp.type non-polymer _chem_comp.pdbx_type HETAIN _chem_comp.formula "C26 H30 N8 O2" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2021-08-31 _chem_comp.pdbx_modified_date 2024-09-27 _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 486.569 _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 7FIC _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site PDBJ _chem_comp.pdbx_pcm Y # 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_backbone_atom_flag _chem_comp_atom.pdbx_n_terminal_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 5YZ C1 C1 C 0 1 N N N N N N -36.996 9.800 -1.214 -5.011 -1.359 -0.569 C1 5YZ 1 5YZ C10 C2 C 0 1 N N N N N N -33.114 9.627 -5.962 -0.671 -1.933 1.236 C10 5YZ 2 5YZ C11 C3 C 0 1 Y N N N N N -31.162 7.505 -1.818 -1.955 3.985 -0.432 C11 5YZ 3 5YZ C12 C4 C 0 1 N N N N N N -33.655 12.467 -6.127 1.851 -0.644 0.816 C12 5YZ 4 5YZ C13 C5 C 0 1 N N N N N N -32.220 10.666 -6.630 0.617 -2.418 1.906 C13 5YZ 5 5YZ C14 C6 C 0 1 Y N N N N N -30.485 8.169 -2.837 -0.721 3.606 0.121 C14 5YZ 6 5YZ C15 C7 C 0 1 Y N N N N N -29.199 7.621 -2.731 0.088 4.689 0.111 C15 5YZ 7 5YZ C16 C8 C 0 1 N N N N N N -32.256 12.605 -8.079 3.014 -2.609 1.621 C16 5YZ 8 5YZ C17 C9 C 0 1 N N N N N N -28.125 8.111 -3.658 1.509 4.740 0.612 C17 5YZ 9 5YZ C18 C10 C 0 1 Y N N N N N -31.463 11.777 -9.066 4.124 -2.477 0.610 C18 5YZ 10 5YZ C19 C11 C 0 1 N N N N N N -28.617 8.391 -5.075 1.979 6.037 1.273 C19 5YZ 11 5YZ C2 C12 C 0 1 Y N N N N N -35.668 9.492 -1.915 -3.901 -0.408 -0.305 C2 5YZ 12 5YZ C20 C13 C 0 1 N N N N N N -27.935 7.068 -4.742 2.484 5.662 -0.122 C20 5YZ 13 5YZ C21 C14 C 0 1 Y N N N N N -30.072 11.718 -8.927 4.889 -1.325 0.571 C21 5YZ 14 5YZ C22 C15 C 0 1 Y N N N N N -32.103 11.098 -10.104 4.379 -3.509 -0.273 C22 5YZ 15 5YZ C23 C16 C 0 1 Y N N N N N -29.323 10.960 -9.813 5.906 -1.202 -0.355 C23 5YZ 16 5YZ C24 C17 C 0 1 Y N N N N N -31.337 10.346 -10.991 5.399 -3.393 -1.197 C24 5YZ 17 5YZ C25 C18 C 0 1 Y N N N N N -29.954 10.285 -10.842 6.161 -2.234 -1.246 C25 5YZ 18 5YZ C26 C19 C 0 1 N N N N N N -27.830 10.888 -9.663 6.739 0.054 -0.398 C26 5YZ 19 5YZ C3 C20 C 0 1 N N N N N N -38.239 9.895 0.967 -5.955 -3.605 -0.542 C3 5YZ 20 5YZ C4 C21 C 0 1 Y N N N N N -34.673 8.691 -1.325 -4.047 0.943 -0.597 C4 5YZ 21 5YZ C5 C22 C 0 1 N N N N N N -38.816 11.204 0.628 -5.544 -4.962 -0.147 C5 5YZ 22 5YZ C6 C23 C 0 1 Y N N N N N -34.257 9.799 -3.786 -1.762 0.002 0.463 C6 5YZ 23 5YZ C7 C24 C 0 1 Y N N N N N -33.462 8.477 -2.009 -2.973 1.799 -0.330 C7 5YZ 24 5YZ C8 C25 C 0 1 N N N N N N -39.372 12.335 0.384 -5.216 -6.044 0.169 C8 5YZ 25 5YZ C9 C26 C 0 1 N N N N N N -34.704 11.562 -5.488 0.563 -0.159 0.146 C9 5YZ 26 5YZ N1 N1 N 0 1 N N N N N N -37.102 9.649 0.054 -4.860 -2.667 -0.282 N1 5YZ 27 5YZ N2 N2 N 0 1 Y N N N N N -35.430 10.030 -3.137 -2.754 -0.838 0.220 N2 5YZ 28 5YZ N3 N3 N 0 1 Y N N N N N -33.294 9.030 -3.222 -1.859 1.295 0.189 N3 5YZ 29 5YZ N4 N4 N 0 1 N N N N N N -34.021 10.343 -5.069 -0.585 -0.485 1.004 N4 5YZ 30 5YZ N5 N5 N 0 1 N N N N N N -32.472 7.650 -1.442 -3.069 3.154 -0.604 N5 5YZ 31 5YZ N6 N6 N 0 1 Y N N N N N -30.403 6.631 -1.139 -1.883 5.254 -0.756 N6 5YZ 32 5YZ N7 N7 N 0 1 N N N N N N -33.056 11.713 -7.232 1.765 -2.092 1.048 N7 5YZ 33 5YZ N8 N8 N 0 1 Y N N N N N -29.128 6.724 -1.729 -0.602 5.717 -0.427 N8 5YZ 34 5YZ O1 O1 O 0 1 N N N N N N -37.935 10.236 -1.900 -6.057 -0.956 -1.038 O1 5YZ 35 5YZ O2 O2 O 0 1 N N N N N N -29.195 9.552 -11.696 7.165 -2.118 -2.154 O2 5YZ 36 5YZ H1 H1 H 0 1 N N N N N N -33.689 9.080 -6.724 -0.801 -2.447 0.284 H1 5YZ 37 5YZ H2 H2 H 0 1 N N N N N N -32.501 8.918 -5.386 -1.521 -2.148 1.884 H2 5YZ 38 5YZ H3 H3 H 0 1 N N N N N N -32.884 12.732 -5.389 2.701 -0.429 0.167 H3 5YZ 39 5YZ H4 H4 H 0 1 N N N N N N -34.128 13.384 -6.508 1.981 -0.130 1.768 H4 5YZ 40 5YZ H5 H5 H 0 1 N N N N N N -31.617 10.183 -7.413 0.733 -1.924 2.871 H5 5YZ 41 5YZ H6 H6 H 0 1 N N N N N N -31.554 11.115 -5.878 0.567 -3.496 2.053 H6 5YZ 42 5YZ H7 H7 H 0 1 N N N N N N -30.854 8.912 -3.528 -0.464 2.624 0.490 H7 5YZ 43 5YZ H8 H8 H 0 1 N N N N N N -31.567 13.188 -7.451 2.886 -3.659 1.885 H8 5YZ 44 5YZ H9 H9 H 0 1 N N N N N N -32.922 13.289 -8.625 3.267 -2.038 2.515 H9 5YZ 45 5YZ H10 H10 H 0 1 N N N N N N -27.257 8.658 -3.263 1.902 3.803 1.006 H10 5YZ 46 5YZ H11 H11 H 0 1 N N N N N N -28.102 9.135 -5.701 1.261 6.854 1.346 H11 5YZ 47 5YZ H12 H12 H 0 1 N N N N N N -29.696 8.416 -5.289 2.682 5.953 2.102 H12 5YZ 48 5YZ H13 H13 H 0 1 N N N N N N -28.522 6.138 -4.718 3.519 5.333 -0.211 H13 5YZ 49 5YZ H14 H14 H 0 1 N N N N N N -26.928 6.856 -5.130 2.098 6.233 -0.967 H14 5YZ 50 5YZ H15 H15 H 0 1 N N N N N N -29.584 12.261 -8.132 4.689 -0.521 1.264 H15 5YZ 51 5YZ H16 H16 H 0 1 N N N N N N -33.176 11.155 -10.217 3.781 -4.408 -0.240 H16 5YZ 52 5YZ H17 H17 H 0 1 N N N N N N -31.817 9.809 -11.796 5.596 -4.198 -1.890 H17 5YZ 53 5YZ H18 H18 H 0 1 N N N N N N -27.363 11.700 -10.241 7.599 -0.058 0.262 H18 5YZ 54 5YZ H19 H19 H 0 1 N N N N N N -27.563 10.993 -8.601 7.083 0.227 -1.417 H19 5YZ 55 5YZ H20 H20 H 0 1 N N N N N N -27.470 9.918 -10.037 6.136 0.900 -0.068 H20 5YZ 56 5YZ H21 H21 H 0 1 N N N N N N -38.997 9.108 0.840 -6.198 -3.594 -1.605 H21 5YZ 57 5YZ H22 H22 H 0 1 N N N N N N -37.887 9.900 2.009 -6.832 -3.308 0.034 H22 5YZ 58 5YZ H23 H23 H 0 1 N N N N N N -34.837 8.244 -0.356 -4.965 1.322 -1.019 H23 5YZ 59 5YZ H24 H24 H 0 1 N N N N N N -39.831 13.269 0.183 -4.923 -7.011 0.451 H24 5YZ 60 5YZ H25 H25 H 0 1 N N N N N N -35.153 12.061 -4.617 0.613 0.920 -0.001 H25 5YZ 61 5YZ H26 H26 H 0 1 N N N N N N -35.491 11.322 -6.219 0.447 -0.653 -0.819 H26 5YZ 62 5YZ H27 H27 H 0 1 N N N N N N -36.276 9.307 0.502 -4.027 -2.988 0.096 H27 5YZ 63 5YZ H28 H28 H 0 1 N N N N N N -32.764 7.096 -0.662 -3.909 3.527 -0.915 H28 5YZ 64 5YZ H31 H31 H 0 1 N N N N N N -28.281 9.623 -11.448 6.889 -1.735 -2.999 H31 5YZ 65 5YZ H29 H29 H 0 1 N N N N N N -28.313 6.214 -1.453 -0.270 6.619 -0.559 H29 5YZ 66 # 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 5YZ O2 C25 SING N N 1 5YZ C24 C25 DOUB Y N 2 5YZ C24 C22 SING Y N 3 5YZ C25 C23 SING Y N 4 5YZ C22 C18 DOUB Y N 5 5YZ C23 C26 SING N N 6 5YZ C23 C21 DOUB Y N 7 5YZ C18 C21 SING Y N 8 5YZ C18 C16 SING N N 9 5YZ C16 N7 SING N N 10 5YZ N7 C13 SING N N 11 5YZ N7 C12 SING N N 12 5YZ C13 C10 SING N N 13 5YZ C12 C9 SING N N 14 5YZ C10 N4 SING N N 15 5YZ C9 N4 SING N N 16 5YZ C19 C20 SING N N 17 5YZ C19 C17 SING N N 18 5YZ N4 C6 SING N N 19 5YZ C20 C17 SING N N 20 5YZ C6 N3 SING Y N 21 5YZ C6 N2 DOUB Y N 22 5YZ C17 C15 SING N N 23 5YZ N3 C7 DOUB Y N 24 5YZ N2 C2 SING Y N 25 5YZ C14 C15 DOUB Y N 26 5YZ C14 C11 SING Y N 27 5YZ C15 N8 SING Y N 28 5YZ C7 N5 SING N N 29 5YZ C7 C4 SING Y N 30 5YZ C2 C4 DOUB Y N 31 5YZ C2 C1 SING N N 32 5YZ O1 C1 DOUB N N 33 5YZ C11 N5 SING N N 34 5YZ C11 N6 DOUB Y N 35 5YZ N8 N6 SING Y N 36 5YZ C1 N1 SING N N 37 5YZ N1 C3 SING N N 38 5YZ C8 C5 TRIP N N 39 5YZ C5 C3 SING N N 40 5YZ C10 H1 SING N N 41 5YZ C10 H2 SING N N 42 5YZ C12 H3 SING N N 43 5YZ C12 H4 SING N N 44 5YZ C13 H5 SING N N 45 5YZ C13 H6 SING N N 46 5YZ C14 H7 SING N N 47 5YZ C16 H8 SING N N 48 5YZ C16 H9 SING N N 49 5YZ C17 H10 SING N N 50 5YZ C19 H11 SING N N 51 5YZ C19 H12 SING N N 52 5YZ C20 H13 SING N N 53 5YZ C20 H14 SING N N 54 5YZ C21 H15 SING N N 55 5YZ C22 H16 SING N N 56 5YZ C24 H17 SING N N 57 5YZ C26 H18 SING N N 58 5YZ C26 H19 SING N N 59 5YZ C26 H20 SING N N 60 5YZ C3 H21 SING N N 61 5YZ C3 H22 SING N N 62 5YZ C4 H23 SING N N 63 5YZ C8 H24 SING N N 64 5YZ C9 H25 SING N N 65 5YZ C9 H26 SING N N 66 5YZ N1 H27 SING N N 67 5YZ N5 H28 SING N N 68 5YZ O2 H31 SING N N 69 5YZ N8 H29 SING N N 70 # 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 5YZ InChI InChI 1.03 "InChI=1S/C26H30N8O2/c1-3-8-27-25(36)21-15-23(29-24-14-20(31-32-24)19-5-6-19)30-26(28-21)34-11-9-33(10-12-34)16-18-4-7-22(35)17(2)13-18/h1,4,7,13-15,19,35H,5-6,8-12,16H2,2H3,(H,27,36)(H2,28,29,30,31,32)" 5YZ InChIKey InChI 1.03 VCHMYWXCLCHLBE-UHFFFAOYSA-N 5YZ SMILES_CANONICAL CACTVS 3.385 "Cc1cc(CN2CCN(CC2)c3nc(Nc4cc([nH]n4)C5CC5)cc(n3)C(=O)NCC#C)ccc1O" 5YZ SMILES CACTVS 3.385 "Cc1cc(CN2CCN(CC2)c3nc(Nc4cc([nH]n4)C5CC5)cc(n3)C(=O)NCC#C)ccc1O" 5YZ SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "Cc1cc(ccc1O)CN2CCN(CC2)c3nc(cc(n3)Nc4cc([nH]n4)C5CC5)C(=O)NCC#C" 5YZ SMILES "OpenEye OEToolkits" 2.0.7 "Cc1cc(ccc1O)CN2CCN(CC2)c3nc(cc(n3)Nc4cc([nH]n4)C5CC5)C(=O)NCC#C" # _pdbx_chem_comp_identifier.comp_id 5YZ _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 "6-[(5-cyclopropyl-1~{H}-pyrazol-3-yl)amino]-2-[4-[(3-methyl-4-oxidanyl-phenyl)methyl]piperazin-1-yl]-~{N}-prop-2-ynyl-pyrimidine-4-carboxamide" # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site 5YZ "Create component" 2021-08-31 PDBJ 5YZ "Initial release" 2022-06-08 RCSB 5YZ "Modify PCM" 2024-09-27 PDBE # _pdbx_chem_comp_pcm.pcm_id 1 _pdbx_chem_comp_pcm.comp_id 5YZ _pdbx_chem_comp_pcm.modified_residue_id LYS _pdbx_chem_comp_pcm.type None _pdbx_chem_comp_pcm.category "Covalent chemical modification" _pdbx_chem_comp_pcm.position "Amino-acid side chain" _pdbx_chem_comp_pcm.polypeptide_position "Any position" _pdbx_chem_comp_pcm.comp_id_linking_atom C26 _pdbx_chem_comp_pcm.modified_residue_id_linking_atom NZ _pdbx_chem_comp_pcm.uniprot_specific_ptm_accession ? _pdbx_chem_comp_pcm.uniprot_generic_ptm_accession ? #