data_R1L # _chem_comp.id R1L _chem_comp.name "(2E)-2-{(3R)-3-[4-amino-3-(2-fluoro-4-phenoxyphenyl)-1H-pyrazolo[3,4-d]pyrimidin-1-yl]piperidine-1-carbonyl}-4-methyl-4-[4-(oxetan-3-yl)piperazin-1-yl]pent-2-enenitrile" _chem_comp.type non-polymer _chem_comp.pdbx_type HETAIN _chem_comp.formula "C36 H40 F N9 O3" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms Rilzabrutinib _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2020-12-23 _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 665.760 _chem_comp.one_letter_code ? _chem_comp.three_letter_code R1L _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 7L5O _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site RCSB _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 R1L C2 C1 C 0 1 Y N N N N N 19.463 4.795 5.040 -5.800 -0.257 1.390 C2 R1L 1 R1L C3 C2 C 0 1 Y N N N N N 18.985 4.760 6.312 -6.912 0.488 1.730 C3 R1L 2 R1L C4 C3 C 0 1 Y N N N N N 18.811 5.960 6.982 -7.219 1.641 1.023 C4 R1L 3 R1L C6 C4 C 0 1 Y N N N N N 17.233 6.620 8.665 -9.399 2.308 0.543 C6 R1L 4 R1L C7 C5 C 0 1 Y N N N N N 17.130 6.883 10.011 -10.558 2.996 0.873 C7 R1L 5 R1L C8 C6 C 0 1 Y N N N N N 16.049 7.571 10.512 -11.657 2.934 0.038 C8 R1L 6 R1L C11 C7 C 0 1 Y N N N N N 16.221 7.012 7.803 -9.347 1.560 -0.625 C11 R1L 7 R1L C12 C8 C 0 1 Y N N N N N 19.138 7.165 6.363 -6.410 2.052 -0.029 C12 R1L 8 R1L C15 C9 C 0 1 Y N N N N N 20.310 5.973 3.019 -3.793 -0.645 -0.039 C15 R1L 9 R1L C18 C10 C 0 1 Y N N N N N 20.683 5.665 0.771 -2.385 -2.114 -1.110 C18 R1L 10 R1L C24 C11 C 0 1 Y N N N N N 19.715 5.464 1.787 -3.696 -1.604 -1.140 C24 R1L 11 R1L C27 C12 C 0 1 N N N N N N 24.201 6.237 1.573 -0.318 -2.267 1.766 C27 R1L 12 R1L C31 C13 C 0 1 N N N N N N 23.015 8.157 0.441 0.430 -0.435 0.242 C31 R1L 13 R1L C32 C14 C 0 1 N N N N N N 24.382 8.898 -1.458 2.867 -0.341 0.028 C32 R1L 14 R1L C34 C15 C 0 1 N N N N N N 25.648 9.190 -2.150 4.217 -0.440 0.619 C34 R1L 15 R1L C35 C16 C 0 1 N N N N N N 25.902 10.578 -2.386 4.678 0.569 1.525 C35 R1L 16 R1L C37 C17 C 0 1 N N N N N N 26.393 8.110 -2.508 5.015 -1.478 0.305 C37 R1L 17 R1L C38 C18 C 0 1 N N N N N N 27.714 8.038 -3.240 6.439 -1.510 0.797 C38 R1L 18 R1L C39 C19 C 0 1 N N N N N N 28.726 7.306 -2.345 6.451 -1.738 2.309 C39 R1L 19 R1L C40 C20 C 0 1 N N N N N N 27.463 7.067 -4.413 7.193 -2.647 0.104 C40 R1L 20 R1L F1 F1 F 0 1 N N N N N N 19.635 3.622 4.395 -5.501 -1.381 2.078 F1 R1L 21 R1L O5 O1 O 0 1 N N N N N N 18.337 5.929 8.260 -8.314 2.372 1.359 O5 R1L 22 R1L C9 C21 C 0 1 Y N N N N N 15.032 7.955 9.657 -11.603 2.188 -1.125 C9 R1L 23 R1L C10 C22 C 0 1 Y N N N N N 15.114 7.663 8.308 -10.449 1.502 -1.456 C10 R1L 24 R1L C13 C23 C 0 1 Y N N N N N 19.635 7.181 5.076 -5.297 1.314 -0.374 C13 R1L 25 R1L C14 C24 C 0 1 Y N N N N N 19.786 5.985 4.391 -4.987 0.150 0.330 C14 R1L 26 R1L N16 N1 N 0 1 Y N N N N N 21.501 6.400 2.705 -2.628 -0.624 0.565 N16 R1L 27 R1L N17 N2 N 0 1 Y N N N N N 21.757 6.251 1.362 -1.748 -1.508 -0.068 N17 R1L 28 R1L N19 N3 N 0 1 Y N N N N N 20.441 5.313 -0.476 -2.030 -3.017 -2.024 N19 R1L 29 R1L C20 C25 C 0 1 Y N N N N N 19.283 4.762 -0.749 -2.887 -3.423 -2.934 C20 R1L 30 R1L N21 N4 N 0 1 Y N N N N N 18.332 4.562 0.133 -4.129 -2.976 -2.995 N21 R1L 31 R1L C22 C26 C 0 1 Y N N N N N 18.490 4.891 1.415 -4.576 -2.071 -2.130 C22 R1L 32 R1L N23 N5 N 0 1 N N N N N N 17.494 4.696 2.312 -5.873 -1.603 -2.203 N23 R1L 33 R1L C25 C27 C 0 1 N N R N N N 23.001 6.634 0.693 -0.358 -1.746 0.328 C25 R1L 34 R1L C28 C28 C 0 1 N N N N N N 25.516 6.717 0.951 1.132 -2.547 2.169 C28 R1L 35 R1L C29 C29 C 0 1 N N N N N N 25.467 8.217 0.697 1.936 -1.245 2.104 C29 R1L 36 R1L N30 N6 N 0 1 N N N N N N 24.317 8.452 -0.191 1.784 -0.662 0.764 N30 R1L 37 R1L O33 O2 O 0 1 N N N N N N 23.358 9.063 -2.107 2.732 0.030 -1.122 O33 R1L 38 R1L N36 N7 N 0 1 N N N N N N 26.083 11.692 -2.556 5.044 1.369 2.243 N36 R1L 39 R1L N41 N8 N 0 1 N N N N N N 28.198 9.366 -3.727 7.092 -0.230 0.489 N41 R1L 40 R1L C42 C30 C 0 1 N N N N N N 28.795 10.424 -2.797 8.433 -0.166 1.087 C42 R1L 41 R1L C43 C31 C 0 1 N N N N N N 28.834 11.650 -3.475 9.046 1.209 0.811 C43 R1L 42 R1L N44 N9 N 0 1 N N N N N N 29.580 11.634 -4.813 9.108 1.433 -0.640 N44 R1L 43 R1L C45 C32 C 0 1 N N N N N N 28.951 10.625 -5.719 7.767 1.368 -1.238 C45 R1L 44 R1L C46 C33 C 0 1 N N N N N N 28.728 9.306 -5.124 7.154 -0.007 -0.962 C46 R1L 45 R1L C47 C34 C 0 1 N N N N N N 29.675 12.908 -5.347 9.761 2.712 -0.948 C47 R1L 46 R1L C48 C35 C 0 1 N N N N N N 30.950 13.655 -4.917 11.251 2.759 -0.560 C48 R1L 47 R1L O49 O3 O 0 1 N N N N N N 31.476 13.394 -6.236 11.446 3.401 -1.836 O49 R1L 48 R1L C50 C36 C 0 1 N N N N N N 30.230 12.915 -6.783 10.252 2.825 -2.404 C50 R1L 49 R1L H1 H1 H 0 1 N N N N N N 18.747 3.820 6.788 -7.544 0.171 2.547 H1 R1L 50 R1L H2 H2 H 0 1 N N N N N N 17.906 6.546 10.682 -10.601 3.578 1.781 H2 R1L 51 R1L H3 H3 H 0 1 N N N N N N 15.995 7.809 11.564 -12.560 3.469 0.295 H3 R1L 52 R1L H4 H4 H 0 1 N N N N N N 16.298 6.810 6.745 -8.446 1.025 -0.884 H4 R1L 53 R1L H5 H5 H 0 1 N N N N N N 19.001 8.095 6.895 -6.652 2.950 -0.577 H5 R1L 54 R1L H6 H6 H 0 1 N N N N N N 24.085 6.693 2.567 -0.743 -1.519 2.435 H6 R1L 55 R1L H7 H7 H 0 1 N N N N N N 24.228 5.142 1.673 -0.898 -3.188 1.835 H7 R1L 56 R1L H8 H8 H 0 1 N N N N N N 22.919 8.703 1.391 0.489 -0.112 -0.797 H8 R1L 57 R1L H9 H9 H 0 1 N N N N N N 22.191 8.441 -0.230 -0.069 0.331 0.836 H9 R1L 58 R1L H10 H10 H 0 1 N N N N N N 25.976 7.155 -2.225 4.634 -2.289 -0.299 H10 R1L 59 R1L H11 H11 H 0 1 N N N N N N 28.966 7.932 -1.473 5.967 -2.687 2.538 H11 R1L 60 R1L H12 H12 H 0 1 N N N N N N 28.293 6.354 -2.004 7.482 -1.760 2.665 H12 R1L 61 R1L H13 H13 H 0 1 N N N N N N 29.644 7.107 -2.917 5.915 -0.928 2.803 H13 R1L 62 R1L H14 H14 H 0 1 N N N N N N 27.109 6.102 -4.021 7.184 -2.485 -0.974 H14 R1L 63 R1L H15 H15 H 0 1 N N N N N N 26.702 7.492 -5.084 8.223 -2.670 0.459 H15 R1L 64 R1L H16 H16 H 0 1 N N N N N N 28.399 6.915 -4.970 6.708 -3.596 0.332 H16 R1L 65 R1L H17 H17 H 0 1 N N N N N N 14.173 8.483 10.043 -12.464 2.141 -1.776 H17 R1L 66 R1L H18 H18 H 0 1 N N N N N N 14.308 7.946 7.647 -10.409 0.920 -2.365 H18 R1L 67 R1L H19 H19 H 0 1 N N N N N N 19.904 8.116 4.607 -4.669 1.634 -1.192 H19 R1L 68 R1L H20 H20 H 0 1 N N N N N N 19.100 4.452 -1.767 -2.564 -4.156 -3.659 H20 R1L 69 R1L H21 H21 H 0 1 N N N N N N 16.703 4.295 1.850 -6.453 -1.890 -2.926 H21 R1L 70 R1L H22 H22 H 0 1 N N N N N N 17.809 4.076 3.031 -6.205 -0.987 -1.530 H22 R1L 71 R1L H23 H23 H 0 1 N N N N N N 23.081 6.114 -0.273 0.090 -2.484 -0.339 H23 R1L 72 R1L H24 H24 H 0 1 N N N N N N 25.678 6.193 -0.003 1.157 -2.941 3.185 H24 R1L 73 R1L H25 H25 H 0 1 N N N N N N 26.345 6.493 1.638 1.565 -3.278 1.485 H25 R1L 74 R1L H26 H26 H 0 1 N N N N N N 26.396 8.551 0.212 1.561 -0.546 2.851 H26 R1L 75 R1L H27 H27 H 0 1 N N N N N N 25.333 8.759 1.645 2.988 -1.456 2.296 H27 R1L 76 R1L H29 H29 H 0 1 N N N N N N 28.171 10.519 -1.896 8.359 -0.322 2.163 H29 R1L 77 R1L H30 H30 H 0 1 N N N N N N 29.814 10.129 -2.507 9.064 -0.940 0.649 H30 R1L 78 R1L H31 H31 H 0 1 N N N N N N 29.325 12.385 -2.821 8.430 1.981 1.272 H31 R1L 79 R1L H32 H32 H 0 1 N N N N N N 27.798 11.965 -3.667 10.052 1.249 1.229 H32 R1L 80 R1L H34 H34 H 0 1 N N N N N N 29.606 10.498 -6.593 7.136 2.142 -0.801 H34 R1L 81 R1L H35 H35 H 0 1 N N N N N N 27.978 11.020 -6.045 7.841 1.524 -2.314 H35 R1L 82 R1L H36 H36 H 0 1 N N N N N N 28.005 8.760 -5.748 7.771 -0.779 -1.423 H36 R1L 83 R1L H37 H37 H 0 1 N N N N N N 29.685 8.763 -5.111 6.148 -0.047 -1.380 H37 R1L 84 R1L H38 H38 H 0 1 N N N N N N 28.771 13.526 -5.243 9.189 3.575 -0.606 H38 R1L 85 R1L H39 H39 H 0 1 N N N N N N 31.507 13.176 -4.098 11.464 3.402 0.294 H39 R1L 86 R1L H40 H40 H 0 1 N N N N N N 30.801 14.720 -4.686 11.718 1.778 -0.482 H40 R1L 87 R1L H41 H41 H 0 1 N N N N N N 29.729 13.618 -7.465 10.415 1.863 -2.890 H41 R1L 88 R1L H42 H42 H 0 1 N N N N N N 30.288 11.924 -7.256 9.674 3.520 -3.012 H42 R1L 89 # 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 R1L C50 O49 SING N N 1 R1L C50 C47 SING N N 2 R1L O49 C48 SING N N 3 R1L C45 C46 SING N N 4 R1L C45 N44 SING N N 5 R1L C47 C48 SING N N 6 R1L C47 N44 SING N N 7 R1L C46 N41 SING N N 8 R1L N44 C43 SING N N 9 R1L C40 C38 SING N N 10 R1L N41 C38 SING N N 11 R1L N41 C42 SING N N 12 R1L C43 C42 SING N N 13 R1L C38 C37 SING N N 14 R1L C38 C39 SING N N 15 R1L N36 C35 TRIP N N 16 R1L C37 C34 DOUB N E 17 R1L C35 C34 SING N N 18 R1L C34 C32 SING N N 19 R1L O33 C32 DOUB N N 20 R1L C32 N30 SING N N 21 R1L C20 N19 DOUB Y N 22 R1L C20 N21 SING Y N 23 R1L N19 C18 SING Y N 24 R1L N30 C31 SING N N 25 R1L N30 C29 SING N N 26 R1L N21 C22 DOUB Y N 27 R1L C31 C25 SING N N 28 R1L C25 N17 SING N N 29 R1L C25 C27 SING N N 30 R1L C29 C28 SING N N 31 R1L C18 N17 SING Y N 32 R1L C18 C24 DOUB Y N 33 R1L C28 C27 SING N N 34 R1L N17 N16 SING Y N 35 R1L C22 C24 SING Y N 36 R1L C22 N23 SING N N 37 R1L C24 C15 SING Y N 38 R1L N16 C15 DOUB Y N 39 R1L C15 C14 SING N N 40 R1L C14 C2 DOUB Y N 41 R1L C14 C13 SING Y N 42 R1L F1 C2 SING N N 43 R1L C2 C3 SING Y N 44 R1L C13 C12 DOUB Y N 45 R1L C3 C4 DOUB Y N 46 R1L C12 C4 SING Y N 47 R1L C4 O5 SING N N 48 R1L C11 C10 DOUB Y N 49 R1L C11 C6 SING Y N 50 R1L O5 C6 SING N N 51 R1L C10 C9 SING Y N 52 R1L C6 C7 DOUB Y N 53 R1L C9 C8 DOUB Y N 54 R1L C7 C8 SING Y N 55 R1L C3 H1 SING N N 56 R1L C7 H2 SING N N 57 R1L C8 H3 SING N N 58 R1L C11 H4 SING N N 59 R1L C12 H5 SING N N 60 R1L C27 H6 SING N N 61 R1L C27 H7 SING N N 62 R1L C31 H8 SING N N 63 R1L C31 H9 SING N N 64 R1L C37 H10 SING N N 65 R1L C39 H11 SING N N 66 R1L C39 H12 SING N N 67 R1L C39 H13 SING N N 68 R1L C40 H14 SING N N 69 R1L C40 H15 SING N N 70 R1L C40 H16 SING N N 71 R1L C9 H17 SING N N 72 R1L C10 H18 SING N N 73 R1L C13 H19 SING N N 74 R1L C20 H20 SING N N 75 R1L N23 H21 SING N N 76 R1L N23 H22 SING N N 77 R1L C25 H23 SING N N 78 R1L C28 H24 SING N N 79 R1L C28 H25 SING N N 80 R1L C29 H26 SING N N 81 R1L C29 H27 SING N N 82 R1L C42 H29 SING N N 83 R1L C42 H30 SING N N 84 R1L C43 H31 SING N N 85 R1L C43 H32 SING N N 86 R1L C45 H34 SING N N 87 R1L C45 H35 SING N N 88 R1L C46 H36 SING N N 89 R1L C46 H37 SING N N 90 R1L C47 H38 SING N N 91 R1L C48 H39 SING N N 92 R1L C48 H40 SING N N 93 R1L C50 H41 SING N N 94 R1L C50 H42 SING N N 95 # 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 R1L SMILES ACDLabs 12.01 "c2(cc(Oc1ccccc1)ccc2c3c7c(n(n3)C4CCCN(C4)C(C(C#N)=[C@H]C(C)(C)N5CCN(CC5)C6COC6)=O)ncnc7N)F" R1L InChI InChI 1.03 "InChI=1S/C36H40FN9O3/c1-36(2,45-15-13-43(14-16-45)26-21-48-22-26)18-24(19-38)35(47)44-12-6-7-25(20-44)46-34-31(33(39)40-23-41-34)32(42-46)29-11-10-28(17-30(29)37)49-27-8-4-3-5-9-27/h3-5,8-11,17-18,23,25-26H,6-7,12-16,20-22H2,1-2H3,(H2,39,40,41)/b24-18+/t25-/m1/s1" R1L InChIKey InChI 1.03 LCFFREMLXLZNHE-GBOLQPHISA-N R1L SMILES_CANONICAL CACTVS 3.385 "CC(C)(\C=C(C#N)\C(=O)N1CCC[C@H](C1)n2nc(c3ccc(Oc4ccccc4)cc3F)c5c(N)ncnc25)N6CCN(CC6)C7COC7" R1L SMILES CACTVS 3.385 "CC(C)(C=C(C#N)C(=O)N1CCC[CH](C1)n2nc(c3ccc(Oc4ccccc4)cc3F)c5c(N)ncnc25)N6CCN(CC6)C7COC7" R1L SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "CC(C)(/C=C(\C#N)/C(=O)N1CCC[C@H](C1)n2c3c(c(n2)c4ccc(cc4F)Oc5ccccc5)c(ncn3)N)N6CCN(CC6)C7COC7" R1L SMILES "OpenEye OEToolkits" 2.0.7 "CC(C)(C=C(C#N)C(=O)N1CCCC(C1)n2c3c(c(n2)c4ccc(cc4F)Oc5ccccc5)c(ncn3)N)N6CCN(CC6)C7COC7" # loop_ _pdbx_chem_comp_identifier.comp_id _pdbx_chem_comp_identifier.type _pdbx_chem_comp_identifier.program _pdbx_chem_comp_identifier.program_version _pdbx_chem_comp_identifier.identifier R1L "SYSTEMATIC NAME" ACDLabs 12.01 "(2E)-2-{(3R)-3-[4-amino-3-(2-fluoro-4-phenoxyphenyl)-1H-pyrazolo[3,4-d]pyrimidin-1-yl]piperidine-1-carbonyl}-4-methyl-4-[4-(oxetan-3-yl)piperazin-1-yl]pent-2-enenitrile" R1L "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 "(~{E})-2-[(3~{R})-3-[4-azanyl-3-(2-fluoranyl-4-phenoxy-phenyl)pyrazolo[3,4-d]pyrimidin-1-yl]piperidin-1-yl]carbonyl-4-methyl-4-[4-(oxetan-3-yl)piperazin-1-yl]pent-2-enenitrile" # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site R1L "Create component" 2020-12-23 RCSB R1L "Modify synonyms" 2021-03-01 PDBE R1L "Initial release" 2022-06-29 RCSB R1L "Modify PCM" 2024-09-27 PDBE # _pdbx_chem_comp_synonyms.ordinal 1 _pdbx_chem_comp_synonyms.comp_id R1L _pdbx_chem_comp_synonyms.name Rilzabrutinib _pdbx_chem_comp_synonyms.provenance ? _pdbx_chem_comp_synonyms.type ? # _pdbx_chem_comp_pcm.pcm_id 1 _pdbx_chem_comp_pcm.comp_id R1L _pdbx_chem_comp_pcm.modified_residue_id CYS _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 C37 _pdbx_chem_comp_pcm.modified_residue_id_linking_atom SG _pdbx_chem_comp_pcm.uniprot_specific_ptm_accession ? _pdbx_chem_comp_pcm.uniprot_generic_ptm_accession ? #