data_XD8 # _chem_comp.id XD8 _chem_comp.name "(5~{S})-1'-[6-azanyl-5-(2-azanyl-3-chloranyl-pyridin-4-yl)sulfanyl-pyrazin-2-yl]spiro[5,7-dihydrocyclopenta[b]pyridine-6,4'-piperidine]-5-amine" _chem_comp.type non-polymer _chem_comp.pdbx_type HETAIN _chem_comp.formula "C21 H23 Cl N8 S" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2023-11-02 _chem_comp.pdbx_modified_date 2024-08-09 _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 454.979 _chem_comp.one_letter_code ? _chem_comp.three_letter_code XD8 _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 8WX7 _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site PDBC # 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 XD8 C4 C1 C 0 1 N N N N N N 16.390 -24.772 25.323 -4.116 0.580 -0.849 C4 XD8 1 XD8 C5 C2 C 0 1 N N S N N N 15.066 -25.174 26.033 -4.425 0.311 0.632 C5 XD8 2 XD8 C6 C3 C 0 1 N N N N N N 16.800 -23.346 25.707 -3.528 1.974 -1.030 C6 XD8 3 XD8 C7 C4 C 0 1 N N N N N N 18.140 -22.981 25.061 -2.143 2.030 -0.380 C7 XD8 4 XD8 C10 C5 C 0 1 N N N N N N 17.540 -25.747 25.634 -3.176 -0.483 -1.404 C10 XD8 5 XD8 N12 N1 N 0 1 Y N N N N N 19.622 -22.729 27.331 0.344 2.077 0.352 N12 XD8 6 XD8 C13 C6 C 0 1 Y N N N N N 20.248 -22.564 28.491 1.590 2.188 0.790 C13 XD8 7 XD8 C20 C7 C 0 1 Y N N N N N 24.671 -23.661 31.130 4.979 -1.120 0.266 C20 XD8 8 XD8 C21 C8 C 0 1 Y N N N N N 26.023 -23.645 30.838 5.667 -2.043 -0.512 C21 XD8 9 XD8 C24 C9 C 0 1 Y N N N N N 24.216 -23.075 28.877 5.892 0.609 -1.118 C24 XD8 10 XD8 C28 C10 C 0 1 Y N N N N N 12.670 -25.609 24.974 -6.280 -1.281 1.619 C28 XD8 11 XD8 C1 C11 C 0 1 Y N N N N N 14.590 -25.138 23.667 -6.315 -0.410 -0.607 C1 XD8 12 XD8 C2 C12 C 0 1 Y N N N N N 14.021 -25.329 24.921 -5.698 -0.507 0.626 C2 XD8 13 XD8 C3 C13 C 0 1 N N N N N N 16.053 -24.836 23.824 -5.497 0.484 -1.517 C3 XD8 14 XD8 N8 N2 N 0 1 N N N N N N 19.210 -23.988 25.340 -1.278 1.007 -0.983 N8 XD8 15 XD8 C9 C14 C 0 1 N N N N N N 18.833 -25.341 24.908 -1.802 -0.343 -0.742 C9 XD8 16 XD8 C11 C15 C 0 1 Y N N N N N 19.869 -23.835 26.577 0.031 1.125 -0.521 C11 XD8 17 XD8 C14 C16 C 0 1 Y N N N N N 21.178 -23.520 28.949 2.571 1.302 0.332 C14 XD8 18 XD8 N15 N3 N 0 1 Y N N N N N 21.406 -24.590 28.211 2.252 0.355 -0.537 N15 XD8 19 XD8 C16 C17 C 0 1 Y N N N N N 20.777 -24.779 27.046 1.007 0.247 -0.973 C16 XD8 20 XD8 N17 N4 N 0 1 N N N N N N 19.985 -21.423 29.208 1.921 3.184 1.704 N17 XD8 21 XD8 S18 S1 S 0 1 N N N N N N 22.018 -23.399 30.504 4.229 1.445 0.911 S18 XD8 22 XD8 C19 C18 C 0 1 Y N N N N N 23.736 -23.373 30.148 5.087 0.234 -0.039 C19 XD8 23 XD8 N22 N5 N 0 1 Y N N N N N 26.414 -23.347 29.628 6.419 -1.643 -1.527 N22 XD8 24 XD8 C23 C19 C 0 1 Y N N N N N 25.570 -23.060 28.648 6.547 -0.365 -1.839 C23 XD8 25 XD8 CL25 CL1 CL 0 0 N N N N N N 24.138 -24.018 32.727 3.994 -1.649 1.594 CL25 XD8 26 XD8 N26 N6 N 0 1 N N N N N N 27.009 -23.967 31.783 5.564 -3.399 -0.224 N26 XD8 27 XD8 N27 N7 N 0 1 N N N N N N 15.258 -26.423 26.801 -3.332 -0.451 1.252 N27 XD8 28 XD8 C29 C20 C 0 1 Y N N N N N 11.965 -25.704 23.771 -7.470 -1.935 1.337 C29 XD8 29 XD8 C30 C21 C 0 1 Y N N N N N 12.604 -25.490 22.562 -8.030 -1.794 0.082 C30 XD8 30 XD8 N31 N8 N 0 1 Y N N N N N 13.896 -25.222 22.524 -7.449 -1.051 -0.837 N31 XD8 31 XD8 H1 H1 H 0 1 N N N N N N 14.760 -24.361 26.707 -4.579 1.250 1.163 H1 XD8 32 XD8 H2 H2 H 0 1 N N N N N N 16.895 -23.279 26.801 -3.440 2.195 -2.094 H2 XD8 33 XD8 H3 H3 H 0 1 N N N N N N 16.028 -22.642 25.362 -4.181 2.708 -0.559 H3 XD8 34 XD8 H4 H4 H 0 1 N N N N N N 18.465 -22.005 25.452 -1.706 3.016 -0.539 H4 XD8 35 XD8 H5 H5 H 0 1 N N N N N N 17.998 -22.911 23.972 -2.236 1.842 0.690 H5 XD8 36 XD8 H6 H6 H 0 1 N N N N N N 17.250 -26.757 25.310 -3.582 -1.472 -1.195 H6 XD8 37 XD8 H7 H7 H 0 1 N N N N N N 17.724 -25.749 26.718 -3.075 -0.352 -2.482 H7 XD8 38 XD8 H8 H8 H 0 1 N N N N N N 23.527 -22.857 28.074 5.999 1.650 -1.384 H8 XD8 39 XD8 H9 H9 H 0 1 N N N N N N 12.171 -25.751 25.921 -5.818 -1.372 2.591 H9 XD8 40 XD8 H10 H10 H 0 1 N N N N N N 16.647 -25.628 23.345 -5.952 1.472 -1.586 H10 XD8 41 XD8 H11 H11 H 0 1 N N N N N N 16.283 -23.869 23.352 -5.408 0.038 -2.507 H11 XD8 42 XD8 H12 H12 H 0 1 N N N N N N 18.666 -25.349 23.821 -1.897 -0.510 0.331 H12 XD8 43 XD8 H13 H13 H 0 1 N N N N N N 19.637 -26.048 25.161 -1.118 -1.079 -1.165 H13 XD8 44 XD8 H14 H14 H 0 1 N N N N N N 20.975 -25.669 26.467 0.749 -0.525 -1.682 H14 XD8 45 XD8 H15 H15 H 0 1 N N N N N N 19.322 -20.862 28.712 1.240 3.798 2.020 H15 XD8 46 XD8 H16 H16 H 0 1 N N N N N N 19.610 -21.670 30.101 2.833 3.265 2.024 H16 XD8 47 XD8 H17 H17 H 0 1 N N N N N N 25.948 -22.814 27.667 7.170 -0.081 -2.674 H17 XD8 48 XD8 H18 H18 H 0 1 N N N N N N 27.911 -23.914 31.355 5.015 -3.697 0.518 H18 XD8 49 XD8 H19 H19 H 0 1 N N N N N N 26.964 -23.321 32.545 6.043 -4.048 -0.764 H19 XD8 50 XD8 H20 H20 H 0 1 N N N N N N 15.945 -26.275 27.512 -3.450 -0.504 2.252 H20 XD8 51 XD8 H21 H21 H 0 1 N N N N N N 14.392 -26.690 27.225 -3.258 -1.372 0.846 H21 XD8 52 XD8 H23 H23 H 0 1 N N N N N N 10.913 -25.946 23.785 -7.950 -2.546 2.087 H23 XD8 53 XD8 H24 H24 H 0 1 N N N N N N 12.041 -25.543 21.642 -8.957 -2.300 -0.148 H24 XD8 54 # 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 XD8 N31 C30 DOUB Y N 1 XD8 N31 C1 SING Y N 2 XD8 C30 C29 SING Y N 3 XD8 C1 C3 SING N N 4 XD8 C1 C2 DOUB Y N 5 XD8 C29 C28 DOUB Y N 6 XD8 C3 C4 SING N N 7 XD8 C9 N8 SING N N 8 XD8 C9 C10 SING N N 9 XD8 C2 C28 SING Y N 10 XD8 C2 C5 SING N N 11 XD8 C7 N8 SING N N 12 XD8 C7 C6 SING N N 13 XD8 C4 C10 SING N N 14 XD8 C4 C6 SING N N 15 XD8 C4 C5 SING N N 16 XD8 N8 C11 SING N N 17 XD8 C5 N27 SING N N 18 XD8 C11 C16 DOUB Y N 19 XD8 C11 N12 SING Y N 20 XD8 C16 N15 SING Y N 21 XD8 N12 C13 DOUB Y N 22 XD8 N15 C14 DOUB Y N 23 XD8 C13 C14 SING Y N 24 XD8 C13 N17 SING N N 25 XD8 C23 C24 DOUB Y N 26 XD8 C23 N22 SING Y N 27 XD8 C24 C19 SING Y N 28 XD8 C14 S18 SING N N 29 XD8 N22 C21 DOUB Y N 30 XD8 C19 S18 SING N N 31 XD8 C19 C20 DOUB Y N 32 XD8 C21 C20 SING Y N 33 XD8 C21 N26 SING N N 34 XD8 C20 CL25 SING N N 35 XD8 C5 H1 SING N N 36 XD8 C6 H2 SING N N 37 XD8 C6 H3 SING N N 38 XD8 C7 H4 SING N N 39 XD8 C7 H5 SING N N 40 XD8 C10 H6 SING N N 41 XD8 C10 H7 SING N N 42 XD8 C24 H8 SING N N 43 XD8 C28 H9 SING N N 44 XD8 C3 H10 SING N N 45 XD8 C3 H11 SING N N 46 XD8 C9 H12 SING N N 47 XD8 C9 H13 SING N N 48 XD8 C16 H14 SING N N 49 XD8 N17 H15 SING N N 50 XD8 N17 H16 SING N N 51 XD8 C23 H17 SING N N 52 XD8 N26 H18 SING N N 53 XD8 N26 H19 SING N N 54 XD8 N27 H20 SING N N 55 XD8 N27 H21 SING N N 56 XD8 C29 H23 SING N N 57 XD8 C30 H24 SING N N 58 # 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 XD8 InChI InChI 1.06 "InChI=1S/C21H23ClN8S/c22-16-14(3-7-27-18(16)24)31-20-19(25)29-15(11-28-20)30-8-4-21(5-9-30)10-13-12(17(21)23)2-1-6-26-13/h1-3,6-7,11,17H,4-5,8-10,23H2,(H2,24,27)(H2,25,29)/t17-/m1/s1" XD8 InChIKey InChI 1.06 YFKOUTGKKFPEOH-QGZVFWFLSA-N XD8 SMILES_CANONICAL CACTVS 3.385 "N[C@@H]1c2cccnc2CC13CCN(CC3)c4cnc(Sc5ccnc(N)c5Cl)c(N)n4" XD8 SMILES CACTVS 3.385 "N[CH]1c2cccnc2CC13CCN(CC3)c4cnc(Sc5ccnc(N)c5Cl)c(N)n4" XD8 SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "c1cc2c(nc1)CC3([C@@H]2N)CCN(CC3)c4cnc(c(n4)N)Sc5ccnc(c5Cl)N" XD8 SMILES "OpenEye OEToolkits" 2.0.7 "c1cc2c(nc1)CC3(C2N)CCN(CC3)c4cnc(c(n4)N)Sc5ccnc(c5Cl)N" # _pdbx_chem_comp_identifier.comp_id XD8 _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 "(5~{S})-1'-[6-azanyl-5-(2-azanyl-3-chloranyl-pyridin-4-yl)sulfanyl-pyrazin-2-yl]spiro[5,7-dihydrocyclopenta[b]pyridine-6,4'-piperidine]-5-amine" # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site XD8 "Create component" 2023-11-02 PDBC XD8 "Initial release" 2024-08-14 RCSB #