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 
# 
