data_XI3
# 
_chem_comp.id                                    XI3 
_chem_comp.name                                  "(3S)-N-[(1-benzothiophen-5-yl)methyl]-1-[(2P)-2-(3-fluoro-4-methylphenyl)-2H-pyrazolo[3,4-d]pyrimidin-4-yl]piperidine-3-carboxamide" 
_chem_comp.type                                  non-polymer 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C27 H25 F N6 O S" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2022-11-21 
_chem_comp.pdbx_modified_date                    2023-11-24 
_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                        500.590 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     XI3 
_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        8F7L 
_chem_comp.pdbx_subcomponent_list                ? 
_chem_comp.pdbx_processing_site                  RCSB 
# 
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 
XI3 C02 C1  C 0 1 N N N N N N 17.332 -0.323 -13.251 2.725   -1.478 -0.119 C02 XI3 1  
XI3 C04 C2  C 0 1 N N N N N N 18.031 -2.726 -12.449 5.159   -1.571 -0.184 C04 XI3 2  
XI3 C05 C3  C 0 1 Y N N N N N 19.131 -2.700 -11.321 6.317   -0.608 -0.228 C05 XI3 3  
XI3 C06 C4  C 0 1 Y N N N N N 20.265 -1.864 -11.444 6.810   -0.179 -1.453 C06 XI3 4  
XI3 C07 C5  C 0 1 Y N N N N N 21.268 -1.804 -10.465 7.866   0.699  -1.505 C07 XI3 5  
XI3 C08 C6  C 0 1 Y N N N N N 21.176 -2.575 -9.299  8.451   1.166  -0.323 C08 XI3 6  
XI3 C10 C7  C 0 1 Y N N N N N 21.263 -3.859 -7.102  9.664   2.141  1.672  C10 XI3 7  
XI3 C11 C8  C 0 1 Y N N N N N 20.161 -4.146 -7.823  8.689   1.326  2.021  C11 XI3 8  
XI3 C12 C9  C 0 1 Y N N N N N 20.049 -3.432 -9.113  7.957   0.736  0.912  C12 XI3 9  
XI3 C13 C10 C 0 1 Y N N N N N 19.065 -3.459 -10.133 6.868   -0.162 0.934  C13 XI3 10 
XI3 C14 C11 C 0 1 N N S N N N 16.311 0.881  -13.227 1.431   -0.707 -0.093 C14 XI3 11 
XI3 C15 C12 C 0 1 N N N N N N 16.817 2.019  -12.282 0.254   -1.684 -0.054 C15 XI3 12 
XI3 C17 C13 C 0 1 Y N N N N N 18.259 1.295  -10.187 -2.083  -1.776 0.116  C17 XI3 13 
XI3 C19 C14 C 0 1 Y N N N N N 20.556 1.757  -9.774  -2.939  -3.911 0.420  C19 XI3 14 
XI3 C21 C15 C 0 1 Y N N N N N 19.593 0.203  -8.355  -4.536  -2.244 0.335  C21 XI3 15 
XI3 C24 C16 C 0 1 Y N N N N N 17.592 -2.192 -6.381  -6.330  0.820  0.122  C24 XI3 16 
XI3 C25 C17 C 0 1 Y N N N N N 17.993 -2.232 -5.038  -7.679  0.518  0.247  C25 XI3 17 
XI3 C26 C18 C 0 1 Y N N N N N 17.507 -3.153 -4.065  -8.619  1.532  0.207  C26 XI3 18 
XI3 C28 C19 C 0 1 Y N N N N N 16.524 -4.134 -4.447  -8.214  2.846  0.041  C28 XI3 19 
XI3 C29 C20 C 0 1 N N N N N N 16.012 -5.107 -3.416  -9.240  3.950  -0.004 C29 XI3 20 
XI3 C30 C21 C 0 1 Y N N N N N 16.120 -4.092 -5.786  -6.871  3.148  -0.084 C30 XI3 21 
XI3 C31 C22 C 0 1 Y N N N N N 16.621 -3.163 -6.728  -5.928  2.139  -0.044 C31 XI3 22 
XI3 C32 C23 C 0 1 Y N N N N N 17.468 -0.537 -8.385  -4.049  -0.026 0.058  C32 XI3 23 
XI3 C33 C24 C 0 1 Y N N N N N 18.335 0.353  -9.063  -3.451  -1.263 0.153  C33 XI3 24 
XI3 C34 C25 C 0 1 N N N N N N 15.693 1.024  -10.372 -1.152  -0.131 -1.272 C34 XI3 25 
XI3 C35 C26 C 0 1 N N N N N N 14.907 0.068  -11.329 -0.017  0.893  -1.348 C35 XI3 26 
XI3 C36 C27 C 0 1 N N N N N N 14.916 0.480  -12.815 1.327   0.159  -1.352 C36 XI3 27 
XI3 F27 F1  F 0 1 N N N N N N 17.953 -3.106 -2.837  -9.933  1.240  0.329  F27 XI3 28 
XI3 N03 N1  N 0 1 N N N N N N 17.120 -1.545 -12.505 3.901   -0.821 -0.159 N03 XI3 29 
XI3 N16 N2  N 0 1 N N N N N N 17.004 1.471  -10.931 -1.008  -0.933 -0.050 N16 XI3 30 
XI3 N18 N3  N 0 1 Y N N N N N 19.372 1.972  -10.526 -1.917  -3.086 0.254  N18 XI3 31 
XI3 N20 N4  N 0 1 Y N N N N N 20.729 0.936  -8.734  -4.192  -3.539 0.465  N20 XI3 32 
XI3 N22 N5  N 0 1 Y N N N N N 19.465 -0.722 -7.325  -5.661  -1.564 0.337  N22 XI3 33 
XI3 N23 N6  N 0 1 Y N N N N N 18.147 -1.176 -7.354  -5.375  -0.204 0.168  N23 XI3 34 
XI3 O01 O1  O 0 1 N N N N N N 18.335 -0.189 -13.910 2.709   -2.691 -0.098 O01 XI3 35 
XI3 S09 S1  S 0 1 Y N N N N N 22.252 -2.695 -7.934  9.792   2.275  -0.071 S09 XI3 36 
XI3 H1  H1  H 0 1 N N N N N N 17.411 -3.621 -12.294 5.184   -2.210 -1.067 H1  XI3 37 
XI3 H2  H2  H 0 1 N N N N N N 18.545 -2.800 -13.418 5.233   -2.187 0.712  H2  XI3 38 
XI3 H3  H3  H 0 1 N N N N N N 20.363 -1.248 -12.326 6.361   -0.537 -2.368 H3  XI3 39 
XI3 H4  H4  H 0 1 N N N N N N 22.120 -1.157 -10.612 8.246   1.029  -2.460 H4  XI3 40 
XI3 H5  H5  H 0 1 N N N N N N 21.499 -4.292 -6.141  10.302  2.661  2.371  H5  XI3 41 
XI3 H6  H6  H 0 1 N N N N N N 19.413 -4.847 -7.483  8.451   1.112  3.053  H6  XI3 42 
XI3 H7  H7  H 0 1 N N N N N N 18.209 -4.102 -9.992  6.472   -0.500 1.880  H7  XI3 43 
XI3 H8  H8  H 0 1 N N N N N N 16.264 1.292  -14.246 1.405   -0.069 0.790  H8  XI3 44 
XI3 H9  H9  H 0 1 N N N N N N 17.774 2.411  -12.657 0.289   -2.331 -0.930 H9  XI3 45 
XI3 H10 H10 H 0 1 N N N N N N 16.075 2.830  -12.251 0.317   -2.292 0.849  H10 XI3 46 
XI3 H11 H11 H 0 1 N N N N N N 21.422 2.326  -10.079 -2.723  -4.963 0.529  H11 XI3 47 
XI3 H12 H12 H 0 1 N N N N N N 18.727 -1.509 -4.716  -7.995  -0.507 0.376  H12 XI3 48 
XI3 H13 H13 H 0 1 N N N N N N 16.645 -6.007 -3.414  -9.416  4.323  1.005  H13 XI3 49 
XI3 H14 H14 H 0 1 N N N N N N 16.040 -4.637 -2.422  -8.873  4.761  -0.632 H14 XI3 50 
XI3 H15 H15 H 0 1 N N N N N N 14.977 -5.388 -3.659  -10.172 3.563  -0.416 H15 XI3 51 
XI3 H16 H16 H 0 1 N N N N N N 15.384 -4.809 -6.119  -6.558  4.173  -0.213 H16 XI3 52 
XI3 H17 H17 H 0 1 N N N N N N 16.252 -3.195 -7.742  -4.879  2.376  -0.142 H17 XI3 53 
XI3 H18 H18 H 0 1 N N N N N N 16.429 -0.697 -8.633  -3.542  0.917  -0.081 H18 XI3 54 
XI3 H19 H19 H 0 1 N N N N N N 15.074 1.913  -10.180 -2.109  0.390  -1.254 H19 XI3 55 
XI3 H20 H20 H 0 1 N N N N N N 15.879 0.495  -9.425  -1.110  -0.785 -2.143 H20 XI3 56 
XI3 H21 H21 H 0 1 N N N N N N 13.861 0.032  -10.991 -0.115  1.478  -2.262 H21 XI3 57 
XI3 H22 H22 H 0 1 N N N N N N 15.352 -0.935 -11.250 -0.067  1.557  -0.484 H22 XI3 58 
XI3 H23 H23 H 0 1 N N N N N N 14.233 1.330  -12.962 2.139   0.886  -1.362 H23 XI3 59 
XI3 H24 H24 H 0 1 N N N N N N 14.583 -0.368 -13.431 1.393   -0.475 -2.236 H24 XI3 60 
XI3 H25 H25 H 0 1 N N N N N N 16.276 -1.604 -11.972 3.914   0.149  -0.172 H25 XI3 61 
# 
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 
XI3 O01 C02 DOUB N N 1  
XI3 C02 C14 SING N N 2  
XI3 C02 N03 SING N N 3  
XI3 C14 C36 SING N N 4  
XI3 C14 C15 SING N N 5  
XI3 C36 C35 SING N N 6  
XI3 N03 C04 SING N N 7  
XI3 C04 C05 SING N N 8  
XI3 C15 N16 SING N N 9  
XI3 C06 C05 DOUB Y N 10 
XI3 C06 C07 SING Y N 11 
XI3 C35 C34 SING N N 12 
XI3 C05 C13 SING Y N 13 
XI3 N16 C34 SING N N 14 
XI3 N16 C17 SING N N 15 
XI3 N18 C17 DOUB Y N 16 
XI3 N18 C19 SING Y N 17 
XI3 C07 C08 DOUB Y N 18 
XI3 C17 C33 SING Y N 19 
XI3 C13 C12 DOUB Y N 20 
XI3 C19 N20 DOUB Y N 21 
XI3 C08 C12 SING Y N 22 
XI3 C08 S09 SING Y N 23 
XI3 C12 C11 SING Y N 24 
XI3 C33 C32 DOUB Y N 25 
XI3 C33 C21 SING Y N 26 
XI3 N20 C21 SING Y N 27 
XI3 C32 N23 SING Y N 28 
XI3 C21 N22 DOUB Y N 29 
XI3 S09 C10 SING Y N 30 
XI3 C11 C10 DOUB Y N 31 
XI3 N23 N22 SING Y N 32 
XI3 N23 C24 SING N N 33 
XI3 C31 C24 DOUB Y N 34 
XI3 C31 C30 SING Y N 35 
XI3 C24 C25 SING Y N 36 
XI3 C30 C28 DOUB Y N 37 
XI3 C25 C26 DOUB Y N 38 
XI3 C28 C26 SING Y N 39 
XI3 C28 C29 SING N N 40 
XI3 C26 F27 SING N N 41 
XI3 C04 H1  SING N N 42 
XI3 C04 H2  SING N N 43 
XI3 C06 H3  SING N N 44 
XI3 C07 H4  SING N N 45 
XI3 C10 H5  SING N N 46 
XI3 C11 H6  SING N N 47 
XI3 C13 H7  SING N N 48 
XI3 C14 H8  SING N N 49 
XI3 C15 H9  SING N N 50 
XI3 C15 H10 SING N N 51 
XI3 C19 H11 SING N N 52 
XI3 C25 H12 SING N N 53 
XI3 C29 H13 SING N N 54 
XI3 C29 H14 SING N N 55 
XI3 C29 H15 SING N N 56 
XI3 C30 H16 SING N N 57 
XI3 C31 H17 SING N N 58 
XI3 C32 H18 SING N N 59 
XI3 C34 H19 SING N N 60 
XI3 C34 H20 SING N N 61 
XI3 C35 H21 SING N N 62 
XI3 C35 H22 SING N N 63 
XI3 C36 H23 SING N N 64 
XI3 C36 H24 SING N N 65 
XI3 N03 H25 SING N N 66 
# 
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 
XI3 SMILES           ACDLabs              12.01 "Cc1ccc(cc1F)n1cc2c(n1)ncnc2N1CCCC(C1)C(=O)NCc1cc2ccsc2cc1"                                                                                                                                              
XI3 InChI            InChI                1.06  "InChI=1S/C27H25FN6OS/c1-17-4-6-21(12-23(17)28)34-15-22-25(32-34)30-16-31-26(22)33-9-2-3-20(14-33)27(35)29-13-18-5-7-24-19(11-18)8-10-36-24/h4-8,10-12,15-16,20H,2-3,9,13-14H2,1H3,(H,29,35)/t20-/m0/s1" 
XI3 InChIKey         InChI                1.06  LQSRIPAMJVTBAV-FQEVSTJZSA-N                                                                                                                                                                              
XI3 SMILES_CANONICAL CACTVS               3.385 "Cc1ccc(cc1F)n2cc3c(ncnc3N4CCC[C@@H](C4)C(=O)NCc5ccc6sccc6c5)n2"                                                                                                                                         
XI3 SMILES           CACTVS               3.385 "Cc1ccc(cc1F)n2cc3c(ncnc3N4CCC[CH](C4)C(=O)NCc5ccc6sccc6c5)n2"                                                                                                                                           
XI3 SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "Cc1ccc(cc1F)n2cc3c(n2)ncnc3N4CCC[C@@H](C4)C(=O)NCc5ccc6c(c5)ccs6"                                                                                                                                       
XI3 SMILES           "OpenEye OEToolkits" 2.0.7 "Cc1ccc(cc1F)n2cc3c(n2)ncnc3N4CCCC(C4)C(=O)NCc5ccc6c(c5)ccs6"                                                                                                                                            
# 
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 
XI3 "SYSTEMATIC NAME" ACDLabs              12.01 "(3S)-N-[(1-benzothiophen-5-yl)methyl]-1-[(2P)-2-(3-fluoro-4-methylphenyl)-2H-pyrazolo[3,4-d]pyrimidin-4-yl]piperidine-3-carboxamide" 
XI3 "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 "(3~{S})-~{N}-(1-benzothiophen-5-ylmethyl)-1-[2-(3-fluoranyl-4-methyl-phenyl)pyrazolo[3,4-d]pyrimidin-4-yl]piperidine-3-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 
XI3 "Create component" 2022-11-21 RCSB 
XI3 "Initial release"  2023-11-29 RCSB 
# 
