data_A1I1R
# 
_chem_comp.id                                    A1I1R 
_chem_comp.name                                  "(4~{S})-2-azanyl-4-methyl-4-[3-[2-[(2~{S})-2-methylpiperazin-1-yl]pyrimidin-4-yl]-1,2,4-oxadiazol-5-yl]-6,7-dihydro-5~{H}-1-benzothiophene-3-carbonitrile" 
_chem_comp.type                                  non-polymer 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C21 H24 N8 O S" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2025-02-11 
_chem_comp.pdbx_modified_date                    2025-08-01 
_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                        436.533 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     A1I1R 
_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        9IAW 
_chem_comp.pdbx_subcomponent_list                ? 
_chem_comp.pdbx_processing_site                  PDBE 
_chem_comp.pdbx_pcm                              ? 
# 
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_n_terminal_atom_flag 
_chem_comp_atom.pdbx_backbone_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 
A1I1R C5   C1  C 0 1 Y N N N N N 21.459 -0.233 5.670 -0.269 -0.730 0.517  C5   A1I1R 1  
A1I1R C8   C2  C 0 1 Y N N N N N 22.760 -1.793 7.055 -1.554 1.257  1.329  C8   A1I1R 2  
A1I1R C10  C3  C 0 1 Y N N N N N 23.999 -2.264 7.413 -2.768 1.904  1.490  C10  A1I1R 3  
A1I1R C13  C4  C 0 1 N N N N N N 16.163 2.125  6.339 5.380  -2.487 0.115  C13  A1I1R 4  
A1I1R C15  C5  C 0 1 Y N N N N N 16.072 0.497  4.492 5.013  -0.202 -0.770 C15  A1I1R 5  
A1I1R C17  C6  C 0 1 N N S N N N 17.955 0.314  6.162 3.278  -1.280 0.705  C17  A1I1R 6  
A1I1R C20  C7  C 0 1 Y N N N N N 16.296 -1.715 3.390 4.089  2.125  -0.770 C20  A1I1R 7  
A1I1R C22  C8  C 0 1 N N N N N N 18.263 -2.457 4.649 2.165  1.605  0.680  C22  A1I1R 8  
A1I1R C26  C9  C 0 1 N N S N N N 26.101 0.551  4.178 -6.165 0.422  0.333  C26  A1I1R 9  
A1I1R C1   C10 C 0 1 Y N N N N N 22.732 -0.832 6.062 -1.545 0.005  0.713  C1   A1I1R 10 
A1I1R C12  C11 C 0 1 N N N N N N 17.650 1.810  6.396 3.852  -2.580 0.138  C12  A1I1R 11 
A1I1R C14  C12 C 0 1 N N N N N N 15.631 1.856  4.944 5.803  -1.482 -0.961 C14  A1I1R 12 
A1I1R C16  C13 C 0 1 Y N N N N N 17.104 -0.212 5.013 3.898  -0.106 -0.036 C16  A1I1R 13 
A1I1R C19  C14 C 0 1 Y N N N N N 17.240 -1.500 4.389 3.354  1.240  -0.030 C19  A1I1R 14 
A1I1R C2   C15 C 0 1 Y N N N N N 19.423 0.169  5.773 1.782  -1.264 0.519  C2   A1I1R 15 
A1I1R C23  C16 C 0 1 N N N N N N 17.658 -0.500 7.440 3.610  -1.179 2.195  C23  A1I1R 16 
A1I1R C27  C17 C 0 1 N N N N N N 27.001 0.243  2.987 -7.456 -0.285 -0.087 C27  A1I1R 17 
A1I1R C29  C18 C 0 1 N N N N N N 28.344 -1.260 4.409 -6.238 -1.491 -1.797 C29  A1I1R 18 
A1I1R C30  C19 C 0 1 N N N N N N 27.488 -0.928 5.612 -4.948 -0.784 -1.376 C30  A1I1R 19 
A1I1R C31  C20 C 0 1 N N N N N N 26.390 1.912  4.784 -6.018 1.726  -0.454 C31  A1I1R 20 
A1I1R C9   C21 C 0 1 Y N N N N N 24.992 -0.909 5.880 -3.837 0.126  0.487  C9   A1I1R 21 
A1I1R N11  N1  N 0 1 Y N N N N N 25.136 -1.848 6.847 -3.875 1.319  1.064  N11  A1I1R 22 
A1I1R N21  N2  N 0 1 N N N N N N 16.109 -2.821 2.631 3.783  3.465  -0.925 N21  A1I1R 23 
A1I1R N24  N3  N 0 1 N N N N N N 19.054 -3.260 4.842 1.222  1.895  1.243  N24  A1I1R 24 
A1I1R N25  N4  N 0 1 N N N N N N 26.137 -0.502 5.207 -5.017 -0.452 0.054  N25  A1I1R 25 
A1I1R N28  N5  N 0 1 N N N N N N 28.367 -0.115 3.465 -7.386 -0.617 -1.517 N28  A1I1R 26 
A1I1R N4   N6  N 0 1 Y N N N N N 21.271 0.519  4.623 -0.126 -1.900 -0.047 N4   A1I1R 27 
A1I1R N6   N7  N 0 1 Y N N N N N 20.319 -0.478 6.416 0.963  -0.310 0.883  N6   A1I1R 28 
A1I1R N7   N8  N 0 1 Y N N N N N 23.834 -0.373 5.458 -2.697 -0.521 0.304  N7   A1I1R 29 
A1I1R O3   O1  O 0 1 Y N N N N N 19.861 0.797  4.679 1.043  -2.220 -0.052 O3   A1I1R 30 
A1I1R S18  S1  S 0 1 Y N N N N N 15.256 -0.359 3.226 5.431  1.351  -1.475 S18  A1I1R 31 
A1I1R H8   H1  H 0 1 N N N N N N 21.856 -2.154 7.524 -0.636 1.713  1.668  H8   A1I1R 32 
A1I1R H10  H2  H 0 1 N N N N N N 24.058 -3.009 8.192 -2.811 2.876  1.959  H10  A1I1R 33 
A1I1R H13B H3  H 0 0 N N N N N N 16.005 3.184  6.592 5.740  -2.152 1.088  H13B A1I1R 34 
A1I1R H13A H4  H 0 0 N N N N N N 15.628 1.491  7.062 5.802  -3.466 -0.112 H13A A1I1R 35 
A1I1R H26  H5  H 0 1 N N N N N N 25.072 0.591  3.791 -6.202 0.644  1.400  H26  A1I1R 36 
A1I1R H12B H6  H 0 0 N N N N N N 18.032 2.096  7.387 3.481  -2.730 -0.876 H12B A1I1R 37 
A1I1R H12A H7  H 0 0 N N N N N N 18.164 2.399  5.622 3.547  -3.417 0.767  H12A A1I1R 38 
A1I1R H14B H8  H 0 0 N N N N N N 16.020 2.617  4.251 6.869  -1.272 -0.866 H14B A1I1R 39 
A1I1R H14A H9  H 0 0 N N N N N N 14.532 1.899  4.957 5.596  -1.896 -1.948 H14A A1I1R 40 
A1I1R H23C H10 H 0 0 N N N N N N 18.273 -0.119 8.269 4.692  -1.185 2.327  H23C A1I1R 41 
A1I1R H23A H11 H 0 0 N N N N N N 16.593 -0.401 7.698 3.200  -0.252 2.597  H23A A1I1R 42 
A1I1R H23B H12 H 0 0 N N N N N N 17.896 -1.559 7.263 3.175  -2.027 2.723  H23B A1I1R 43 
A1I1R H27B H13 H 0 0 N N N N N N 27.062 1.128  2.337 -7.575 -1.200 0.493  H27B A1I1R 44 
A1I1R H27A H14 H 0 0 N N N N N N 26.580 -0.600 2.420 -8.306 0.373  0.093  H27A A1I1R 45 
A1I1R H29A H15 H 0 0 N N N N N N 27.929 -2.142 3.900 -6.201 -1.712 -2.863 H29A A1I1R 46 
A1I1R H29B H16 H 0 0 N N N N N N 29.370 -1.477 4.742 -6.343 -2.420 -1.236 H29B A1I1R 47 
A1I1R H30B H17 H 0 0 N N N N N N 27.406 -1.820 6.250 -4.097 -1.442 -1.556 H30B A1I1R 48 
A1I1R H30A H18 H 0 0 N N N N N N 27.966 -0.115 6.178 -4.829 0.131  -1.957 H30A A1I1R 49 
A1I1R H31B H19 H 0 0 N N N N N N 25.716 2.085  5.636 -5.982 1.504  -1.521 H31B A1I1R 50 
A1I1R H31C H20 H 0 0 N N N N N N 27.434 1.945  5.129 -6.869 2.374  -0.247 H31C A1I1R 51 
A1I1R H31A H21 H 0 0 N N N N N N 26.229 2.692  4.026 -5.098 2.228  -0.156 H31A A1I1R 52 
A1I1R H21A H22 H 0 0 N N N N N N 15.323 -2.683 2.028 2.999  3.837  -0.491 H21A A1I1R 53 
A1I1R H21B H23 H 0 0 N N N N N N 16.926 -2.989 2.080 4.352  4.033  -1.467 H21B A1I1R 54 
A1I1R H28A H24 H 0 0 N N N N N N 28.931 -0.358 2.676 -8.247 -1.038 -1.833 H28A A1I1R 55 
# 
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 
A1I1R N21 C20  SING N N 1  
A1I1R C27 N28  SING N N 2  
A1I1R C27 C26  SING N N 3  
A1I1R S18 C20  SING Y N 4  
A1I1R S18 C15  SING Y N 5  
A1I1R C20 C19  DOUB Y N 6  
A1I1R N28 C29  SING N N 7  
A1I1R C26 C31  SING N N 8  
A1I1R C26 N25  SING N N 9  
A1I1R C19 C22  SING N N 10 
A1I1R C19 C16  SING Y N 11 
A1I1R C29 C30  SING N N 12 
A1I1R C15 C14  SING N N 13 
A1I1R C15 C16  DOUB Y N 14 
A1I1R N4  O3   SING Y N 15 
A1I1R N4  C5   DOUB Y N 16 
A1I1R C22 N24  TRIP N N 17 
A1I1R O3  C2   SING Y N 18 
A1I1R C14 C13  SING N N 19 
A1I1R C16 C17  SING N N 20 
A1I1R N25 C30  SING N N 21 
A1I1R N25 C9   SING N N 22 
A1I1R N7  C9   DOUB Y N 23 
A1I1R N7  C1   SING Y N 24 
A1I1R C5  C1   SING N N 25 
A1I1R C5  N6   SING Y N 26 
A1I1R C2  C17  SING N N 27 
A1I1R C2  N6   DOUB Y N 28 
A1I1R C9  N11  SING Y N 29 
A1I1R C1  C8   DOUB Y N 30 
A1I1R C17 C12  SING N N 31 
A1I1R C17 C23  SING N N 32 
A1I1R C13 C12  SING N N 33 
A1I1R N11 C10  DOUB Y N 34 
A1I1R C8  C10  SING Y N 35 
A1I1R C8  H8   SING N N 36 
A1I1R C10 H10  SING N N 37 
A1I1R C13 H13B SING N N 38 
A1I1R C13 H13A SING N N 39 
A1I1R C26 H26  SING N N 40 
A1I1R C12 H12B SING N N 41 
A1I1R C12 H12A SING N N 42 
A1I1R C14 H14B SING N N 43 
A1I1R C14 H14A SING N N 44 
A1I1R C23 H23C SING N N 45 
A1I1R C23 H23A SING N N 46 
A1I1R C23 H23B SING N N 47 
A1I1R C27 H27B SING N N 48 
A1I1R C27 H27A SING N N 49 
A1I1R C29 H29A SING N N 50 
A1I1R C29 H29B SING N N 51 
A1I1R C30 H30B SING N N 52 
A1I1R C30 H30A SING N N 53 
A1I1R C31 H31B SING N N 54 
A1I1R C31 H31C SING N N 55 
A1I1R C31 H31A SING N N 56 
A1I1R N21 H21A SING N N 57 
A1I1R N21 H21B SING N N 58 
A1I1R N28 H28A SING N N 59 
# 
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 
A1I1R InChI            InChI                1.06  "InChI=1S/C21H24N8OS/c1-12-11-24-8-9-29(12)20-25-7-5-14(26-20)18-27-19(30-28-18)21(2)6-3-4-15-16(21)13(10-22)17(23)31-15/h5,7,12,24H,3-4,6,8-9,11,23H2,1-2H3/t12-,21-/m0/s1" 
A1I1R InChIKey         InChI                1.06  QNZGWBDPZZTGGM-QKVFXAPYSA-N                                                                                                                                                  
A1I1R SMILES_CANONICAL CACTVS               3.385 "C[C@H]1CNCCN1c2nccc(n2)c3noc(n3)[C@@]4(C)CCCc5sc(N)c(C#N)c45"                                                                                                               
A1I1R SMILES           CACTVS               3.385 "C[CH]1CNCCN1c2nccc(n2)c3noc(n3)[C]4(C)CCCc5sc(N)c(C#N)c45"                                                                                                                  
A1I1R SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "C[C@H]1CNCCN1c2nccc(n2)c3nc(on3)[C@]4(CCCc5c4c(c(s5)N)C#N)C"                                                                                                                
A1I1R SMILES           "OpenEye OEToolkits" 2.0.7 "CC1CNCCN1c2nccc(n2)c3nc(on3)C4(CCCc5c4c(c(s5)N)C#N)C"                                                                                                                       
# 
_pdbx_chem_comp_identifier.comp_id           A1I1R 
_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        "(4~{S})-2-azanyl-4-methyl-4-[3-[2-[(2~{S})-2-methylpiperazin-1-yl]pyrimidin-4-yl]-1,2,4-oxadiazol-5-yl]-6,7-dihydro-5~{H}-1-benzothiophene-3-carbonitrile" 
# 
loop_
_pdbx_chem_comp_audit.comp_id 
_pdbx_chem_comp_audit.action_type 
_pdbx_chem_comp_audit.date 
_pdbx_chem_comp_audit.processing_site 
A1I1R "Create component" 2025-02-11 PDBE 
A1I1R "Initial release"  2025-08-06 RCSB 
# 
