data_A1B3S
# 
_chem_comp.id                                    A1B3S 
_chem_comp.name                                  "(3S)-1-{[5-(methylsulfanyl)pyrimidin-4-yl]acetyl}piperidine-3-carboxamide" 
_chem_comp.type                                  non-polymer 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C13 H18 N4 O2 S" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2025-03-21 
_chem_comp.pdbx_modified_date                    2025-03-28 
_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                        294.373 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     A1B3S 
_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        7I5B 
_chem_comp.pdbx_subcomponent_list                ? 
_chem_comp.pdbx_processing_site                  RCSB 
_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 
A1B3S N1  N1  N 0 1 Y N N N N N 7.807  11.230 25.630 2.495  1.980  0.701  N1  A1B3S 1  
A1B3S N3  N2  N 0 1 N N N N N N 11.145 13.527 17.861 -4.643 0.807  -2.216 N3  A1B3S 2  
A1B3S C4  C1  C 0 1 Y N N N N N 8.814  11.002 24.775 2.252  0.684  0.600  C4  A1B3S 3  
A1B3S C5  C2  C 0 1 N N N N N N 9.610  12.214 24.377 0.988  0.096  1.171  C5  A1B3S 4  
A1B3S C6  C3  C 0 1 N N N N N N 9.305  12.660 22.957 -0.096 0.120  0.123  C6  A1B3S 5  
A1B3S C7  C4  C 0 1 N N N N N N 11.196 14.298 23.149 -1.619 -0.907 1.741  C7  A1B3S 6  
A1B3S C8  C5  C 0 1 N N N N N N 12.481 14.285 22.335 -2.853 -0.196 2.304  C8  A1B3S 7  
A1B3S C10 C6  C 0 1 N N S N N N 11.109 14.005 20.225 -3.615 0.364  -0.011 C10 A1B3S 8  
A1B3S O1  O1  O 0 1 N N N N N N 10.584 15.601 18.510 -5.792 -0.277 -0.658 O1  A1B3S 9  
A1B3S C11 C7  C 0 1 N N N N N N 10.921 14.447 18.784 -4.762 0.274  -0.984 C11 A1B3S 10 
A1B3S C9  C8  C 0 1 N N N N N N 12.235 14.791 20.911 -4.006 -0.315 1.304  C9  A1B3S 11 
A1B3S C12 C9  C 0 1 N N N N N N 9.854  14.148 21.090 -2.388 -0.341 -0.600 C12 A1B3S 12 
A1B3S N2  N3  N 0 1 N N N N N N 10.104 13.617 22.433 -1.322 -0.358 0.411  N2  A1B3S 13 
A1B3S O   O2  O 0 1 N N N N N N 8.333  12.227 22.354 0.137  0.571  -0.979 O   A1B3S 14 
A1B3S C1  C10 C 0 1 Y N N N N N 9.096  9.690  24.319 3.183  -0.130 -0.043 C1  A1B3S 15 
A1B3S S   S1  S 0 1 N N N N N N 10.375 9.339  23.154 2.909  -1.863 -0.206 S   A1B3S 16 
A1B3S C   C11 C 0 1 N N N N N N 10.315 7.561  23.030 4.385  -2.428 -1.096 C   A1B3S 17 
A1B3S C3  C12 C 0 1 Y N N N N N 7.099  10.177 26.039 3.599  2.502  0.203  C3  A1B3S 18 
A1B3S N   N4  N 0 1 Y N N N N N 7.261  8.907  25.684 4.503  1.767  -0.411 N   A1B3S 19 
A1B3S C2  C13 C 0 1 Y N N N N N 8.260  8.680  24.831 4.335  0.463  -0.554 C2  A1B3S 20 
A1B3S H15 H1  H 0 1 N N N N N N 11.043 13.755 16.893 -3.819 1.248  -2.477 H15 A1B3S 21 
A1B3S H14 H2  H 0 1 N N N N N N 11.417 12.603 18.131 -5.382 0.749  -2.843 H14 A1B3S 22 
A1B3S H6  H3  H 0 1 N N N N N N 9.370  13.037 25.066 1.172  -0.933 1.479  H6  A1B3S 23 
A1B3S H7  H4  H 0 1 N N N N N N 10.681 11.974 24.451 0.672  0.682  2.034  H7  A1B3S 24 
A1B3S H9  H5  H 0 1 N N N N N N 10.904 15.341 23.341 -0.768 -0.741 2.403  H9  A1B3S 25 
A1B3S H8  H6  H 0 1 N N N N N N 11.372 13.785 24.106 -1.817 -1.976 1.662  H8  A1B3S 26 
A1B3S H10 H7  H 0 1 N N N N N N 13.223 14.934 22.824 -3.141 -0.659 3.248  H10 A1B3S 27 
A1B3S H11 H8  H 0 1 N N N N N N 12.867 13.256 22.289 -2.623 0.857  2.470  H11 A1B3S 28 
A1B3S H   H9  H 0 1 N N N N N N 11.395 12.943 20.220 -3.378 1.411  0.177  H   A1B3S 29 
A1B3S H12 H10 H 0 1 N N N N N N 11.956 15.854 20.952 -4.219 -1.368 1.119  H12 A1B3S 30 
A1B3S H13 H11 H 0 1 N N N N N N 13.159 14.677 20.326 -4.893 0.169  1.712  H13 A1B3S 31 
A1B3S H16 H12 H 0 1 N N N N N N 9.583  15.211 21.164 -2.651 -1.363 -0.872 H16 A1B3S 32 
A1B3S H17 H13 H 0 1 N N N N N N 9.027  13.590 20.626 -2.048 0.197  -1.484 H17 A1B3S 33 
A1B3S H2  H14 H 0 1 N N N N N N 11.081 7.216  22.319 5.274  -2.197 -0.509 H2  A1B3S 34 
A1B3S H1  H15 H 0 1 N N N N N N 10.507 7.118  24.018 4.324  -3.504 -1.255 H1  A1B3S 35 
A1B3S H3  H16 H 0 1 N N N N N N 9.321  7.252  22.676 4.445  -1.921 -2.059 H3  A1B3S 36 
A1B3S H5  H17 H 0 1 N N N N N N 6.302  10.380 26.739 3.766  3.565  0.303  H5  A1B3S 37 
A1B3S H4  H18 H 0 1 N N N N N N 8.438  7.663  24.515 5.081  -0.134 -1.058 H4  A1B3S 38 
# 
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 
A1B3S C   S   SING N N 1  
A1B3S S   C1  SING N N 2  
A1B3S C1  C2  DOUB Y N 3  
A1B3S C2  N   SING Y N 4  
A1B3S N   C3  DOUB Y N 5  
A1B3S C3  N1  SING Y N 6  
A1B3S N1  C4  DOUB Y N 7  
A1B3S C1  C4  SING Y N 8  
A1B3S C4  C5  SING N N 9  
A1B3S C5  C6  SING N N 10 
A1B3S O   C6  DOUB N N 11 
A1B3S C6  N2  SING N N 12 
A1B3S N2  C7  SING N N 13 
A1B3S C7  C8  SING N N 14 
A1B3S C8  C9  SING N N 15 
A1B3S C9  C10 SING N N 16 
A1B3S C10 C11 SING N N 17 
A1B3S N3  C11 SING N N 18 
A1B3S C11 O1  DOUB N N 19 
A1B3S C12 C10 SING N N 20 
A1B3S N2  C12 SING N N 21 
A1B3S N3  H15 SING N N 22 
A1B3S N3  H14 SING N N 23 
A1B3S C5  H6  SING N N 24 
A1B3S C5  H7  SING N N 25 
A1B3S C7  H9  SING N N 26 
A1B3S C7  H8  SING N N 27 
A1B3S C8  H10 SING N N 28 
A1B3S C8  H11 SING N N 29 
A1B3S C10 H   SING N N 30 
A1B3S C9  H12 SING N N 31 
A1B3S C9  H13 SING N N 32 
A1B3S C12 H16 SING N N 33 
A1B3S C12 H17 SING N N 34 
A1B3S C   H2  SING N N 35 
A1B3S C   H1  SING N N 36 
A1B3S C   H3  SING N N 37 
A1B3S C3  H5  SING N N 38 
A1B3S C2  H4  SING N N 39 
# 
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 
A1B3S SMILES           ACDLabs              14.52   "O=C(Cc1ncncc1SC)N1CCCC(C1)C(N)=O"                                                                                        
A1B3S InChI            InChI                1.06    "InChI=1S/C13H18N4O2S/c1-20-11-6-15-8-16-10(11)5-12(18)17-4-2-3-9(7-17)13(14)19/h6,8-9H,2-5,7H2,1H3,(H2,14,19)/t9-/m0/s1" 
A1B3S InChIKey         InChI                1.06    STOZPWZNKNIBMH-VIFPVBQESA-N                                                                                               
A1B3S SMILES_CANONICAL CACTVS               3.385   "CSc1cncnc1CC(=O)N2CCC[C@@H](C2)C(N)=O"                                                                                   
A1B3S SMILES           CACTVS               3.385   "CSc1cncnc1CC(=O)N2CCC[CH](C2)C(N)=O"                                                                                     
A1B3S SMILES_CANONICAL "OpenEye OEToolkits" 3.1.0.0 "CSc1cncnc1CC(=O)N2CCC[C@@H](C2)C(=O)N"                                                                                   
A1B3S SMILES           "OpenEye OEToolkits" 3.1.0.0 "CSc1cncnc1CC(=O)N2CCCC(C2)C(=O)N"                                                                                        
# 
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 
A1B3S "SYSTEMATIC NAME" ACDLabs              14.52   "(3S)-1-{[5-(methylsulfanyl)pyrimidin-4-yl]acetyl}piperidine-3-carboxamide"      
A1B3S "SYSTEMATIC NAME" "OpenEye OEToolkits" 3.1.0.0 "(3~{S})-1-[2-(5-methylsulfanylpyrimidin-4-yl)ethanoyl]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 
A1B3S "Create component" 2025-03-21 RCSB 
A1B3S "Initial release"  2025-04-02 RCSB 
# 
