data_YP5
# 
_chem_comp.id                                    YP5 
_chem_comp.name                                  "(2-{[(2S)-5-chloro-2,3-dihydro-1H-inden-2-yl]amino}pyrimidin-5-yl)[(4s,6S)-6-hydroxy-6-methyl-1-azaspiro[3.3]heptan-1-yl]methanone" 
_chem_comp.type                                  non-polymer 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C21 H23 Cl N4 O2" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2023-06-19 
_chem_comp.pdbx_modified_date                    2024-12-13 
_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                        398.886 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     YP5 
_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        7G3N 
_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_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 
YP5 C11  C1  C  0 1 Y N N N N N -14.257 9.550  48.071 -2.082 -0.308 -0.156 C11  YP5 1  
YP5 C16  C2  C  0 1 Y N N N N N -13.130 8.941  47.551 -1.017 0.369  -0.765 C16  YP5 2  
YP5 C18  C3  C  0 1 N N R N N N -13.288 5.486  45.393 2.830  -0.932 -0.422 C18  YP5 3  
YP5 C19  C4  C  0 1 N N N N N N -12.816 6.189  44.071 4.023  -1.874 -0.691 C19  YP5 4  
YP5 C20  C5  C  0 1 Y N N N N N -12.106 5.027  43.380 5.256  -1.022 -0.483 C20  YP5 5  
YP5 C21  C6  C  0 1 Y N N N N N -11.158 5.050  42.406 6.566  -1.228 -0.881 C21  YP5 6  
YP5 C22  C7  C  0 1 Y N N N N N -10.623 3.819  41.931 7.541  -0.298 -0.573 C22  YP5 7  
YP5 C23  C8  C  0 1 Y N N N N N -11.063 2.703  42.509 7.207  0.843  0.134  C23  YP5 8  
YP5 C24  C9  C  0 1 Y N N N N N -12.027 2.625  43.469 5.899  1.050  0.531  C24  YP5 9  
YP5 C25  C10 C  0 1 Y N N N N N -12.519 3.847  43.950 4.922  0.118  0.224  C25  YP5 10 
YP5 C26  C11 C  0 1 N N N N N N -13.571 4.051  45.009 3.441  0.110  0.539  C26  YP5 11 
YP5 C28  C12 C  0 1 N N N N N N -13.115 13.950 49.369 -6.679 0.492  1.116  C28  YP5 12 
YP5 C1   C13 C  0 1 N N N N N N -14.578 15.809 50.675 -8.142 2.202  -0.120 C1   YP5 13 
YP5 C2   C14 C  0 1 N N N N N N -14.421 14.331 50.213 -6.788 1.493  -0.048 C2   YP5 14 
YP5 O3   O1  O  0 1 N N N N N N -15.649 13.925 49.577 -5.685 2.397  -0.130 O3   YP5 15 
YP5 C4   C15 C  0 1 N N N N N N -13.913 13.223 51.294 -6.672 0.289  -1.000 C4   YP5 16 
YP5 C5   C16 C  0 1 N N N N N N -12.899 12.619 50.225 -5.952 -0.434 0.141  C5   YP5 17 
YP5 C6   C17 C  0 1 N N N N N N -11.492 12.043 50.691 -6.019 -1.955 0.286  C6   YP5 18 
YP5 C7   C18 C  0 1 N N N N N N -11.646 10.907 49.620 -4.603 -1.849 0.886  C7   YP5 19 
YP5 N8   N1  N  0 1 N N N N N N -13.104 11.283 49.529 -4.493 -0.567 0.160  N8   YP5 20 
YP5 C9   C19 C  0 1 N N N N N N -14.195 10.828 48.826 -3.468 0.178  -0.298 C9   YP5 21 
YP5 O10  O2  O  0 1 N N N N N N -15.216 11.479 48.801 -3.685 1.250  -0.829 O10  YP5 22 
YP5 C12  C20 C  0 1 Y N N N N N -15.467 8.937  47.863 -1.797 -1.461 0.588  C12  YP5 23 
YP5 N13  N2  N  0 1 Y N N N N N -15.615 7.788  47.160 -0.545 -1.865 0.687  N13  YP5 24 
YP5 C14  C21 C  0 1 Y N N N N N -14.386 7.252  46.701 0.436  -1.197 0.094  C14  YP5 25 
YP5 N15  N3  N  0 1 Y N N N N N -13.161 7.821  46.907 0.207  -0.101 -0.618 N15  YP5 26 
YP5 N17  N4  N  0 1 N N N N N N -14.465 6.116  46.000 1.731  -1.654 0.223  N17  YP5 27 
YP5 CL27 CL1 CL 0 0 N N N N N N -10.434 1.174  41.833 8.429  2.013  0.522  CL27 YP5 28 
YP5 H40  H1  H  0 1 N N N N N N -12.175 9.426  47.690 -1.195 1.261  -1.347 H40  YP5 29 
YP5 H42  H2  H  0 1 N N N N N N -12.452 5.505  46.108 2.495  -0.458 -1.345 H42  YP5 30 
YP5 H44  H3  H  0 1 N N N N N N -13.668 6.555  43.479 4.014  -2.706 0.013  H44  YP5 31 
YP5 H43  H4  H  0 1 N N N N N N -12.127 7.022  44.277 3.988  -2.245 -1.716 H43  YP5 32 
YP5 H45  H5  H  0 1 N N N N N N -10.815 5.989  41.998 6.827  -2.118 -1.433 H45  YP5 33 
YP5 H46  H6  H  0 1 N N N N N N -9.892  3.792  41.136 8.562  -0.462 -0.885 H46  YP5 34 
YP5 H47  H7  H  0 1 N N N N N N -12.391 1.677  43.838 5.639  1.940  1.084  H47  YP5 35 
YP5 H48  H8  H  0 1 N N N N N N -13.432 3.367  45.859 3.010  1.094  0.355  H48  YP5 36 
YP5 H49  H9  H  0 1 N N N N N N -14.586 3.930  44.603 3.277  -0.188 1.574  H49  YP5 37 
YP5 H51  H10 H  0 1 N N N N N N -13.315 13.764 48.303 -6.052 0.841  1.937  H51  YP5 38 
YP5 H50  H11 H  0 1 N N N N N N -12.296 14.678 49.467 -7.641 0.105  1.453  H50  YP5 39 
YP5 H31  H12 H  0 1 N N N N N N -13.651 16.141 51.164 -8.294 2.593  -1.126 H31  YP5 40 
YP5 H29  H13 H  0 1 N N N N N N -14.780 16.446 49.802 -8.936 1.493  0.117  H29  YP5 41 
YP5 H30  H14 H  0 1 N N N N N N -15.415 15.884 51.385 -8.162 3.023  0.596  H30  YP5 42 
YP5 H32  H15 H  0 1 N N N N N N -15.564 13.032 49.265 -5.742 3.144  0.482  H32  YP5 43 
YP5 H33  H16 H  0 1 N N N N N N -13.424 13.655 52.180 -7.631 -0.157 -1.261 H33  YP5 44 
YP5 H34  H17 H  0 1 N N N N N N -14.696 12.520 51.614 -6.039 0.476  -1.868 H34  YP5 45 
YP5 H36  H18 H  0 1 N N N N N N -10.643 12.720 50.516 -6.773 -2.297 0.995  H36  YP5 46 
YP5 H35  H19 H  0 1 N N N N N N -11.469 11.687 51.731 -6.056 -2.486 -0.665 H35  YP5 47 
YP5 H38  H20 H  0 1 N N N N N N -11.072 11.067 48.695 -4.593 -1.742 1.970  H38  YP5 48 
YP5 H37  H21 H  0 1 N N N N N N -11.457 9.891  49.998 -3.917 -2.616 0.527  H37  YP5 49 
YP5 H39  H22 H  0 1 N N N N N N -16.350 9.396  48.283 -2.591 -2.010 1.073  H39  YP5 50 
YP5 H41  H23 H  0 1 N N N N N N -14.858 5.435  46.617 1.914  -2.453 0.741  H41  YP5 51 
# 
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 
YP5 C1  C2   SING N N 1  
YP5 C2  O3   SING N N 2  
YP5 C2  C4   SING N N 3  
YP5 C2  C28  SING N N 4  
YP5 C4  C5   SING N N 5  
YP5 C5  C6   SING N N 6  
YP5 C5  N8   SING N N 7  
YP5 C5  C28  SING N N 8  
YP5 C6  C7   SING N N 9  
YP5 C7  N8   SING N N 10 
YP5 N8  C9   SING N N 11 
YP5 C9  O10  DOUB N N 12 
YP5 C9  C11  SING N N 13 
YP5 C11 C12  DOUB Y N 14 
YP5 C11 C16  SING Y N 15 
YP5 C12 N13  SING Y N 16 
YP5 N13 C14  DOUB Y N 17 
YP5 C14 N15  SING Y N 18 
YP5 C14 N17  SING N N 19 
YP5 N15 C16  DOUB Y N 20 
YP5 N17 C18  SING N N 21 
YP5 C18 C19  SING N N 22 
YP5 C18 C26  SING N N 23 
YP5 C19 C20  SING N N 24 
YP5 C20 C21  DOUB Y N 25 
YP5 C20 C25  SING Y N 26 
YP5 C21 C22  SING Y N 27 
YP5 C22 C23  DOUB Y N 28 
YP5 C23 C24  SING Y N 29 
YP5 C23 CL27 SING N N 30 
YP5 C24 C25  DOUB Y N 31 
YP5 C25 C26  SING N N 32 
YP5 C16 H40  SING N N 33 
YP5 C18 H42  SING N N 34 
YP5 C19 H44  SING N N 35 
YP5 C19 H43  SING N N 36 
YP5 C21 H45  SING N N 37 
YP5 C22 H46  SING N N 38 
YP5 C24 H47  SING N N 39 
YP5 C26 H48  SING N N 40 
YP5 C26 H49  SING N N 41 
YP5 C28 H51  SING N N 42 
YP5 C28 H50  SING N N 43 
YP5 C1  H31  SING N N 44 
YP5 C1  H29  SING N N 45 
YP5 C1  H30  SING N N 46 
YP5 O3  H32  SING N N 47 
YP5 C4  H33  SING N N 48 
YP5 C4  H34  SING N N 49 
YP5 C6  H36  SING N N 50 
YP5 C6  H35  SING N N 51 
YP5 C7  H38  SING N N 52 
YP5 C7  H37  SING N N 53 
YP5 C12 H39  SING N N 54 
YP5 N17 H41  SING N N 55 
# 
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 
YP5 SMILES           ACDLabs              12.01 "O=C(c1cnc(NC2Cc3ccc(Cl)cc3C2)nc1)N1CCC21CC(C)(O)C2"                                                                                                                                      
YP5 InChI            InChI                1.06  "InChI=1S/C21H23ClN4O2/c1-20(28)11-21(12-20)4-5-26(21)18(27)15-9-23-19(24-10-15)25-17-7-13-2-3-16(22)6-14(13)8-17/h2-3,6,9-10,17,28H,4-5,7-8,11-12H2,1H3,(H,23,24,25)/t17-,20-,21+/m0/s1" 
YP5 InChIKey         InChI                1.06  FMXQAKFCTVPOGB-DZFGPLHGSA-N                                                                                                                                                               
YP5 SMILES_CANONICAL CACTVS               3.385 "C[C@@]1(O)C[C@@]2(CCN2C(=O)c3cnc(N[C@@H]4Cc5ccc(Cl)cc5C4)nc3)C1"                                                                                                                         
YP5 SMILES           CACTVS               3.385 "C[C]1(O)C[C]2(CCN2C(=O)c3cnc(N[CH]4Cc5ccc(Cl)cc5C4)nc3)C1"                                                                                                                               
YP5 SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "CC1(CC2(C1)CCN2C(=O)c3cnc(nc3)N[C@@H]4Cc5ccc(cc5C4)Cl)O"                                                                                                                                 
YP5 SMILES           "OpenEye OEToolkits" 2.0.7 "CC1(CC2(C1)CCN2C(=O)c3cnc(nc3)NC4Cc5ccc(cc5C4)Cl)O"                                                                                                                                      
# 
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 
YP5 "SYSTEMATIC NAME" ACDLabs              12.01 "(2-{[(2S)-5-chloro-2,3-dihydro-1H-inden-2-yl]amino}pyrimidin-5-yl)[(4s,6S)-6-hydroxy-6-methyl-1-azaspiro[3.3]heptan-1-yl]methanone"    
YP5 "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 "[2-[[(2~{R})-5-chloranyl-2,3-dihydro-1~{H}-inden-2-yl]amino]pyrimidin-5-yl]-(6-methyl-6-oxidanyl-1-azaspiro[3.3]heptan-1-yl)methanone" 
# 
loop_
_pdbx_chem_comp_audit.comp_id 
_pdbx_chem_comp_audit.action_type 
_pdbx_chem_comp_audit.date 
_pdbx_chem_comp_audit.processing_site 
YP5 "Create component" 2023-06-19 RCSB 
YP5 "Initial release"  2024-12-18 RCSB 
# 
