data_Y6X
# 
_chem_comp.id                                    Y6X 
_chem_comp.name                                  "(2R)-6-chloro-2-{[5-(6-oxa-1-azaspiro[3.3]heptane-1-carbonyl)pyrimidin-2-yl]amino}-2,3-dihydro-1H-indene-4-carbonitrile" 
_chem_comp.type                                  non-polymer 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C20 H18 Cl N5 O2" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2023-06-12 
_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                        395.842 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     Y6X 
_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        7G3T 
_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 
Y6X C10 C1  C  0 1 Y N N N N N -12.146 5.367  43.919 4.207  0.669  0.194  C10 Y6X 1  
Y6X C11 C2  C  0 1 N N N N N N -12.874 6.495  44.626 3.087  1.681  0.302  C11 Y6X 2  
Y6X C16 C3  C  0 1 Y N N N N N -14.410 7.587  47.226 -0.517 1.429  -0.638 C16 Y6X 3  
Y6X C18 C4  C  0 1 Y N N N N N -13.095 9.337  47.965 -2.672 1.951  -1.258 C18 Y6X 4  
Y6X C19 C5  C  0 1 Y N N N N N -14.215 10.004 48.451 -3.138 0.883  -0.479 C19 Y6X 5  
Y6X C20 C6  C  0 1 N N N N N N -14.148 14.627 48.767 -6.844 -2.141 -0.134 C20 Y6X 6  
Y6X C22 C7  C  0 1 N N N N N N -14.784 14.171 50.768 -7.628 -0.290 0.487  C22 Y6X 7  
Y6X C23 C8  C  0 1 N N N N N N -15.206 13.664 49.327 -6.301 -1.010 0.746  C23 Y6X 8  
Y6X C24 C9  C  0 1 N N N N N N -16.631 13.743 48.685 -5.813 -1.279 2.166  C24 Y6X 9  
Y6X C25 C10 C  0 1 N N N N N N -16.520 12.286 48.287 -4.429 -1.214 1.502  C25 Y6X 10 
Y6X C27 C11 C  0 1 N N N N N N -14.099 11.337 49.031 -4.580 0.576  -0.400 C27 Y6X 11 
Y6X C1  C12 C  0 1 N N N N N N -13.504 4.345  45.598 2.309  -0.275 -0.862 C1  Y6X 12 
Y6X N2  N1  N  0 1 N N N N N N -10.686 7.700  41.793 6.365  2.805  1.904  N2  Y6X 13 
Y6X C3  C13 C  0 1 N N N N N N -10.926 6.700  42.238 5.994  1.885  1.350  C3  Y6X 14 
Y6X C4  C14 C  0 1 Y N N N N N -11.250 5.440  42.864 5.527  0.725  0.652  C4  Y6X 15 
Y6X C5  C15 C  0 1 Y N N N N N -10.667 4.253  42.367 6.388  -0.350 0.430  C5  Y6X 16 
Y6X CL6 CL1 CL 0 0 N N N N N N -10.334 1.619  42.320 6.996  -2.807 -0.522 CL6 Y6X 17 
Y6X C7  C16 C  0 1 Y N N N N N -11.021 3.067  42.930 5.930  -1.466 -0.243 C7  Y6X 18 
Y6X C8  C17 C  0 1 Y N N N N N -11.960 2.963  44.024 4.623  -1.516 -0.694 C8  Y6X 19 
Y6X C9  C18 C  0 1 Y N N N N N -12.498 4.136  44.485 3.760  -0.454 -0.472 C9  Y6X 20 
Y6X C12 C19 C  0 1 N N S N N N -13.319 5.814  45.946 1.796  0.886  0.013  C12 Y6X 21 
Y6X N13 N2  N  0 1 N N N N N N -14.509 6.460  46.561 0.831  1.709  -0.720 N13 Y6X 22 
Y6X C14 C20 C  0 1 Y N N N N N -15.431 9.331  48.331 -2.200 0.114  0.222  C14 Y6X 23 
Y6X N15 N3  N  0 1 Y N N N N N -15.550 8.145  47.752 -0.919 0.412  0.113  N15 Y6X 24 
Y6X N17 N4  N  0 1 Y N N N N N -13.153 8.177  47.356 -1.375 2.186  -1.310 N17 Y6X 25 
Y6X O21 O1  O  0 1 N N N N N N -13.668 14.872 50.130 -7.717 -1.131 -0.683 O21 Y6X 26 
Y6X N26 N5  N  0 1 N N N N N N -15.145 12.262 48.953 -5.022 -0.369 0.452  N26 Y6X 27 
Y6X O28 O2  O  0 1 N N N N N N -13.080 11.695 49.606 -5.368 1.176  -1.105 O28 Y6X 28 
Y6X H33 H1  H  0 1 N N N N N N -12.202 7.344  44.821 3.055  2.104  1.306  H33 Y6X 29 
Y6X H34 H2  H  0 1 N N N N N N -13.740 6.839  44.042 3.219  2.471  -0.438 H34 Y6X 30 
Y6X H38 H3  H  0 1 N N N N N N -12.127 9.799  48.096 -3.364 2.567  -1.813 H38 Y6X 31 
Y6X H40 H4  H  0 1 N N N N N N -13.408 14.150 48.107 -6.118 -2.533 -0.847 H40 Y6X 32 
Y6X H39 H5  H  0 1 N N N N N N -14.565 15.515 48.269 -7.365 -2.921 0.421  H39 Y6X 33 
Y6X H42 H6  H  0 1 N N N N N N -14.486 13.374 51.465 -8.394 -0.493 1.235  H42 Y6X 34 
Y6X H41 H7  H  0 1 N N N N N N -15.519 14.828 51.256 -7.519 0.771  0.264  H41 Y6X 35 
Y6X H43 H8  H  0 1 N N N N N N -17.438 13.954 49.403 -6.012 -0.470 2.869  H43 Y6X 36 
Y6X H44 H9  H  0 1 N N N N N N -16.705 14.438 47.836 -6.080 -2.263 2.553  H44 Y6X 37 
Y6X H45 H10 H  0 1 N N N N N N -17.266 11.627 48.755 -3.683 -0.697 2.106  H45 Y6X 38 
Y6X H46 H11 H  0 1 N N N N N N -16.505 12.109 47.201 -4.079 -2.179 1.135  H46 Y6X 39 
Y6X H29 H12 H  0 1 N N N N N N -13.279 3.702  46.461 2.233  -0.014 -1.918 H29 Y6X 40 
Y6X H30 H13 H  0 1 N N N N N N -14.528 4.146  45.249 1.743  -1.183 -0.654 H30 Y6X 41 
Y6X H31 H14 H  0 1 N N N N N N -9.954  4.287  41.556 7.408  -0.310 0.783  H31 Y6X 42 
Y6X H32 H15 H  0 1 N N N N N N -12.224 2.009  44.456 4.272  -2.391 -1.220 H32 Y6X 43 
Y6X H35 H16 H  0 1 N N N N N N -12.481 5.889  46.655 1.360  0.506  0.937  H35 Y6X 44 
Y6X H36 H17 H  0 1 N N N N N N -15.155 6.627  45.817 1.139  2.452  -1.263 H36 Y6X 45 
Y6X H37 H18 H  0 1 N N N N N N -16.319 9.799  48.729 -2.520 -0.717 0.833  H37 Y6X 46 
# 
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 
Y6X C1  C12 SING N N 1  
Y6X C1  C9  SING N N 2  
Y6X N2  C3  TRIP N N 3  
Y6X C3  C4  SING N N 4  
Y6X C4  C10 DOUB Y N 5  
Y6X C4  C5  SING Y N 6  
Y6X C5  C7  DOUB Y N 7  
Y6X CL6 C7  SING N N 8  
Y6X C7  C8  SING Y N 9  
Y6X C8  C9  DOUB Y N 10 
Y6X C9  C10 SING Y N 11 
Y6X C10 C11 SING N N 12 
Y6X C11 C12 SING N N 13 
Y6X C12 N13 SING N N 14 
Y6X N13 C16 SING N N 15 
Y6X C14 C19 DOUB Y N 16 
Y6X C14 N15 SING Y N 17 
Y6X N15 C16 DOUB Y N 18 
Y6X C16 N17 SING Y N 19 
Y6X N17 C18 DOUB Y N 20 
Y6X C18 C19 SING Y N 21 
Y6X C19 C27 SING N N 22 
Y6X C20 C23 SING N N 23 
Y6X C20 O21 SING N N 24 
Y6X O21 C22 SING N N 25 
Y6X C22 C23 SING N N 26 
Y6X C23 N26 SING N N 27 
Y6X C23 C24 SING N N 28 
Y6X C24 C25 SING N N 29 
Y6X C25 N26 SING N N 30 
Y6X N26 C27 SING N N 31 
Y6X C27 O28 DOUB N N 32 
Y6X C11 H33 SING N N 33 
Y6X C11 H34 SING N N 34 
Y6X C18 H38 SING N N 35 
Y6X C20 H40 SING N N 36 
Y6X C20 H39 SING N N 37 
Y6X C22 H42 SING N N 38 
Y6X C22 H41 SING N N 39 
Y6X C24 H43 SING N N 40 
Y6X C24 H44 SING N N 41 
Y6X C25 H45 SING N N 42 
Y6X C25 H46 SING N N 43 
Y6X C1  H29 SING N N 44 
Y6X C1  H30 SING N N 45 
Y6X C5  H31 SING N N 46 
Y6X C8  H32 SING N N 47 
Y6X C12 H35 SING N N 48 
Y6X N13 H36 SING N N 49 
Y6X C14 H37 SING N N 50 
# 
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 
Y6X SMILES           ACDLabs              12.01 "O=C(N1CCC21COC2)c1cnc(NC2Cc3cc(Cl)cc(C#N)c3C2)nc1"                                                                                                                     
Y6X InChI            InChI                1.06  "InChI=1S/C20H18ClN5O2/c21-15-3-12-5-16(6-17(12)13(4-15)7-22)25-19-23-8-14(9-24-19)18(27)26-2-1-20(26)10-28-11-20/h3-4,8-9,16H,1-2,5-6,10-11H2,(H,23,24,25)/t16-/m1/s1" 
Y6X InChIKey         InChI                1.06  IEGMVFCMBVSNLK-MRXNPFEDSA-N                                                                                                                                             
Y6X SMILES_CANONICAL CACTVS               3.385 "Clc1cc2C[C@@H](Cc2c(c1)C#N)Nc3ncc(cn3)C(=O)N4CCC45COC5"                                                                                                                
Y6X SMILES           CACTVS               3.385 "Clc1cc2C[CH](Cc2c(c1)C#N)Nc3ncc(cn3)C(=O)N4CCC45COC5"                                                                                                                  
Y6X SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "c1c(cc(c2c1C[C@@H](C2)Nc3ncc(cn3)C(=O)N4CCC45COC5)C#N)Cl"                                                                                                              
Y6X SMILES           "OpenEye OEToolkits" 2.0.7 "c1c(cc(c2c1CC(C2)Nc3ncc(cn3)C(=O)N4CCC45COC5)C#N)Cl"                                                                                                                   
# 
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 
Y6X "SYSTEMATIC NAME" ACDLabs              12.01 "(2R)-6-chloro-2-{[5-(6-oxa-1-azaspiro[3.3]heptane-1-carbonyl)pyrimidin-2-yl]amino}-2,3-dihydro-1H-indene-4-carbonitrile"           
Y6X "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 "(2~{S})-6-chloranyl-2-[[5-(6-oxa-1-azaspiro[3.3]heptan-1-ylcarbonyl)pyrimidin-2-yl]amino]-2,3-dihydro-1~{H}-indene-4-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 
Y6X "Create component" 2023-06-12 RCSB 
Y6X "Initial release"  2024-12-18 RCSB 
# 
