data_6Y1
# 
_chem_comp.id                                    6Y1 
_chem_comp.name                                  "~{N}-(1-adamantyl)-2-selanyl-benzamide" 
_chem_comp.type                                  NON-POLYMER 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C17 H21 N O Se" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         "Adamantyl Ebselen (open form)" 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2016-07-21 
_chem_comp.pdbx_modified_date                    2024-09-27 
_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                        334.315 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     6Y1 
_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        5KWI 
_chem_comp.pdbx_subcomponent_list                ? 
_chem_comp.pdbx_processing_site                  RCSB 
_chem_comp.pdbx_pcm                              Y 
# 
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 
6Y1 SE05 SE1 SE 0 0 N N N N N N 27.873 57.400 195.120 -2.751 1.716  0.018  SE05 6Y1 1  
6Y1 C06  C1  C  0 1 Y N N N N N 29.200 56.259 195.886 -2.940 -0.235 0.007  C06  6Y1 2  
6Y1 C07  C2  C  0 1 Y N N N N N 29.477 56.358 197.239 -1.806 -1.047 0.001  C07  6Y1 3  
6Y1 C08  C3  C  0 1 N N N N N N 28.714 57.387 198.088 -0.458 -0.440 0.002  C08  6Y1 4  
6Y1 N09  N1  N  0 1 N N N N N N 28.727 57.149 199.500 0.636  -1.227 -0.004 N09  6Y1 5  
6Y1 C10  C4  C  0 1 N N N N N N 28.063 58.023 200.478 1.972  -0.626 -0.002 C10  6Y1 6  
6Y1 C11  C5  C  0 1 N N N N N N 28.705 59.340 200.510 3.029  -1.731 -0.009 C11  6Y1 7  
6Y1 C12  C6  C  0 1 N N N N N N 28.086 60.251 201.515 4.424  -1.103 -0.008 C12  6Y1 8  
6Y1 C13  C7  C  0 1 N N N N N N 26.651 60.352 201.333 4.591  -0.228 -1.252 C13  6Y1 9  
6Y1 C14  C8  C  0 1 N N N N N N 26.600 58.125 200.295 2.139  0.249  -1.246 C14  6Y1 10 
6Y1 C15  C9  C  0 1 N N N N N N 25.986 59.036 201.299 3.534  0.877  -1.244 C15  6Y1 11 
6Y1 C16  C10 C  0 1 N N N N N N 26.190 58.391 202.670 3.704  1.737  0.010  C16  6Y1 12 
6Y1 C17  C11 C  0 1 N N N N N N 27.665 58.245 202.979 3.537  0.863  1.254  C17  6Y1 13 
6Y1 C18  C12 C  0 1 N N N N N N 28.329 59.594 202.881 4.595  -0.243 1.246  C18  6Y1 14 
6Y1 C19  C13 C  0 1 N N N N N N 28.276 57.396 201.866 2.142  0.234  1.252  C19  6Y1 15 
6Y1 O20  O1  O  0 1 N N N N N N 28.128 58.338 197.641 -0.336 0.769  0.009  O20  6Y1 16 
6Y1 C21  C14 C  0 1 Y N N N N N 30.437 55.543 197.816 -1.949 -2.436 -0.007 C21  6Y1 17 
6Y1 C22  C15 C  0 1 Y N N N N N 31.128 54.603 197.040 -3.209 -2.996 -0.008 C22  6Y1 18 
6Y1 C23  C16 C  0 1 Y N N N N N 30.850 54.501 195.676 -4.330 -2.185 -0.002 C23  6Y1 19 
6Y1 C24  C17 C  0 1 Y N N N N N 29.881 55.324 195.104 -4.195 -0.808 0.011  C24  6Y1 20 
6Y1 H1   H1  H  0 1 N N N N N N 27.325 58.273 196.154 -2.725 2.021  -1.512 H1   6Y1 21 
6Y1 H2   H2  H  0 1 N N N N N N 29.214 56.344 199.839 0.539  -2.193 -0.009 H2   6Y1 22 
6Y1 H3   H3  H  0 1 N N N N N N 29.768 59.209 200.760 2.910  -2.354 0.877  H3   6Y1 23 
6Y1 H4   H4  H  0 1 N N N N N N 28.617 59.800 199.515 2.908  -2.344 -0.903 H4   6Y1 24 
6Y1 H5   H5  H  0 1 N N N N N N 28.562 61.242 201.484 5.178  -1.890 -0.013 H5   6Y1 25 
6Y1 H6   H6  H  0 1 N N N N N N 26.453 60.871 200.384 5.585  0.219  -1.251 H6   6Y1 26 
6Y1 H7   H7  H  0 1 N N N N N N 26.231 60.937 202.165 4.470  -0.841 -2.145 H7   6Y1 27 
6Y1 H8   H8  H  0 1 N N N N N N 26.392 58.513 199.287 2.018  -0.364 -2.140 H8   6Y1 28 
6Y1 H9   H9  H  0 1 N N N N N N 26.156 57.124 200.402 1.386  1.036  -1.241 H9   6Y1 29 
6Y1 H10  H10 H  0 1 N N N N N N 24.910 59.153 201.100 3.653  1.500  -2.131 H10  6Y1 30 
6Y1 H11  H11 H  0 1 N N N N N N 25.721 59.022 203.439 4.698  2.185  0.011  H11  6Y1 31 
6Y1 H12  H12 H  0 1 N N N N N N 25.720 57.396 202.675 2.951  2.525  0.015  H12  6Y1 32 
6Y1 H13  H13 H  0 1 N N N N N N 27.826 57.786 203.965 3.658  1.475  2.148  H13  6Y1 33 
6Y1 H14  H14 H  0 1 N N N N N N 29.412 59.469 203.029 4.476  -0.866 2.133  H14  6Y1 34 
6Y1 H15  H15 H  0 1 N N N N N N 27.925 60.248 203.668 5.588  0.205  1.248  H15  6Y1 35 
6Y1 H16  H16 H  0 1 N N N N N N 27.808 56.401 201.881 1.389  1.022  1.258  H16  6Y1 36 
6Y1 H17  H17 H  0 1 N N N N N N 29.356 57.296 202.048 2.023  -0.389 2.139  H17  6Y1 37 
6Y1 H18  H18 H  0 1 N N N N N N 30.654 55.633 198.870 -1.075 -3.070 -0.012 H18  6Y1 38 
6Y1 H19  H19 H  0 1 N N N N N N 31.870 53.962 197.494 -3.322 -4.070 -0.014 H19  6Y1 39 
6Y1 H20  H20 H  0 1 N N N N N N 31.384 53.787 195.066 -5.315 -2.628 -0.003 H20  6Y1 40 
6Y1 H21  H21 H  0 1 N N N N N N 29.656 55.238 194.051 -5.074 -0.181 0.015  H21  6Y1 41 
# 
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 
6Y1 C24  C23 DOUB Y N 1  
6Y1 C24  C06 SING Y N 2  
6Y1 SE05 C06 SING N N 3  
6Y1 C23  C22 SING Y N 4  
6Y1 C06  C07 DOUB Y N 5  
6Y1 C22  C21 DOUB Y N 6  
6Y1 C07  C21 SING Y N 7  
6Y1 C07  C08 SING N N 8  
6Y1 O20  C08 DOUB N N 9  
6Y1 C08  N09 SING N N 10 
6Y1 N09  C10 SING N N 11 
6Y1 C14  C10 SING N N 12 
6Y1 C14  C15 SING N N 13 
6Y1 C10  C11 SING N N 14 
6Y1 C10  C19 SING N N 15 
6Y1 C11  C12 SING N N 16 
6Y1 C15  C13 SING N N 17 
6Y1 C15  C16 SING N N 18 
6Y1 C13  C12 SING N N 19 
6Y1 C12  C18 SING N N 20 
6Y1 C19  C17 SING N N 21 
6Y1 C16  C17 SING N N 22 
6Y1 C18  C17 SING N N 23 
6Y1 SE05 H1  SING N N 24 
6Y1 N09  H2  SING N N 25 
6Y1 C11  H3  SING N N 26 
6Y1 C11  H4  SING N N 27 
6Y1 C12  H5  SING N N 28 
6Y1 C13  H6  SING N N 29 
6Y1 C13  H7  SING N N 30 
6Y1 C14  H8  SING N N 31 
6Y1 C14  H9  SING N N 32 
6Y1 C15  H10 SING N N 33 
6Y1 C16  H11 SING N N 34 
6Y1 C16  H12 SING N N 35 
6Y1 C17  H13 SING N N 36 
6Y1 C18  H14 SING N N 37 
6Y1 C18  H15 SING N N 38 
6Y1 C19  H16 SING N N 39 
6Y1 C19  H17 SING N N 40 
6Y1 C21  H18 SING N N 41 
6Y1 C22  H19 SING N N 42 
6Y1 C23  H20 SING N N 43 
6Y1 C24  H21 SING N N 44 
# 
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 
6Y1 InChI            InChI                1.03  "InChI=1S/C17H21NOSe/c19-16(14-3-1-2-4-15(14)20)18-17-8-11-5-12(9-17)7-13(6-11)10-17/h1-4,11-13,20H,5-10H2,(H,18,19)/t11-,12+,13-,17-" 
6Y1 InChIKey         InChI                1.03  CBUMZOCCFOYBIQ-FBBPANFNSA-N                                                                                                            
6Y1 SMILES_CANONICAL CACTVS               3.385 "[SeH]c1ccccc1C(=O)NC23CC4CC(CC(C4)C2)C3"                                                                                              
6Y1 SMILES           CACTVS               3.385 "[SeH]c1ccccc1C(=O)NC23CC4CC(CC(C4)C2)C3"                                                                                              
6Y1 SMILES_CANONICAL "OpenEye OEToolkits" 2.0.5 "c1ccc(c(c1)C(=O)NC23CC4CC(C2)CC(C4)C3)[SeH]"                                                                                          
6Y1 SMILES           "OpenEye OEToolkits" 2.0.5 "c1ccc(c(c1)C(=O)NC23CC4CC(C2)CC(C4)C3)[SeH]"                                                                                          
# 
_pdbx_chem_comp_identifier.comp_id           6Y1 
_pdbx_chem_comp_identifier.type              "SYSTEMATIC NAME" 
_pdbx_chem_comp_identifier.program           "OpenEye OEToolkits" 
_pdbx_chem_comp_identifier.program_version   2.0.5 
_pdbx_chem_comp_identifier.identifier        "~{N}-(1-adamantyl)-2-selanyl-benzamide" 
# 
loop_
_pdbx_chem_comp_audit.comp_id 
_pdbx_chem_comp_audit.action_type 
_pdbx_chem_comp_audit.date 
_pdbx_chem_comp_audit.processing_site 
6Y1 "Create component" 2016-07-21 RCSB 
6Y1 "Initial release"  2017-03-29 RCSB 
6Y1 "Modify synonyms"  2020-06-05 PDBE 
6Y1 "Modify PCM"       2024-09-27 PDBE 
# 
_pdbx_chem_comp_synonyms.ordinal      1 
_pdbx_chem_comp_synonyms.comp_id      6Y1 
_pdbx_chem_comp_synonyms.name         "Adamantyl Ebselen (open form)" 
_pdbx_chem_comp_synonyms.provenance   ? 
_pdbx_chem_comp_synonyms.type         ? 
# 
_pdbx_chem_comp_pcm.pcm_id                             1 
_pdbx_chem_comp_pcm.comp_id                            6Y1 
_pdbx_chem_comp_pcm.modified_residue_id                CYS 
_pdbx_chem_comp_pcm.type                               None 
_pdbx_chem_comp_pcm.category                           "Covalent chemical modification" 
_pdbx_chem_comp_pcm.position                           "Amino-acid side chain" 
_pdbx_chem_comp_pcm.polypeptide_position               "Any position" 
_pdbx_chem_comp_pcm.comp_id_linking_atom               SE05 
_pdbx_chem_comp_pcm.modified_residue_id_linking_atom   SG 
_pdbx_chem_comp_pcm.uniprot_specific_ptm_accession     ? 
_pdbx_chem_comp_pcm.uniprot_generic_ptm_accession      ? 
# 
