data_X9L
# 
_chem_comp.id                                    X9L 
_chem_comp.name                                  "5'-S-(2-{[(3-bromophenyl)methyl]amino}ethyl)-5'-thioadenosine" 
_chem_comp.type                                  non-polymer 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C19 H23 Br N6 O3 S" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2023-10-26 
_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                        495.393 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     X9L 
_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        8UQH 
_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 
X9L C13  C1  C  0 1 N N S N N N -10.746 11.826 -76.286 2.807  2.022  -0.197 C13  X9L 1  
X9L C17  C2  C  0 1 N N N N N N -12.955 16.116 -76.830 -2.381 1.195  1.187  C17  X9L 2  
X9L C20  C3  C  0 1 Y N N N N N -12.411 19.715 -76.021 -6.101 0.788  1.010  C20  X9L 3  
X9L C21  C4  C  0 1 Y N N N N N -12.893 19.892 -74.732 -6.591 -0.414 0.534  C21  X9L 4  
X9L C22  C5  C  0 1 Y N N N N N -13.132 21.170 -74.248 -7.848 -0.470 -0.040 C22  X9L 5  
X9L C24  C6  C  0 1 Y N N N N N -12.886 22.267 -75.060 -8.615 0.677  -0.138 C24  X9L 6  
X9L C26  C7  C  0 1 Y N N N N N -12.164 20.811 -76.829 -6.868 1.934  0.913  C26  X9L 7  
X9L C02  C8  C  0 1 Y N N N N N -10.641 6.813  -80.952 8.006  -2.824 0.260  C02  X9L 8  
X9L C04  C9  C  0 1 Y N N N N N -10.827 5.879  -78.851 8.859  -0.779 0.907  C04  X9L 9  
X9L C06  C10 C  0 1 Y N N N N N -10.386 8.177  -79.012 6.645  -0.834 0.293  C06  X9L 10 
X9L C07  C11 C  0 1 Y N N N N N -10.398 8.092  -80.371 6.759  -2.212 0.045  C07  X9L 11 
X9L C09  C12 C  0 1 Y N N N N N -9.999  10.174 -79.793 4.714  -1.644 -0.398 C09  X9L 12 
X9L C11  C13 C  0 1 N N R N N N -10.053 9.961  -77.318 4.744  0.827  0.112  C11  X9L 13 
X9L C14  C14 C  0 1 N N N N N N -11.107 12.966 -77.028 1.347  1.921  -0.641 C14  X9L 14 
X9L C16  C15 C  0 1 N N N N N N -12.635 15.135 -75.702 -1.365 1.489  0.082  C16  X9L 15 
X9L C19  C16 C  0 1 N N N N N N -12.145 18.309 -76.556 -4.734 0.847  1.641  C19  X9L 16 
X9L C25  C17 C  0 1 Y N N N N N -12.402 22.088 -76.348 -8.125 1.878  0.339  C25  X9L 17 
X9L C27  C18 C  0 1 N N S N N N -9.184  11.734 -76.154 3.702  2.444  -1.383 C27  X9L 18 
X9L C29  C19 C  0 1 N N R N N N -8.837  11.044 -77.125 5.005  1.640  -1.175 C29  X9L 19 
X9L N01  N1  N  0 1 N N N N N N -10.666 6.657  -82.395 8.180  -4.177 0.027  N01  X9L 20 
X9L N03  N2  N  0 1 Y N N N N N -10.846 5.760  -80.171 9.015  -2.072 0.687  N03  X9L 21 
X9L N05  N3  N  0 1 Y N N N N N -10.604 7.047  -78.278 7.710  -0.164 0.719  N05  X9L 22 
X9L N08  N4  N  0 1 Y N N N N N -10.154 9.347  -80.839 5.545  -2.644 -0.374 N08  X9L 23 
X9L N10  N5  N  0 1 Y N N N N N -10.135 9.465  -78.671 5.344  -0.504 0.006  N10  X9L 24 
X9L N18  N6  N  0 1 N N N N N N -13.265 17.426 -76.284 -3.730 1.129  0.607  N18  X9L 25 
X9L O12  O1  O  0 1 N N N N N N -11.145 10.580 -77.031 3.305  0.725  0.198  O12  X9L 26 
X9L O28  O2  O  0 1 N N N N N N -8.829  11.034 -74.854 3.967  3.847  -1.336 O28  X9L 27 
X9L O30  O3  O  0 1 N N N N N N -7.563  10.337 -76.823 6.115  2.523  -0.993 O30  X9L 28 
X9L S15  S1  S  0 1 N N N N N N -10.979 14.434 -75.966 0.300  1.570  0.798  S15  X9L 29 
X9L BR23 BR1 BR 0 0 N N N N N N -13.808 21.424 -72.443 -8.518 -2.114 -0.692 BR23 X9L 30 
X9L H1   H1  H  0 1 N N N N N N -11.198 11.832 -75.283 2.906  2.732  0.624  H1   X9L 31 
X9L H2   H2  H  0 1 N N N N N N -13.821 15.746 -77.399 -2.141 0.241  1.657  H2   X9L 32 
X9L H3   H3  H  0 1 N N N N N N -12.085 16.198 -77.498 -2.345 1.987  1.935  H3   X9L 33 
X9L H4   H4  H  0 1 N N N N N N -13.082 19.034 -74.105 -5.991 -1.309 0.610  H4   X9L 34 
X9L H5   H5  H  0 1 N N N N N N -13.072 23.264 -74.689 -9.597 0.634  -0.586 H5   X9L 35 
X9L H6   H6  H  0 1 N N N N N N -11.787 20.671 -77.831 -6.485 2.873  1.285  H6   X9L 36 
X9L H7   H7  H  0 1 N N N N N N -10.996 5.008  -78.236 9.705  -0.205 1.254  H7   X9L 37 
X9L H8   H8  H  0 1 N N N N N N -9.798  11.234 -79.850 3.677  -1.707 -0.694 H8   X9L 38 
X9L H9   H9  H  0 1 N N N N N N -9.857  9.126  -76.629 5.139  1.355  0.981  H9   X9L 39 
X9L H10  H10 H  0 1 N N N N N N -10.431 13.074 -77.889 1.039  2.865  -1.093 H10  X9L 40 
X9L H11  H11 H  0 1 N N N N N N -12.142 12.860 -77.386 1.243  1.118  -1.370 H11  X9L 41 
X9L H12  H12 H  0 1 N N N N N N -12.661 15.663 -74.737 -1.401 0.697  -0.665 H12  X9L 42 
X9L H13  H13 H  0 1 N N N N N N -13.380 14.326 -75.697 -1.605 2.443  -0.388 H13  X9L 43 
X9L H14  H14 H  0 1 N N N N N N -11.243 17.905 -76.072 -4.715 1.637  2.392  H14  X9L 44 
X9L H15  H15 H  0 1 N N N N N N -11.985 18.362 -77.643 -4.510 -0.109 2.114  H15  X9L 45 
X9L H16  H16 H  0 1 N N N N N N -12.211 22.945 -76.976 -8.723 2.774  0.263  H16  X9L 46 
X9L H17  H17 H  0 1 N N N N N N -8.766  12.751 -76.151 3.233  2.176  -2.330 H17  X9L 47 
X9L H18  H18 H  0 1 N N N N N N -8.736  11.610 -78.063 5.184  0.973  -2.018 H18  X9L 48 
X9L H19  H19 H  0 1 N N N N N N -10.849 5.701  -82.624 7.437  -4.714 -0.289 H19  X9L 49 
X9L H20  H20 H  0 1 N N N N N N -11.385 7.235  -82.780 9.045  -4.588 0.179  H20  X9L 50 
X9L H21  H21 H  0 1 N N N N N N -14.092 17.786 -76.716 -3.951 1.979  0.110  H21  X9L 51 
X9L H23  H23 H  0 1 N N N N N N -9.100  11.572 -74.120 4.525  4.167  -2.059 H23  X9L 52 
X9L H24  H24 H  0 1 N N N N N N -6.866  10.973 -76.713 6.323  3.057  -1.772 H24  X9L 53 
# 
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 
X9L N01 C02  SING N N 1  
X9L C02 C07  DOUB Y N 2  
X9L C02 N03  SING Y N 3  
X9L N08 C07  SING Y N 4  
X9L N08 C09  DOUB Y N 5  
X9L C07 C06  SING Y N 6  
X9L N03 C04  DOUB Y N 7  
X9L C09 N10  SING Y N 8  
X9L C06 N10  SING Y N 9  
X9L C06 N05  DOUB Y N 10 
X9L C04 N05  SING Y N 11 
X9L N10 C11  SING N N 12 
X9L C11 C29  SING N N 13 
X9L C11 O12  SING N N 14 
X9L C29 O30  SING N N 15 
X9L C29 C27  SING N N 16 
X9L O12 C13  SING N N 17 
X9L C14 C13  SING N N 18 
X9L C14 S15  SING N N 19 
X9L C17 N18  SING N N 20 
X9L C17 C16  SING N N 21 
X9L C26 C25  DOUB Y N 22 
X9L C26 C20  SING Y N 23 
X9L C19 N18  SING N N 24 
X9L C19 C20  SING N N 25 
X9L C25 C24  SING Y N 26 
X9L C13 C27  SING N N 27 
X9L C27 O28  SING N N 28 
X9L C20 C21  DOUB Y N 29 
X9L S15 C16  SING N N 30 
X9L C24 C22  DOUB Y N 31 
X9L C21 C22  SING Y N 32 
X9L C22 BR23 SING N N 33 
X9L C13 H1   SING N N 34 
X9L C17 H2   SING N N 35 
X9L C17 H3   SING N N 36 
X9L C21 H4   SING N N 37 
X9L C24 H5   SING N N 38 
X9L C26 H6   SING N N 39 
X9L C04 H7   SING N N 40 
X9L C09 H8   SING N N 41 
X9L C11 H9   SING N N 42 
X9L C14 H10  SING N N 43 
X9L C14 H11  SING N N 44 
X9L C16 H12  SING N N 45 
X9L C16 H13  SING N N 46 
X9L C19 H14  SING N N 47 
X9L C19 H15  SING N N 48 
X9L C25 H16  SING N N 49 
X9L C27 H17  SING N N 50 
X9L C29 H18  SING N N 51 
X9L N01 H19  SING N N 52 
X9L N01 H20  SING N N 53 
X9L N18 H21  SING N N 54 
X9L O28 H23  SING N N 55 
X9L O30 H24  SING N N 56 
# 
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 
X9L SMILES           ACDLabs              12.01 "Brc1cccc(c1)CNCCSCC1OC(n2cnc3c(N)ncnc32)C(O)C1O"                                                                                                                                                       
X9L InChI            InChI                1.06  "InChI=1S/C19H23BrN6O3S/c20-12-3-1-2-11(6-12)7-22-4-5-30-8-13-15(27)16(28)19(29-13)26-10-25-14-17(21)23-9-24-18(14)26/h1-3,6,9-10,13,15-16,19,22,27-28H,4-5,7-8H2,(H2,21,23,24)/t13-,15-,16-,19-/m1/s1" 
X9L InChIKey         InChI                1.06  JGFTVBMOETWOQF-NVQRDWNXSA-N                                                                                                                                                                             
X9L SMILES_CANONICAL CACTVS               3.385 "Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CSCCNCc4cccc(Br)c4)[C@@H](O)[C@H]3O"                                                                                                                                     
X9L SMILES           CACTVS               3.385 "Nc1ncnc2n(cnc12)[CH]3O[CH](CSCCNCc4cccc(Br)c4)[CH](O)[CH]3O"                                                                                                                                           
X9L SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "c1cc(cc(c1)Br)CNCCSC[C@@H]2[C@H]([C@H]([C@@H](O2)n3cnc4c3ncnc4N)O)O"                                                                                                                                   
X9L SMILES           "OpenEye OEToolkits" 2.0.7 "c1cc(cc(c1)Br)CNCCSCC2C(C(C(O2)n3cnc4c3ncnc4N)O)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 
X9L "SYSTEMATIC NAME" ACDLabs              12.01 "5'-S-(2-{[(3-bromophenyl)methyl]amino}ethyl)-5'-thioadenosine"                                                         
X9L "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 "(2~{R},3~{R},4~{S},5~{S})-2-(6-aminopurin-9-yl)-5-[2-[(3-bromophenyl)methylamino]ethylsulfanylmethyl]oxolane-3,4-diol" 
# 
loop_
_pdbx_chem_comp_audit.comp_id 
_pdbx_chem_comp_audit.action_type 
_pdbx_chem_comp_audit.date 
_pdbx_chem_comp_audit.processing_site 
X9L "Create component" 2023-10-26 RCSB 
X9L "Initial release"  2025-04-02 RCSB 
# 
