data_YDO
# 
_chem_comp.id                                    YDO 
_chem_comp.name                                  "5'-deoxy-5'-(ethylsulfamamido)adenosine" 
_chem_comp.type                                  non-polymer 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C12 H19 N7 O5 S" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2023-12-01 
_chem_comp.pdbx_modified_date                    2023-12-08 
_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                        373.388 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     YDO 
_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        8V5G 
_chem_comp.pdbx_subcomponent_list                ? 
_chem_comp.pdbx_processing_site                  RCSB 
# 
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 
YDO N1  N1  N 0 1 N N N N N N 22.885 -32.016 15.822 -6.039 2.716  -0.306 N1  YDO 1  
YDO N3  N2  N 0 1 N N N N N N 18.689 -30.242 21.757 3.070  -0.242 0.752  N3  YDO 2  
YDO C4  C1  C 0 1 N N R N N N 21.592 -32.789 21.644 -1.191 -0.895 0.266  C4  YDO 3  
YDO C5  C2  C 0 1 N N R N N N 22.276 -31.857 22.642 -1.135 -1.880 -0.922 C5  YDO 4  
YDO C6  C3  C 0 1 N N S N N N 21.135 -30.919 23.035 0.364  -2.237 -1.043 C6  YDO 5  
YDO C7  C4  C 0 1 N N R N N N 19.948 -31.872 23.039 1.035  -1.425 0.087  C7  YDO 6  
YDO C8  C5  C 0 1 N N N N N N 18.608 -31.227 22.835 2.400  -0.905 -0.369 C8  YDO 7  
YDO C10 C6  C 0 1 N N N N N N 21.032 -26.677 20.756 4.976  3.453  -1.471 C10 YDO 8  
YDO C1  C7  C 0 1 Y N N N N N 22.805 -32.721 16.947 -5.443 1.532  0.092  C1  YDO 9  
YDO C11 C8  C 0 1 Y N N N N N 21.523 -31.076 19.769 -1.951 1.362  -0.571 C11 YDO 10 
YDO C12 C9  C 0 1 Y N N N N N 23.177 -34.765 18.044 -5.598 -0.561 1.052  C12 YDO 11 
YDO C2  C10 C 0 1 Y N N N N N 22.311 -32.194 18.151 -4.068 1.317  -0.104 C2  YDO 12 
YDO C3  C11 C 0 1 Y N N N N N 22.293 -33.045 19.228 -3.520 0.095  0.321  C3  YDO 13 
YDO C9  C12 C 0 1 N N N N N N 20.073 -27.807 20.737 4.337  2.534  -0.427 C9  YDO 14 
YDO N2  N3  N 0 1 Y N N N N N 21.781 -32.324 20.274 -2.184 0.152  0.013  N2  YDO 15 
YDO N4  N4  N 0 1 N N N N N N 19.035 -27.655 21.750 4.906  1.190  -0.547 N4  YDO 16 
YDO N5  N5  N 0 1 Y N N N N N 21.821 -30.948 18.502 -3.057 2.043  -0.639 N5  YDO 17 
YDO N6  N6  N 0 1 Y N N N N N 22.714 -34.313 19.202 -4.315 -0.806 0.888  N6  YDO 18 
YDO N7  N7  N 0 1 Y N N N N N 23.231 -34.010 16.937 -6.157 0.574  0.674  N7  YDO 19 
YDO O1  O1  O 0 1 N N N N N N 22.740 -32.594 23.747 -1.906 -3.049 -0.640 O1  YDO 20 
YDO O2  O2  O 0 1 N N N N N N 21.340 -30.348 24.319 0.563  -3.637 -0.839 O2  YDO 21 
YDO O3  O3  O 0 1 N N N N N N 16.973 -28.726 20.919 5.026  0.755  1.880  O3  YDO 22 
YDO O4  O4  O 0 1 N N N N N N 17.535 -28.755 23.315 5.323  -1.111 0.244  O4  YDO 23 
YDO O5  O5  O 0 1 N N N N N N 20.204 -32.784 21.953 0.134  -0.324 0.336  O5  YDO 24 
YDO S1  S1  S 0 1 N N N N N N 17.943 -28.830 21.954 4.691  0.088  0.671  S1  YDO 25 
YDO H1  H1  H 0 1 N N N N N N 23.273 -32.586 15.098 -5.506 3.410  -0.726 H1  YDO 26 
YDO H2  H2  H 0 1 N N N N N N 21.971 -31.712 15.554 -6.989 2.851  -0.169 H2  YDO 27 
YDO H3  H3  H 0 1 N N N N N N 18.305 -30.668 20.938 2.564  0.005  1.542  H3  YDO 28 
YDO H4  H4  H 0 1 N N N N N N 22.007 -33.801 21.757 -1.425 -1.426 1.189  H4  YDO 29 
YDO H5  H5  H 0 1 N N N N N N 23.082 -31.294 22.150 -1.487 -1.399 -1.834 H5  YDO 30 
YDO H6  H6  H 0 1 N N N N N N 20.999 -30.147 22.264 0.752  -1.932 -2.015 H6  YDO 31 
YDO H7  H7  H 0 1 N N N N N N 19.939 -32.421 23.992 1.143  -2.037 0.982  H7  YDO 32 
YDO H8  H8  H 0 1 N N N N N N 18.299 -30.726 23.764 2.264  -0.194 -1.184 H8  YDO 33 
YDO H9  H9  H 0 1 N N N N N N 17.869 -31.997 22.570 3.010  -1.740 -0.714 H9  YDO 34 
YDO H10 H10 H 0 1 N N N N N N 21.796 -26.830 19.979 6.052  3.498  -1.305 H10 YDO 35 
YDO H11 H11 H 0 1 N N N N N N 20.495 -25.737 20.561 4.777  3.062  -2.469 H11 YDO 36 
YDO H12 H12 H 0 1 N N N N N N 21.517 -26.625 21.742 4.552  4.454  -1.382 H12 YDO 37 
YDO H13 H13 H 0 1 N N N N N N 21.112 -30.273 20.362 -0.990 1.703  -0.926 H13 YDO 38 
YDO H14 H14 H 0 1 N N N N N N 23.526 -35.786 17.990 -6.216 -1.315 1.516  H14 YDO 39 
YDO H15 H15 H 0 1 N N N N N N 19.599 -27.854 19.746 4.536  2.925  0.571  H15 YDO 40 
YDO H16 H16 H 0 1 N N N N N N 20.621 -28.742 20.926 3.261  2.489  -0.592 H16 YDO 41 
YDO H17 H17 H 0 1 N N N N N N 19.500 -27.535 22.627 5.410  0.945  -1.339 H17 YDO 42 
YDO H18 H18 H 0 1 N N N N N N 23.164 -32.008 24.363 -1.906 -3.702 -1.353 H18 YDO 43 
YDO H19 H19 H 0 1 N N N N N N 20.614 -29.773 24.530 0.112  -4.197 -1.486 H19 YDO 44 
# 
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 
YDO N1  C1  SING N N 1  
YDO N7  C1  DOUB Y N 2  
YDO N7  C12 SING Y N 3  
YDO C1  C2  SING Y N 4  
YDO C12 N6  DOUB Y N 5  
YDO C2  N5  SING Y N 6  
YDO C2  C3  DOUB Y N 7  
YDO N5  C11 DOUB Y N 8  
YDO N6  C3  SING Y N 9  
YDO C3  N2  SING Y N 10 
YDO C11 N2  SING Y N 11 
YDO N2  C4  SING N N 12 
YDO C9  C10 SING N N 13 
YDO C9  N4  SING N N 14 
YDO O3  S1  DOUB N N 15 
YDO C4  O5  SING N N 16 
YDO C4  C5  SING N N 17 
YDO N4  S1  SING N N 18 
YDO N3  S1  SING N N 19 
YDO N3  C8  SING N N 20 
YDO O5  C7  SING N N 21 
YDO S1  O4  DOUB N N 22 
YDO C5  C6  SING N N 23 
YDO C5  O1  SING N N 24 
YDO C8  C7  SING N N 25 
YDO C6  C7  SING N N 26 
YDO C6  O2  SING N N 27 
YDO N1  H1  SING N N 28 
YDO N1  H2  SING N N 29 
YDO N3  H3  SING N N 30 
YDO C4  H4  SING N N 31 
YDO C5  H5  SING N N 32 
YDO C6  H6  SING N N 33 
YDO C7  H7  SING N N 34 
YDO C8  H8  SING N N 35 
YDO C8  H9  SING N N 36 
YDO C10 H10 SING N N 37 
YDO C10 H11 SING N N 38 
YDO C10 H12 SING N N 39 
YDO C11 H13 SING N N 40 
YDO C12 H14 SING N N 41 
YDO C9  H15 SING N N 42 
YDO C9  H16 SING N N 43 
YDO N4  H17 SING N N 44 
YDO O1  H18 SING N N 45 
YDO O2  H19 SING N N 46 
# 
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 
YDO SMILES           ACDLabs              12.01 "CCNS(=O)(=O)NCC1OC(n2cnc3c(N)ncnc32)C(O)C1O"                                                                                                                         
YDO InChI            InChI                1.06  "InChI=1S/C12H19N7O5S/c1-2-17-25(22,23)18-3-6-8(20)9(21)12(24-6)19-5-16-7-10(13)14-4-15-11(7)19/h4-6,8-9,12,17-18,20-21H,2-3H2,1H3,(H2,13,14,15)/t6-,8-,9-,12-/m1/s1" 
YDO InChIKey         InChI                1.06  YOSUWZOUTJPARI-WOUKDFQISA-N                                                                                                                                           
YDO SMILES_CANONICAL CACTVS               3.385 "CCN[S](=O)(=O)NC[C@H]1O[C@H]([C@H](O)[C@@H]1O)n2cnc3c(N)ncnc23"                                                                                                      
YDO SMILES           CACTVS               3.385 "CCN[S](=O)(=O)NC[CH]1O[CH]([CH](O)[CH]1O)n2cnc3c(N)ncnc23"                                                                                                           
YDO SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "CCNS(=O)(=O)NC[C@@H]1[C@H]([C@H]([C@@H](O1)n2cnc3c2ncnc3N)O)O"                                                                                                       
YDO SMILES           "OpenEye OEToolkits" 2.0.7 "CCNS(=O)(=O)NCC1C(C(C(O1)n2cnc3c2ncnc3N)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 
YDO "SYSTEMATIC NAME" ACDLabs              12.01 "5'-deoxy-5'-(ethylsulfamamido)adenosine"                                                         
YDO "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 "(2~{R},3~{R},4~{S},5~{R})-2-(6-aminopurin-9-yl)-5-[(ethylsulfamoylamino)methyl]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 
YDO "Create component" 2023-12-01 RCSB 
YDO "Initial release"  2023-12-13 RCSB 
# 
