data_YVU
# 
_chem_comp.id                                    YVU 
_chem_comp.name                                  "5'-S-[2-(benzylcarbamamido)ethyl]-5'-thioadenosine" 
_chem_comp.type                                  non-polymer 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C20 H25 N7 O4 S" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2023-02-24 
_chem_comp.pdbx_modified_date                    2023-04-21 
_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                        459.522 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     YVU 
_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        8G2G 
_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.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 
YVU N1  N1  N 0 1 Y N N 18.778 19.658 38.055 -8.521 1.918  0.174  N1  YVU 1  
YVU C7  C1  C 0 1 N N N 16.010 12.033 39.098 -0.762 -1.876 -0.398 C7  YVU 2  
YVU C8  C2  C 0 1 N N N 17.198 9.732  40.198 1.921  -1.047 0.026  C8  YVU 3  
YVU N2  N2  N 0 1 Y N N 18.320 17.935 39.679 -7.205 0.033  0.415  N2  YVU 4  
YVU C9  C3  C 0 1 N N N 17.702 9.955  41.613 2.969  -0.488 0.990  C9  YVU 5  
YVU O1  O1  O 0 1 N N N 18.485 7.417  42.614 5.234  0.440  2.121  O1  YVU 6  
YVU C1  C4  C 0 1 Y N N 18.950 19.018 39.215 -8.377 0.631  0.434  C1  YVU 7  
YVU C5  C5  C 0 1 N N R 16.657 15.325 39.921 -4.168 -0.916 0.235  C5  YVU 8  
YVU C6  C6  C 0 1 N N S 16.582 13.016 40.101 -2.164 -2.075 0.179  C6  YVU 9  
YVU N3  N3  N 0 1 Y N N 16.150 17.299 36.908 -4.948 2.535  -0.413 N3  YVU 10 
YVU C4  C7  C 0 1 Y N N 15.878 16.332 37.750 -4.106 1.548  -0.306 C4  YVU 11 
YVU C3  C8  C 0 1 Y N N 17.124 18.041 37.560 -6.201 2.088  -0.157 C3  YVU 12 
YVU O3  O2  O 0 1 N N N 14.974 15.909 41.640 -5.485 -2.447 -1.161 O3  YVU 13 
YVU C2  C9  C 0 1 Y N N 17.424 17.480 38.793 -6.101 0.715  0.127  C2  YVU 14 
YVU N4  N4  N 0 1 Y N N 16.626 16.363 38.899 -4.768 0.404  0.026  N4  YVU 15 
YVU C10 C10 C 0 1 N N N 19.343 8.228  42.286 5.328  0.120  0.951  C10 YVU 16 
YVU N6  N5  N 0 1 N N N 20.653 7.930  42.375 6.508  0.242  0.312  N6  YVU 17 
YVU C11 C11 C 0 1 N N N 21.072 6.647  42.912 7.678  0.759  1.025  C11 YVU 18 
YVU C12 C12 C 0 1 Y N N 20.993 5.486  41.954 8.860  0.795  0.091  C12 YVU 19 
YVU C17 C13 C 0 1 Y N N 20.830 5.686  40.586 9.692  -0.304 -0.013 C17 YVU 20 
YVU C16 C14 C 0 1 Y N N 20.901 4.619  39.704 10.773 -0.273 -0.874 C16 YVU 21 
YVU C15 C15 C 0 1 Y N N 21.126 3.341  40.175 11.023 0.857  -1.630 C15 YVU 22 
YVU C14 C16 C 0 1 Y N N 21.286 3.132  41.532 10.191 1.956  -1.526 C14 YVU 23 
YVU C13 C17 C 0 1 Y N N 21.197 4.193  42.416 9.110  1.925  -0.664 C13 YVU 24 
YVU N5  N6  N 0 1 N N N 19.058 9.454  41.795 4.251  -0.356 0.295  N5  YVU 25 
YVU S   S1  S 0 1 N N N 15.573 10.481 39.874 0.333  -1.211 0.887  S   YVU 26 
YVU O   O3  O 0 1 N N N 17.035 14.119 39.290 -2.751 -0.799 0.487  O   YVU 27 
YVU C18 C18 C 0 1 N N S 15.551 13.581 41.086 -3.070 -2.756 -0.865 C18 YVU 28 
YVU O2  O4  O 0 1 N N N 15.988 13.524 42.441 -3.557 -4.003 -0.368 O2  YVU 29 
YVU C19 C19 C 0 1 N N R 15.317 15.016 40.583 -4.237 -1.758 -1.064 C19 YVU 30 
YVU C   C20 C 0 1 Y N N 17.836 19.206 37.199 -7.475 2.681  -0.124 C   YVU 31 
YVU N   N7  N 0 1 N N N 17.577 19.930 36.108 -7.635 4.029  -0.396 N   YVU 32 
YVU H1  H1  H 0 1 N N N 16.760 11.843 38.317 -0.373 -2.833 -0.746 H1  YVU 33 
YVU H2  H2  H 0 1 N N N 15.109 12.471 38.643 -0.808 -1.178 -1.233 H2  YVU 34 
YVU H3  H3  H 0 1 N N N 17.122 8.649  40.023 1.807  -0.369 -0.820 H3  YVU 35 
YVU H4  H4  H 0 1 N N N 17.926 10.166 39.497 2.242  -2.025 -0.333 H4  YVU 36 
YVU H5  H5  H 0 1 N N N 17.690 11.034 41.828 2.647  0.490  1.349  H5  YVU 37 
YVU H6  H6  H 0 1 N N N 17.034 9.434  42.314 3.082  -1.166 1.836  H6  YVU 38 
YVU H7  H7  H 0 1 N N N 19.703 19.434 39.868 -9.254 0.048  0.672  H7  YVU 39 
YVU H8  H8  H 0 1 N N N 17.384 15.594 40.701 -4.663 -1.435 1.056  H8  YVU 40 
YVU H9  H9  H 0 1 N N N 17.416 12.556 40.652 -2.111 -2.688 1.079  H9  YVU 41 
YVU H10 H10 H 0 1 N N N 15.130 15.577 37.556 -3.039 1.625  -0.458 H10 YVU 42 
YVU H11 H11 H 0 1 N N N 14.133 15.660 42.005 -5.576 -2.988 -1.957 H11 YVU 43 
YVU H12 H12 H 0 1 N N N 21.338 8.592  42.071 6.582  -0.013 -0.621 H12 YVU 44 
YVU H13 H13 H 0 1 N N N 20.433 6.417  43.777 7.468  1.767  1.385  H13 YVU 45 
YVU H14 H14 H 0 1 N N N 22.117 6.743  43.243 7.903  0.111  1.872  H14 YVU 46 
YVU H15 H15 H 0 1 N N N 20.647 6.681  40.209 9.497  -1.187 0.577  H15 YVU 47 
YVU H16 H16 H 0 1 N N N 20.780 4.788  38.644 11.424 -1.132 -0.955 H16 YVU 48 
YVU H17 H17 H 0 1 N N N 21.177 2.510  39.488 11.869 0.882  -2.301 H17 YVU 49 
YVU H18 H18 H 0 1 N N N 21.481 2.137  41.904 10.386 2.839  -2.116 H18 YVU 50 
YVU H19 H19 H 0 1 N N N 21.287 4.013  43.477 8.458  2.783  -0.586 H19 YVU 51 
YVU H20 H20 H 0 1 N N N 19.820 10.051 41.543 4.326  -0.611 -0.638 H20 YVU 52 
YVU H21 H21 H 0 1 N N N 14.614 13.016 40.971 -2.529 -2.904 -1.800 H21 YVU 53 
YVU H22 H22 H 0 1 N N N 15.315 13.885 43.007 -4.133 -4.475 -0.985 H22 YVU 54 
YVU H23 H23 H 0 1 N N N 14.529 15.003 39.816 -4.069 -1.134 -1.942 H23 YVU 55 
YVU H24 H24 H 0 1 N N N 18.160 20.742 36.100 -6.864 4.575  -0.613 H24 YVU 56 
YVU H25 H25 H 0 1 N N N 17.760 19.381 35.293 -8.519 4.426  -0.370 H25 YVU 57 
# 
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 
YVU N   C   SING N N 1  
YVU N3  C3  SING Y N 2  
YVU N3  C4  DOUB Y N 3  
YVU C   C3  SING Y N 4  
YVU C   N1  DOUB Y N 5  
YVU C3  C2  DOUB Y N 6  
YVU C4  N4  SING Y N 7  
YVU N1  C1  SING Y N 8  
YVU C2  N4  SING Y N 9  
YVU C2  N2  SING Y N 10 
YVU N4  C5  SING N N 11 
YVU C7  S   SING N N 12 
YVU C7  C6  SING N N 13 
YVU C1  N2  DOUB Y N 14 
YVU O   C5  SING N N 15 
YVU O   C6  SING N N 16 
YVU C16 C15 DOUB Y N 17 
YVU C16 C17 SING Y N 18 
YVU S   C8  SING N N 19 
YVU C5  C19 SING N N 20 
YVU C6  C18 SING N N 21 
YVU C15 C14 SING Y N 22 
YVU C8  C9  SING N N 23 
YVU C19 C18 SING N N 24 
YVU C19 O3  SING N N 25 
YVU C17 C12 DOUB Y N 26 
YVU C18 O2  SING N N 27 
YVU C14 C13 DOUB Y N 28 
YVU C9  N5  SING N N 29 
YVU N5  C10 SING N N 30 
YVU C12 C13 SING Y N 31 
YVU C12 C11 SING N N 32 
YVU C10 N6  SING N N 33 
YVU C10 O1  DOUB N N 34 
YVU N6  C11 SING N N 35 
YVU C7  H1  SING N N 36 
YVU C7  H2  SING N N 37 
YVU C8  H3  SING N N 38 
YVU C8  H4  SING N N 39 
YVU C9  H5  SING N N 40 
YVU C9  H6  SING N N 41 
YVU C1  H7  SING N N 42 
YVU C5  H8  SING N N 43 
YVU C6  H9  SING N N 44 
YVU C4  H10 SING N N 45 
YVU O3  H11 SING N N 46 
YVU N6  H12 SING N N 47 
YVU C11 H13 SING N N 48 
YVU C11 H14 SING N N 49 
YVU C17 H15 SING N N 50 
YVU C16 H16 SING N N 51 
YVU C15 H17 SING N N 52 
YVU C14 H18 SING N N 53 
YVU C13 H19 SING N N 54 
YVU N5  H20 SING N N 55 
YVU C18 H21 SING N N 56 
YVU O2  H22 SING N N 57 
YVU C19 H23 SING N N 58 
YVU N   H24 SING N N 59 
YVU N   H25 SING N N 60 
# 
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 
YVU SMILES           ACDLabs              12.01 "Nc1ncnc2c1ncn2C1OC(CSCCNC(=O)NCc2ccccc2)C(O)C1O"                                                                                                                                                                
YVU InChI            InChI                1.06  "InChI=1S/C20H25N7O4S/c21-17-14-18(25-10-24-17)27(11-26-14)19-16(29)15(28)13(31-19)9-32-7-6-22-20(30)23-8-12-4-2-1-3-5-12/h1-5,10-11,13,15-16,19,28-29H,6-9H2,(H2,21,24,25)(H2,22,23,30)/t13-,15-,16-,19-/m1/s1" 
YVU InChIKey         InChI                1.06  UTFOOFWJWOBJJY-NVQRDWNXSA-N                                                                                                                                                                                      
YVU SMILES_CANONICAL CACTVS               3.385 "Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CSCCNC(=O)NCc4ccccc4)[C@@H](O)[C@H]3O"                                                                                                                                            
YVU SMILES           CACTVS               3.385 "Nc1ncnc2n(cnc12)[CH]3O[CH](CSCCNC(=O)NCc4ccccc4)[CH](O)[CH]3O"                                                                                                                                                  
YVU SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "c1ccc(cc1)CNC(=O)NCCSC[C@@H]2[C@H]([C@H]([C@@H](O2)n3cnc4c3ncnc4N)O)O"                                                                                                                                          
YVU SMILES           "OpenEye OEToolkits" 2.0.7 "c1ccc(cc1)CNC(=O)NCCSCC2C(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 
YVU "SYSTEMATIC NAME" ACDLabs              12.01 "5'-S-[2-(benzylcarbamamido)ethyl]-5'-thioadenosine"                                                                             
YVU "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 "1-[2-[[(2~{S},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methylsulfanyl]ethyl]-3-(phenylmethyl)urea" 
# 
loop_
_pdbx_chem_comp_audit.comp_id 
_pdbx_chem_comp_audit.action_type 
_pdbx_chem_comp_audit.date 
_pdbx_chem_comp_audit.processing_site 
YVU "Create component" 2023-02-24 RCSB 
YVU "Initial release"  2023-04-26 RCSB 
# 
