data_YB5
# 
_chem_comp.id                                    YB5 
_chem_comp.name                                  "5'-S-{3-[N'-(cyclohexylmethyl)carbamimidamido]propyl}-N-(3-phenylpropyl)-5'-thioadenosine" 
_chem_comp.type                                  non-polymer 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C30 H44 N8 O3 S" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2023-01-20 
_chem_comp.pdbx_modified_date                    2023-05-05 
_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                        596.787 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     YB5 
_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        8FS2 
_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 
YB5 C4  C1  C 0 1 N N S -35.365 -0.696 15.181 0.516   -4.889 0.753  C4  YB5 1  
YB5 C5  C2  C 0 1 N N R -34.652 0.165  14.116 1.921   -4.239 0.788  C5  YB5 2  
YB5 C7  C3  C 0 1 N N S -34.279 -0.964 16.229 -0.326  -3.920 -0.099 C7  YB5 3  
YB5 C8  C4  C 0 1 N N N -34.243 -2.425 16.635 -1.522  -3.417 0.714  C8  YB5 4  
YB5 C10 C5  C 0 1 N N N -34.469 -4.131 14.376 -3.922  -1.903 0.779  C10 YB5 5  
YB5 C17 C6  C 0 1 N N N -33.958 -2.274 8.696  -11.012 2.900  -0.057 C17 YB5 6  
YB5 C20 C7  C 0 1 N N N -35.379 0.285  9.468  -13.552 3.500  -1.387 C20 YB5 7  
YB5 C21 C8  C 0 1 N N N -35.054 -0.083 8.030  -12.392 2.846  -2.139 C21 YB5 8  
YB5 C22 C9  C 0 1 N N N -35.028 -1.599 7.840  -11.564 2.003  -1.166 C22 YB5 9  
YB5 C11 C10 C 0 1 N N N -34.136 -3.958 12.910 -4.921  -1.021 0.025  C11 YB5 10 
YB5 C12 C11 C 0 1 N N N -34.859 -4.931 12.006 -6.049  -0.605 0.971  C12 YB5 11 
YB5 C14 C12 C 0 1 N N N -33.387 -5.703 10.075 -8.110  0.736  0.900  C14 YB5 12 
YB5 C16 C13 C 0 1 N N N -34.502 -3.525 9.368  -10.184 2.057  0.916  C16 YB5 13 
YB5 C18 C14 C 0 1 N N N -33.427 -1.282 9.724  -12.172 3.555  0.696  C18 YB5 14 
YB5 C19 C15 C 0 1 N N N -34.560 -0.551 10.439 -13.000 4.397  -0.277 C19 YB5 15 
YB5 C25 C16 C 0 1 N N R -33.356 0.545  14.818 1.879   -3.307 -0.449 C25 YB5 16 
YB5 C27 C17 C 0 1 Y N N -31.843 0.156  12.819 2.546   -0.957 0.185  C27 YB5 17 
YB5 C29 C18 C 0 1 Y N N -30.422 1.715  13.039 4.659   -0.950 -0.300 C29 YB5 18 
YB5 C30 C19 C 0 1 Y N N -31.317 1.859  14.083 4.164   -2.229 -0.606 C30 YB5 19 
YB5 C32 C20 C 0 1 Y N N -30.223 3.601  14.898 6.266   -2.861 -1.288 C32 YB5 20 
YB5 C34 C21 C 0 1 Y N N -29.351 2.640  12.992 6.023   -0.696 -0.525 C34 YB5 21 
YB5 C36 C22 C 0 1 N N N -28.851 2.599  10.575 7.991   0.792  -0.485 C36 YB5 22 
YB5 C37 C23 C 0 1 N N N -28.529 1.254  9.992  8.333   2.231  -0.093 C37 YB5 23 
YB5 C38 C24 C 0 1 N N N -28.274 1.317  8.492  9.820   2.489  -0.345 C38 YB5 24 
YB5 C39 C25 C 0 1 Y N N -29.455 1.474  7.563  10.156  3.906  0.042  C39 YB5 25 
YB5 C40 C26 C 0 1 Y N N -30.704 0.972  7.906  10.562  4.193  1.332  C40 YB5 26 
YB5 C41 C27 C 0 1 Y N N -31.765 1.053  7.019  10.870  5.493  1.686  C41 YB5 27 
YB5 C42 C28 C 0 1 Y N N -31.592 1.637  5.779  10.773  6.506  0.751  C42 YB5 28 
YB5 C43 C29 C 0 1 Y N N -30.356 2.140  5.428  10.367  6.219  -0.539 C43 YB5 29 
YB5 C44 C30 C 0 1 Y N N -29.294 2.060  6.313  10.064  4.918  -0.895 C44 YB5 30 
YB5 N13 N1  N 0 1 N N N -33.938 -5.815 11.302 -7.005  0.239  0.250  N13 YB5 31 
YB5 N15 N2  N 0 1 N N N -33.616 -4.680 9.223  -9.007  1.528  0.223  N15 YB5 32 
YB5 N23 N3  N 0 1 N N N -32.610 -6.666 9.712  -8.307  0.456  2.158  N23 YB5 33 
YB5 N26 N4  N 0 1 Y N N -32.236 0.846  13.937 2.828   -2.202 -0.295 N26 YB5 34 
YB5 N28 N5  N 0 1 Y N N -30.768 0.631  12.244 3.621   -0.225 0.181  N28 YB5 35 
YB5 N31 N6  N 0 1 Y N N -31.275 2.787  15.048 4.996   -3.145 -1.093 N31 YB5 36 
YB5 N33 N7  N 0 1 Y N N -29.277 3.585  13.953 6.777   -1.674 -1.016 N33 YB5 37 
YB5 N35 N8  N 0 1 N N N -28.474 2.698  11.976 6.567   0.545  -0.244 N35 YB5 38 
YB5 O24 O1  O 0 1 N N N -33.034 -0.575 15.610 0.522   -2.815 -0.454 O24 YB5 39 
YB5 O3  O2  O 0 1 N N N -36.505 -0.084 15.782 0.575   -6.176 0.135  O3  YB5 40 
YB5 O6  O3  O 0 1 N N N -35.354 1.354  13.786 2.943   -5.228 0.648  O6  YB5 41 
YB5 S9  S1  S 0 1 N N N -33.239 -3.336 15.436 -2.585  -2.396 -0.343 S9  YB5 42 
YB5 H1  H1  H 0 1 N N N -35.651 -1.653 14.720 0.105   -4.968 1.759  H1  YB5 43 
YB5 H2  H2  H 0 1 N N N -34.438 -0.443 13.225 2.061   -3.664 1.704  H2  YB5 44 
YB5 H3  H3  H 0 1 N N N -34.475 -0.344 17.117 -0.677  -4.426 -0.999 H3  YB5 45 
YB5 H4  H4  H 0 1 N N N -35.265 -2.831 16.646 -2.091  -4.269 1.087  H4  YB5 46 
YB5 H5  H5  H 0 1 N N N -33.799 -2.520 17.637 -1.165  -2.822 1.554  H5  YB5 47 
YB5 H6  H6  H 0 1 N N N -35.454 -3.683 14.574 -3.506  -1.345 1.617  H6  YB5 48 
YB5 H7  H7  H 0 1 N N N -34.501 -5.205 14.610 -4.431  -2.792 1.151  H7  YB5 49 
YB5 H8  H8  H 0 1 N N N -33.126 -2.568 8.039  -10.381 3.674  -0.495 H8  YB5 50 
YB5 H9  H9  H 0 1 N N N -35.151 1.349  9.628  -14.142 4.101  -2.080 H9  YB5 51 
YB5 H10 H10 H 0 1 N N N -36.449 0.107  9.653  -14.183 2.727  -0.948 H10 YB5 52 
YB5 H11 H11 H 0 1 N N N -34.068 0.328  7.768  -12.785 2.207  -2.929 H11 YB5 53 
YB5 H12 H12 H 0 1 N N N -35.819 0.349  7.368  -11.761 3.619  -2.577 H12 YB5 54 
YB5 H13 H13 H 0 1 N N N -36.011 -2.007 8.117  -10.737 1.537  -1.702 H13 YB5 55 
YB5 H14 H14 H 0 1 N N N -34.825 -1.819 6.782  -12.195 1.230  -0.728 H14 YB5 56 
YB5 H15 H15 H 0 1 N N N -33.053 -4.101 12.780 -4.412  -0.132 -0.347 H15 YB5 57 
YB5 H16 H16 H 0 1 N N N -34.409 -2.936 12.610 -5.337  -1.579 -0.813 H16 YB5 58 
YB5 H17 H17 H 0 1 N N N -35.440 -4.362 11.265 -6.558  -1.495 1.344  H17 YB5 59 
YB5 H18 H18 H 0 1 N N N -35.541 -5.542 12.616 -5.632  -0.047 1.810  H18 YB5 60 
YB5 H19 H19 H 0 1 N N N -34.636 -3.318 10.440 -9.865  2.678  1.753  H19 YB5 61 
YB5 H20 H20 H 0 1 N N N -35.475 -3.770 8.918  -10.790 1.231  1.286  H20 YB5 62 
YB5 H21 H21 H 0 1 N N N -32.828 -1.826 10.469 -12.803 2.781  1.134  H21 YB5 63 
YB5 H22 H22 H 0 1 N N N -32.793 -0.543 9.212  -11.779 4.194  1.486  H22 YB5 64 
YB5 H23 H23 H 0 1 N N N -34.131 0.110  11.207 -12.369 5.171  -0.715 H23 YB5 65 
YB5 H24 H24 H 0 1 N N N -35.218 -1.291 10.918 -13.826 4.864  0.259  H24 YB5 66 
YB5 H25 H25 H 0 1 N N N -33.553 1.414  15.462 2.087   -3.869 -1.360 H25 YB5 67 
YB5 H26 H26 H 0 1 N N N -32.375 -0.706 12.445 1.572   -0.627 0.515  H26 YB5 68 
YB5 H27 H27 H 0 1 N N N -30.125 4.377  15.642 6.915   -3.627 -1.685 H27 YB5 69 
YB5 H28 H28 H 0 1 N N N -28.309 3.370  10.007 8.212   0.641  -1.541 H28 YB5 70 
YB5 H29 H29 H 0 1 N N N -29.934 2.773  10.487 8.586   0.101  0.113  H29 YB5 71 
YB5 H30 H30 H 0 1 N N N -29.375 0.577  10.178 7.738   2.921  -0.690 H30 YB5 72 
YB5 H31 H31 H 0 1 N N N -27.629 0.861  10.487 8.112   2.382  0.964  H31 YB5 73 
YB5 H32 H32 H 0 1 N N N -27.762 0.385  8.211  10.415  1.798  0.253  H32 YB5 74 
YB5 H33 H33 H 0 1 N N N -27.605 2.171  8.313  10.041  2.338  -1.401 H33 YB5 75 
YB5 H34 H34 H 0 1 N N N -30.849 0.514  8.873  10.638  3.402  2.062  H34 YB5 76 
YB5 H35 H35 H 0 1 N N N -32.731 0.658  7.298  11.187  5.717  2.694  H35 YB5 77 
YB5 H36 H36 H 0 1 N N N -32.420 1.700  5.088  11.013  7.522  1.028  H36 YB5 78 
YB5 H37 H37 H 0 1 N N N -30.216 2.598  4.460  10.290  7.011  -1.270 H37 YB5 79 
YB5 H38 H38 H 0 1 N N N -28.331 2.457  6.029  9.747   4.694  -1.903 H38 YB5 80 
YB5 H39 H39 H 0 1 N N N -33.672 -6.635 11.809 -6.858  0.447  -0.686 H39 YB5 81 
YB5 H40 H40 H 0 1 N N N -33.103 -4.718 8.365  -8.860  1.736  -0.713 H40 YB5 82 
YB5 H41 H41 H 0 1 N N N -32.532 -7.371 10.417 -7.674  -0.103 2.635  H41 YB5 83 
YB5 H42 H42 H 0 1 N N N -27.823 1.955  12.136 6.006   1.251  0.114  H42 YB5 84 
YB5 H43 H43 H 0 1 N N N -36.883 -0.676 16.422 1.094   -6.826 0.629  H43 YB5 85 
YB5 H44 H44 H 0 1 N N N -36.166 1.131  13.347 3.009   -5.835 1.398  H44 YB5 86 
# 
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 
YB5 C43 C42 DOUB Y N 1  
YB5 C43 C44 SING Y N 2  
YB5 C42 C41 SING Y N 3  
YB5 C44 C39 DOUB Y N 4  
YB5 C41 C40 DOUB Y N 5  
YB5 C39 C40 SING Y N 6  
YB5 C39 C38 SING N N 7  
YB5 C22 C21 SING N N 8  
YB5 C22 C17 SING N N 9  
YB5 C21 C20 SING N N 10 
YB5 C38 C37 SING N N 11 
YB5 C17 C16 SING N N 12 
YB5 C17 C18 SING N N 13 
YB5 N15 C16 SING N N 14 
YB5 N15 C14 SING N N 15 
YB5 C20 C19 SING N N 16 
YB5 N23 C14 DOUB N N 17 
YB5 C18 C19 SING N N 18 
YB5 C37 C36 SING N N 19 
YB5 C14 N13 SING N N 20 
YB5 C36 N35 SING N N 21 
YB5 N13 C12 SING N N 22 
YB5 N35 C34 SING N N 23 
YB5 C12 C11 SING N N 24 
YB5 N28 C27 DOUB Y N 25 
YB5 N28 C29 SING Y N 26 
YB5 C27 N26 SING Y N 27 
YB5 C11 C10 SING N N 28 
YB5 C34 C29 DOUB Y N 29 
YB5 C34 N33 SING Y N 30 
YB5 C29 C30 SING Y N 31 
YB5 O6  C5  SING N N 32 
YB5 N26 C30 SING Y N 33 
YB5 N26 C25 SING N N 34 
YB5 N33 C32 DOUB Y N 35 
YB5 C30 N31 DOUB Y N 36 
YB5 C5  C25 SING N N 37 
YB5 C5  C4  SING N N 38 
YB5 C10 S9  SING N N 39 
YB5 C25 O24 SING N N 40 
YB5 C32 N31 SING Y N 41 
YB5 C4  O3  SING N N 42 
YB5 C4  C7  SING N N 43 
YB5 S9  C8  SING N N 44 
YB5 O24 C7  SING N N 45 
YB5 C7  C8  SING N N 46 
YB5 C4  H1  SING N N 47 
YB5 C5  H2  SING N N 48 
YB5 C7  H3  SING N N 49 
YB5 C8  H4  SING N N 50 
YB5 C8  H5  SING N N 51 
YB5 C10 H6  SING N N 52 
YB5 C10 H7  SING N N 53 
YB5 C17 H8  SING N N 54 
YB5 C20 H9  SING N N 55 
YB5 C20 H10 SING N N 56 
YB5 C21 H11 SING N N 57 
YB5 C21 H12 SING N N 58 
YB5 C22 H13 SING N N 59 
YB5 C22 H14 SING N N 60 
YB5 C11 H15 SING N N 61 
YB5 C11 H16 SING N N 62 
YB5 C12 H17 SING N N 63 
YB5 C12 H18 SING N N 64 
YB5 C16 H19 SING N N 65 
YB5 C16 H20 SING N N 66 
YB5 C18 H21 SING N N 67 
YB5 C18 H22 SING N N 68 
YB5 C19 H23 SING N N 69 
YB5 C19 H24 SING N N 70 
YB5 C25 H25 SING N N 71 
YB5 C27 H26 SING N N 72 
YB5 C32 H27 SING N N 73 
YB5 C36 H28 SING N N 74 
YB5 C36 H29 SING N N 75 
YB5 C37 H30 SING N N 76 
YB5 C37 H31 SING N N 77 
YB5 C38 H32 SING N N 78 
YB5 C38 H33 SING N N 79 
YB5 C40 H34 SING N N 80 
YB5 C41 H35 SING N N 81 
YB5 C42 H36 SING N N 82 
YB5 C43 H37 SING N N 83 
YB5 C44 H38 SING N N 84 
YB5 N13 H39 SING N N 85 
YB5 N15 H40 SING N N 86 
YB5 N23 H41 SING N N 87 
YB5 N35 H42 SING N N 88 
YB5 O3  H43 SING N N 89 
YB5 O6  H44 SING N N 90 
# 
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 
YB5 SMILES           ACDLabs              12.01 "N=C(NCC1CCCCC1)NCCCSCC1OC(n2cnc3c(NCCCc4ccccc4)ncnc32)C(O)C1O"                                                                                                                                                                                                    
YB5 InChI            InChI                1.06  "InChI=1S/C30H44N8O3S/c31-30(34-17-22-11-5-2-6-12-22)33-15-8-16-42-18-23-25(39)26(40)29(41-23)38-20-37-24-27(35-19-36-28(24)38)32-14-7-13-21-9-3-1-4-10-21/h1,3-4,9-10,19-20,22-23,25-26,29,39-40H,2,5-8,11-18H2,(H3,31,33,34)(H,32,35,36)/t23-,25-,26-,29-/m1/s1" 
YB5 InChIKey         InChI                1.06  IFVSTAFZZAWVFJ-CTDWIVFPSA-N                                                                                                                                                                                                                                        
YB5 SMILES_CANONICAL CACTVS               3.385 "O[C@H]1[C@@H](O)[C@@H](O[C@@H]1CSCCCNC(=N)NCC2CCCCC2)n3cnc4c(NCCCc5ccccc5)ncnc34"                                                                                                                                                                                 
YB5 SMILES           CACTVS               3.385 "O[CH]1[CH](O)[CH](O[CH]1CSCCCNC(=N)NCC2CCCCC2)n3cnc4c(NCCCc5ccccc5)ncnc34"                                                                                                                                                                                        
YB5 SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "[H]/N=C(/NCCCSC[C@@H]1[C@H]([C@H]([C@@H](O1)n2cnc3c2ncnc3NCCCc4ccccc4)O)O)\NCC5CCCCC5"                                                                                                                                                                            
YB5 SMILES           "OpenEye OEToolkits" 2.0.7 "c1ccc(cc1)CCCNc2c3c(ncn2)n(cn3)C4C(C(C(O4)CSCCCNC(=N)NCC5CCCCC5)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 
YB5 "SYSTEMATIC NAME" ACDLabs              12.01 "5'-S-{3-[N'-(cyclohexylmethyl)carbamimidamido]propyl}-N-(3-phenylpropyl)-5'-thioadenosine"                                                                
YB5 "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 "1-[3-[[(2~{S},3~{S},4~{R},5~{R})-3,4-bis(oxidanyl)-5-[6-(3-phenylpropylamino)purin-9-yl]oxolan-2-yl]methylsulfanyl]propyl]-3-(cyclohexylmethyl)guanidine" 
# 
loop_
_pdbx_chem_comp_audit.comp_id 
_pdbx_chem_comp_audit.action_type 
_pdbx_chem_comp_audit.date 
_pdbx_chem_comp_audit.processing_site 
YB5 "Create component" 2023-01-20 RCSB 
YB5 "Initial release"  2023-05-10 RCSB 
# 
