data_YB0
# 
_chem_comp.id                                    YB0 
_chem_comp.name                                  "5'-S-{2-[N'-(cyclohexylmethyl)carbamimidamido]ethyl}-N-(3-phenylpropyl)-5'-thioadenosine" 
_chem_comp.type                                  non-polymer 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C29 H42 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                        582.761 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     YB0 
_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        8FS1 
_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 
YB0 C5  C1  C 0 1 N N S -34.360 -1.121 16.053 -0.953  3.321  -0.169 C5  YB0 1  
YB0 C6  C2  C 0 1 N N N -34.322 -2.634 16.141 -2.229  2.693  -0.733 C6  YB0 2  
YB0 C8  C3  C 0 1 N N N -34.527 -4.220 13.773 -4.549  1.125  -0.266 C8  YB0 3  
YB0 N12 N1  N 0 1 N N N -33.860 -4.382 10.255 -8.592  -1.475 0.089  N12 YB0 4  
YB0 C13 C4  C 0 1 N N N -33.825 -3.859 8.895  -9.564  -2.286 0.828  C13 YB0 5  
YB0 C15 C5  C 0 1 N N N -35.748 -2.306 9.397  -11.639 -3.663 0.623  C15 YB0 6  
YB0 C17 C6  C 0 1 N N N -35.339 0.146  9.793  -13.540 -2.856 -0.783 C17 YB0 7  
YB0 C22 C7  C 0 1 N N R -33.436 0.574  14.816 1.283   2.963  0.210  C22 YB0 8  
YB0 C24 C8  C 0 1 Y N N -31.856 0.248  12.855 2.278   0.758  -0.509 C24 YB0 9  
YB0 C26 C9  C 0 1 Y N N -30.529 1.886  13.098 4.335   0.966  0.145  C26 YB0 10 
YB0 C11 C10 C 0 1 N N N -34.549 -5.470 10.604 -7.485  -0.974 0.732  C11 YB0 11 
YB0 C14 C11 C 0 1 N N N -34.348 -2.434 8.799  -10.691 -2.715 -0.114 C14 YB0 12 
YB0 C16 C12 C 0 1 N N N -35.852 -1.154 10.395 -12.766 -4.091 -0.318 C16 YB0 13 
YB0 C18 C13 C 0 1 N N N -33.896 0.001  9.331  -12.592 -1.908 -1.520 C18 YB0 14 
YB0 C19 C14 C 0 1 N N N -33.407 -1.440 9.474  -11.465 -1.480 -0.579 C19 YB0 15 
YB0 C2  C15 C 0 1 N N S -35.461 -0.653 15.092 -0.248  4.170  -1.250 C2  YB0 16 
YB0 C27 C16 C 0 1 Y N N -31.462 1.990  14.119 3.665   2.153  0.487  C27 YB0 17 
YB0 C29 C17 C 0 1 Y N N -30.521 3.816  14.923 5.618   2.977  1.376  C29 YB0 18 
YB0 C3  C18 C 0 1 N N R -34.721 0.239  14.075 1.257   3.929  -0.995 C3  YB0 19 
YB0 C31 C19 C 0 1 Y N N -29.523 2.886  13.067 5.699   0.858  0.465  C31 YB0 20 
YB0 C33 C20 C 0 1 N N N -28.272 1.925  11.136 7.833   -0.381 0.495  C33 YB0 21 
YB0 C34 C21 C 0 1 N N N -28.990 2.308  9.861  8.377   -1.738 0.045  C34 YB0 22 
YB0 C35 C22 C 0 1 N N N -28.768 1.291  8.752  9.861   -1.836 0.401  C35 YB0 23 
YB0 C36 C23 C 0 1 Y N N -29.642 1.516  7.543  10.397  -3.173 -0.042 C36 YB0 24 
YB0 C37 C24 C 0 1 Y N N -30.972 1.115  7.545  10.929  -3.319 -1.310 C37 YB0 25 
YB0 C38 C25 C 0 1 Y N N -31.765 1.291  6.423  11.420  -4.545 -1.717 C38 YB0 26 
YB0 C39 C26 C 0 1 Y N N -31.239 1.870  5.286  11.379  -5.627 -0.856 C39 YB0 27 
YB0 C40 C27 C 0 1 Y N N -29.920 2.272  5.271  10.847  -5.481 0.411  C40 YB0 28 
YB0 C41 C28 C 0 1 Y N N -29.126 2.098  6.392  10.361  -4.253 0.821  C41 YB0 29 
YB0 C9  C29 C 0 1 N N N -33.734 -5.175 12.899 -5.394  0.321  0.724  C9  YB0 30 
YB0 N10 N2  N 0 1 N N N -34.515 -5.859 11.879 -6.574  -0.213 0.039  N10 YB0 31 
YB0 N20 N3  N 0 1 N N N -35.206 -6.129 9.714  -7.300  -1.220 1.999  N20 YB0 32 
YB0 N23 N4  N 0 1 Y N N -32.313 0.924  13.954 2.369   1.990  0.067  N23 YB0 33 
YB0 N25 N5  N 0 1 Y N N -30.791 0.781  12.305 3.433   0.159  -0.462 N25 YB0 34 
YB0 N28 N6  N 0 1 Y N N -31.515 2.934  15.061 4.340   3.123  1.096  N28 YB0 35 
YB0 N30 N7  N 0 1 Y N N -29.551 3.850  14.004 6.289   1.881  1.075  N30 YB0 36 
YB0 N32 N8  N 0 1 N N N -28.508 2.906  12.181 6.411   -0.287 0.154  N32 YB0 37 
YB0 O1  O1  O 0 1 N N N -36.504 0.008  15.803 -0.568  5.553  -1.088 O1  YB0 38 
YB0 O21 O2  O 0 1 N N N -33.113 -0.592 15.544 0.002   2.294  0.178  O21 YB0 39 
YB0 O4  O3  O 0 1 N N N -35.411 1.447  13.777 1.913   5.155  -0.668 O4  YB0 40 
YB0 S7  S1  S 0 1 N N N -33.347 -3.252 14.750 -3.089  1.786  0.582  S7  YB0 41 
YB0 H1  H1  H 0 1 N N N -34.563 -0.709 17.052 -1.185  3.933  0.702  H1  YB0 42 
YB0 H2  H2  H 0 1 N N N -35.344 -3.037 16.088 -2.879  3.477  -1.119 H2  YB0 43 
YB0 H3  H3  H 0 1 N N N -33.856 -2.941 17.089 -1.970  2.005  -1.538 H3  YB0 44 
YB0 H4  H4  H 0 1 N N N -35.130 -3.549 13.143 -4.233  0.477  -1.083 H4  YB0 45 
YB0 H5  H5  H 0 1 N N N -35.190 -4.788 14.442 -5.142  1.948  -0.664 H5  YB0 46 
YB0 H6  H6  H 0 1 N N N -33.342 -3.901 10.962 -8.730  -1.292 -0.853 H6  YB0 47 
YB0 H7  H7  H 0 1 N N N -34.443 -4.504 8.254  -9.069  -3.171 1.228  H7  YB0 48 
YB0 H8  H8  H 0 1 N N N -32.785 -3.877 8.538  -9.979  -1.699 1.647  H8  YB0 49 
YB0 H9  H9  H 0 1 N N N -36.466 -2.133 8.582  -11.087 -4.543 0.955  H9  YB0 50 
YB0 H10 H10 H 0 1 N N N -35.999 -3.244 9.913  -12.062 -3.153 1.488  H10 YB0 51 
YB0 H11 H11 H 0 1 N N N -35.396 0.941  10.551 -14.343 -3.162 -1.454 H11 YB0 52 
YB0 H12 H12 H 0 1 N N N -35.967 0.416  8.931  -13.963 -2.346 0.082  H12 YB0 53 
YB0 H13 H13 H 0 1 N N N -33.638 1.406  15.507 1.396   3.522  1.139  H13 YB0 54 
YB0 H14 H14 H 0 1 N N N -32.330 -0.645 12.475 1.380   0.339  -0.938 H14 YB0 55 
YB0 H15 H15 H 0 1 N N N -34.411 -2.168 7.734  -10.267 -3.225 -0.979 H15 YB0 56 
YB0 H16 H16 H 0 1 N N N -36.905 -1.024 10.684 -12.342 -4.602 -1.183 H16 YB0 57 
YB0 H17 H17 H 0 1 N N N -35.255 -1.397 11.286 -13.441 -4.767 0.207  H17 YB0 58 
YB0 H18 H18 H 0 1 N N N -33.257 0.658  9.940  -12.168 -2.418 -2.386 H18 YB0 59 
YB0 H19 H19 H 0 1 N N N -33.827 0.299  8.274  -13.143 -1.028 -1.852 H19 YB0 60 
YB0 H20 H20 H 0 1 N N N -33.338 -1.687 10.544 -11.888 -0.969 0.286  H20 YB0 61 
YB0 H21 H21 H 0 1 N N N -32.412 -1.524 9.013  -10.790 -0.804 -1.104 H21 YB0 62 
YB0 H22 H22 H 0 1 N N N -35.861 -1.530 14.562 -0.528  3.828  -2.247 H22 YB0 63 
YB0 H23 H23 H 0 1 N N N -30.498 4.610  15.654 6.136   3.785  1.871  H23 YB0 64 
YB0 H24 H24 H 0 1 N N N -34.496 -0.336 13.165 1.721   3.466  -1.865 H24 YB0 65 
YB0 H25 H25 H 0 1 N N N -28.638 0.944  11.474 7.955   -0.280 1.573  H25 YB0 66 
YB0 H26 H26 H 0 1 N N N -27.192 1.865  10.936 8.381   0.415  -0.009 H26 YB0 67 
YB0 H27 H27 H 0 1 N N N -28.618 3.287  9.524  7.829   -2.534 0.549  H27 YB0 68 
YB0 H28 H28 H 0 1 N N N -30.068 2.377  10.068 8.255   -1.839 -1.034 H28 YB0 69 
YB0 H29 H29 H 0 1 N N N -28.979 0.288  9.152  10.410  -1.040 -0.103 H29 YB0 70 
YB0 H30 H30 H 0 1 N N N -27.716 1.345  8.436  9.984   -1.736 1.480  H30 YB0 71 
YB0 H31 H31 H 0 1 N N N -31.392 0.661  8.431  10.961  -2.474 -1.982 H31 YB0 72 
YB0 H32 H32 H 0 1 N N N -32.797 0.974  6.438  11.835  -4.659 -2.707 H32 YB0 73 
YB0 H33 H33 H 0 1 N N N -31.858 2.008  4.412  11.762  -6.585 -1.174 H33 YB0 74 
YB0 H34 H34 H 0 1 N N N -29.505 2.724  4.382  10.814  -6.326 1.084  H34 YB0 75 
YB0 H35 H35 H 0 1 N N N -28.095 2.418  6.371  9.946   -4.139 1.811  H35 YB0 76 
YB0 H36 H36 H 0 1 N N N -33.279 -5.936 13.549 -4.801  -0.503 1.123  H36 YB0 77 
YB0 H37 H37 H 0 1 N N N -32.942 -4.601 12.396 -5.711  0.969  1.541  H37 YB0 78 
YB0 H38 H38 H 0 1 N N N -35.052 -6.659 12.147 -6.712  -0.030 -0.903 H38 YB0 79 
YB0 H39 H39 H 0 1 N N N -35.661 -6.931 10.102 -6.519  -0.867 2.452  H39 YB0 80 
YB0 H40 H40 H 0 1 N N N -27.675 2.905  12.735 5.969   -1.027 -0.291 H40 YB0 81 
YB0 H41 H41 H 0 1 N N N -36.911 -0.601 16.407 -0.152  6.132  -1.741 H41 YB0 82 
YB0 H42 H42 H 0 1 N N N -36.216 1.247  13.314 1.926   5.799  -1.389 H42 YB0 83 
# 
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 
YB0 C40 C39 DOUB Y N 1  
YB0 C40 C41 SING Y N 2  
YB0 C39 C38 SING Y N 3  
YB0 C41 C36 DOUB Y N 4  
YB0 C38 C37 DOUB Y N 5  
YB0 C36 C37 SING Y N 6  
YB0 C36 C35 SING N N 7  
YB0 C35 C34 SING N N 8  
YB0 C14 C13 SING N N 9  
YB0 C14 C15 SING N N 10 
YB0 C14 C19 SING N N 11 
YB0 C13 N12 SING N N 12 
YB0 C18 C19 SING N N 13 
YB0 C18 C17 SING N N 14 
YB0 C15 C16 SING N N 15 
YB0 N20 C11 DOUB N N 16 
YB0 C17 C16 SING N N 17 
YB0 C34 C33 SING N N 18 
YB0 N12 C11 SING N N 19 
YB0 C11 N10 SING N N 20 
YB0 C33 N32 SING N N 21 
YB0 N10 C9  SING N N 22 
YB0 N32 C31 SING N N 23 
YB0 N25 C24 DOUB Y N 24 
YB0 N25 C26 SING Y N 25 
YB0 C24 N23 SING Y N 26 
YB0 C9  C8  SING N N 27 
YB0 C31 C26 DOUB Y N 28 
YB0 C31 N30 SING Y N 29 
YB0 C26 C27 SING Y N 30 
YB0 C8  S7  SING N N 31 
YB0 O4  C3  SING N N 32 
YB0 N23 C27 SING Y N 33 
YB0 N23 C22 SING N N 34 
YB0 N30 C29 DOUB Y N 35 
YB0 C3  C22 SING N N 36 
YB0 C3  C2  SING N N 37 
YB0 C27 N28 DOUB Y N 38 
YB0 S7  C6  SING N N 39 
YB0 C22 O21 SING N N 40 
YB0 C29 N28 SING Y N 41 
YB0 C2  O1  SING N N 42 
YB0 C2  C5  SING N N 43 
YB0 O21 C5  SING N N 44 
YB0 C5  C6  SING N N 45 
YB0 C5  H1  SING N N 46 
YB0 C6  H2  SING N N 47 
YB0 C6  H3  SING N N 48 
YB0 C8  H4  SING N N 49 
YB0 C8  H5  SING N N 50 
YB0 N12 H6  SING N N 51 
YB0 C13 H7  SING N N 52 
YB0 C13 H8  SING N N 53 
YB0 C15 H9  SING N N 54 
YB0 C15 H10 SING N N 55 
YB0 C17 H11 SING N N 56 
YB0 C17 H12 SING N N 57 
YB0 C22 H13 SING N N 58 
YB0 C24 H14 SING N N 59 
YB0 C14 H15 SING N N 60 
YB0 C16 H16 SING N N 61 
YB0 C16 H17 SING N N 62 
YB0 C18 H18 SING N N 63 
YB0 C18 H19 SING N N 64 
YB0 C19 H20 SING N N 65 
YB0 C19 H21 SING N N 66 
YB0 C2  H22 SING N N 67 
YB0 C29 H23 SING N N 68 
YB0 C3  H24 SING N N 69 
YB0 C33 H25 SING N N 70 
YB0 C33 H26 SING N N 71 
YB0 C34 H27 SING N N 72 
YB0 C34 H28 SING N N 73 
YB0 C35 H29 SING N N 74 
YB0 C35 H30 SING N N 75 
YB0 C37 H31 SING N N 76 
YB0 C38 H32 SING N N 77 
YB0 C39 H33 SING N N 78 
YB0 C40 H34 SING N N 79 
YB0 C41 H35 SING N N 80 
YB0 C9  H36 SING N N 81 
YB0 C9  H37 SING N N 82 
YB0 N10 H38 SING N N 83 
YB0 N20 H39 SING N N 84 
YB0 N32 H40 SING N N 85 
YB0 O1  H41 SING N N 86 
YB0 O4  H42 SING N N 87 
# 
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 
YB0 SMILES           ACDLabs              12.01 "N=C(NCC1CCCCC1)NCCSCC1OC(n2cnc3c(NCCCc4ccccc4)ncnc32)C(O)C1O"                                                                                                                                                                                                 
YB0 InChI            InChI                1.06  "InChI=1S/C29H42N8O3S/c30-29(33-16-21-10-5-2-6-11-21)32-14-15-41-17-22-24(38)25(39)28(40-22)37-19-36-23-26(34-18-35-27(23)37)31-13-7-12-20-8-3-1-4-9-20/h1,3-4,8-9,18-19,21-22,24-25,28,38-39H,2,5-7,10-17H2,(H3,30,32,33)(H,31,34,35)/t22-,24-,25-,28-/m1/s1" 
YB0 InChIKey         InChI                1.06  IJAWJZSCQJWFLW-ZYWWQZICSA-N                                                                                                                                                                                                                                    
YB0 SMILES_CANONICAL CACTVS               3.385 "O[C@H]1[C@@H](O)[C@@H](O[C@@H]1CSCCNC(=N)NCC2CCCCC2)n3cnc4c(NCCCc5ccccc5)ncnc34"                                                                                                                                                                              
YB0 SMILES           CACTVS               3.385 "O[CH]1[CH](O)[CH](O[CH]1CSCCNC(=N)NCC2CCCCC2)n3cnc4c(NCCCc5ccccc5)ncnc34"                                                                                                                                                                                     
YB0 SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "[H]/N=C(/NCCSC[C@@H]1[C@H]([C@H]([C@@H](O1)n2cnc3c2ncnc3NCCCc4ccccc4)O)O)\NCC5CCCCC5"                                                                                                                                                                         
YB0 SMILES           "OpenEye OEToolkits" 2.0.7 "c1ccc(cc1)CCCNc2c3c(ncn2)n(cn3)C4C(C(C(O4)CSCCNC(=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 
YB0 "SYSTEMATIC NAME" ACDLabs              12.01 "5'-S-{2-[N'-(cyclohexylmethyl)carbamimidamido]ethyl}-N-(3-phenylpropyl)-5'-thioadenosine"                                                                
YB0 "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 "1-[2-[[(2~{S},3~{S},4~{R},5~{R})-3,4-bis(oxidanyl)-5-[6-(3-phenylpropylamino)purin-9-yl]oxolan-2-yl]methylsulfanyl]ethyl]-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 
YB0 "Create component" 2023-01-20 RCSB 
YB0 "Initial release"  2023-05-10 RCSB 
# 
