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 #