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 #