data_T3D # _chem_comp.id T3D _chem_comp.name "(~{E})-6-[2-[3-[[(2~{R})-4-[[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-4-oxidanyl-3-phosphonooxy-oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-3,3-dimethyl-2-oxidanyl-butanoyl]amino]propanoylamino]ethylsulfanyl]-6-oxidanylidene-hex-3-enoic acid" _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C27 H42 N7 O19 P3 S" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2019-08-19 _chem_comp.pdbx_modified_date 2019-12-06 _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 893.644 _chem_comp.one_letter_code ? _chem_comp.three_letter_code T3D _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 6SLB _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site EBI # # 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 T3D O1 OCD O 0 1 N N N 2.685 8.723 23.365 15.901 6.448 -1.704 O1 T3D 1 T3D C1 CCC C 0 1 N N N 2.493 9.366 22.303 15.469 5.582 -0.773 C1 T3D 2 T3D O2 OCE O 0 1 N N N 2.937 9.116 21.145 14.445 5.803 -0.172 O2 T3D 3 T3D C2 CCB C 0 1 N N N 1.587 10.549 22.424 16.261 4.334 -0.480 C2 T3D 4 T3D C3 CCA C 0 1 N N N 0.259 9.873 22.162 15.565 3.539 0.595 C3 T3D 5 T3D C4 CBZ C 0 1 N N N -0.467 9.138 23.297 15.251 2.285 0.383 C4 T3D 6 T3D C5 CBX C 0 1 N N N -1.778 8.531 22.954 14.555 1.491 1.458 C5 T3D 7 T3D C6 CBW C 0 1 N N N -2.396 7.708 24.136 13.282 0.904 0.905 C6 T3D 8 T3D O3 OBY O 0 1 N N N -3.219 6.849 23.829 12.970 1.110 -0.249 O3 T3D 9 T3D S1 SBV S 0 1 N N N -1.766 7.960 25.892 12.276 -0.055 1.905 S1 T3D 10 T3D C7 CBU C 0 1 N N N -2.988 6.930 26.797 10.958 -0.456 0.731 C7 T3D 11 T3D C8 CBT C 0 1 N N N -2.399 5.571 26.612 9.911 -1.333 1.421 C8 T3D 12 T3D N1 NBS N 0 1 N N N -3.280 4.569 27.264 8.844 -1.658 0.472 N1 T3D 13 T3D C9 CBQ C 0 1 N N N -3.332 4.377 28.585 7.806 -2.425 0.860 C9 T3D 14 T3D O4 OBR O 0 1 N N N -2.854 5.192 29.392 7.756 -2.847 1.996 O4 T3D 15 T3D C10 CBP C 0 1 N N N -4.164 3.174 29.061 6.708 -2.760 -0.116 C10 T3D 16 T3D C11 CBO C 0 1 N N N -3.256 2.448 30.036 5.661 -3.636 0.573 C11 T3D 17 T3D N2 NBN N 0 1 N N N -3.973 1.213 30.501 4.594 -3.961 -0.376 N2 T3D 18 T3D C12 CBL C 0 1 N N N -4.971 1.193 31.385 3.557 -4.729 0.012 C12 T3D 19 T3D O5 OBM O 0 1 N N N -5.309 2.178 32.039 3.552 -5.227 1.118 O5 T3D 20 T3D C13 CBJ C 0 1 N N R -5.582 -0.193 31.637 2.403 -4.968 -0.927 C13 T3D 21 T3D O6 OBK O 0 1 N N N -4.633 -1.232 31.220 2.754 -4.519 -2.237 O6 T3D 22 T3D C14 CBG C 0 1 N N N -6.893 -0.402 30.852 1.177 -4.196 -0.435 C14 T3D 23 T3D C15 CBH C 0 1 N N N -6.658 -0.092 29.330 0.711 -4.776 0.901 C15 T3D 24 T3D C16 CBI C 0 1 N N N -8.038 0.502 31.342 1.542 -2.721 -0.251 C16 T3D 25 T3D C17 CBF C 0 1 N N N -7.342 -1.857 30.943 0.051 -4.317 -1.464 C17 T3D 26 T3D O7 OBE O 0 1 N N N -7.319 -2.362 32.330 -1.094 -3.596 -1.005 O7 T3D 27 T3D P1 PBB P 0 1 N N N -7.340 -3.930 32.468 -2.468 -3.508 -1.840 P1 T3D 28 T3D O8 OBC O 0 1 N N N -7.557 -4.248 33.913 -2.210 -2.711 -3.215 O8 T3D 29 T3D O9 OBD O 0 1 N N N -8.257 -4.461 31.442 -2.948 -4.874 -2.145 O9 T3D 30 T3D O10 OBA O 0 1 N N N -5.888 -4.449 32.042 -3.577 -2.731 -0.969 O10 T3D 31 T3D P2 PAX P 0 1 N N N -4.478 -4.175 32.836 -5.185 -2.659 -1.013 P2 T3D 32 T3D O11 OAY O 0 1 N N N -4.436 -5.186 33.929 -5.801 -3.962 -0.297 O11 T3D 33 T3D O12 OAZ O 0 1 N N N -4.282 -2.777 33.196 -5.637 -2.609 -2.421 O12 T3D 34 T3D O13 O5* O 0 1 N N N -3.425 -4.547 31.687 -5.683 -1.336 -0.242 O13 T3D 35 T3D C18 C5* C 0 1 N N N -3.330 -5.862 31.205 -7.053 -0.933 -0.196 C18 T3D 36 T3D C19 C4* C 0 1 N N R -2.060 -5.884 30.340 -7.177 0.360 0.614 C19 T3D 37 T3D O14 O4* O 0 1 N N N -2.097 -4.961 29.119 -6.587 1.463 -0.106 O14 T3D 38 T3D C20 C3* C 0 1 N N S -0.819 -5.432 31.146 -8.663 0.748 0.784 C20 T3D 39 T3D O15 O3* O 0 1 N N N 0.336 -6.148 30.667 -9.148 0.325 2.060 O15 T3D 40 T3D P3 PAQ P 0 1 N N N 0.960 -7.433 31.440 -10.374 -0.704 2.235 P3 T3D 41 T3D O16 OAS O 0 1 N N N -0.055 -8.438 31.198 -11.723 -0.032 1.669 O16 T3D 42 T3D O17 OAT O 0 1 N N N 2.205 -7.666 30.790 -10.087 -1.945 1.482 O17 T3D 43 T3D O18 OAR O 0 1 N N N 1.083 -6.935 32.811 -10.562 -1.054 3.795 O18 T3D 44 T3D C21 C2* C 0 1 N N R -0.742 -3.939 30.679 -8.661 2.290 0.686 C21 T3D 45 T3D O19 O2* O 0 1 N N N 0.512 -3.263 30.849 -9.145 2.869 1.899 O19 T3D 46 T3D C22 C1* C 0 1 N N R -1.036 -4.042 29.216 -7.175 2.651 0.468 C22 T3D 47 T3D N3 NAJ N 0 1 Y N N -1.595 -2.752 28.719 -7.055 3.779 -0.458 N3 T3D 48 T3D C23 CAI C 0 1 Y N N -2.752 -2.111 28.992 -6.908 3.700 -1.811 C23 T3D 49 T3D N4 NAH N 0 1 Y N N -2.737 -0.917 28.388 -6.832 4.895 -2.321 N4 T3D 50 T3D C24 CAG C 0 1 Y N N -1.567 -0.829 27.706 -6.925 5.814 -1.331 C24 T3D 51 T3D C25 CAF C 0 1 Y N N -0.868 -1.933 27.972 -7.075 5.110 -0.124 C25 T3D 52 T3D N5 NAE N 0 1 Y N N 0.375 -2.090 27.534 -7.190 5.791 1.011 N5 T3D 53 T3D C26 CAD C 0 1 Y N N 1.083 -1.195 26.753 -7.164 7.107 1.010 C26 T3D 54 T3D N6 NAC N 0 1 Y N N 0.284 -0.028 26.519 -7.025 7.812 -0.098 N6 T3D 55 T3D C27 CAB C 0 1 Y N N -0.969 0.105 26.954 -6.911 7.219 -1.282 C27 T3D 56 T3D N7 NAA N 0 1 N N N -1.636 1.223 26.635 -6.766 7.966 -2.437 N7 T3D 57 T3D H1 H1 H 0 1 N N N 3.241 7.974 23.186 15.360 7.234 -1.857 H1 T3D 58 T3D H2 H2 H 0 1 N N N 1.812 11.317 21.670 16.338 3.731 -1.385 H2 T3D 59 T3D H3 H3 H 0 1 N N N 1.629 10.997 23.428 17.259 4.609 -0.140 H3 T3D 60 T3D H4 H4 H 0 1 N N N -0.179 9.908 21.175 15.326 4.003 1.541 H4 T3D 61 T3D H5 H5 H 0 1 N N N -0.048 9.066 24.290 15.490 1.821 -0.562 H5 T3D 62 T3D H6 H6 H 0 1 N N N -2.477 9.336 22.683 15.209 0.687 1.796 H6 T3D 63 T3D H7 H7 H 0 1 N N N -1.640 7.860 22.093 14.319 2.144 2.298 H7 T3D 64 T3D H8 H8 H 0 1 N N N -3.042 7.207 27.860 10.489 0.464 0.383 H8 T3D 65 T3D H9 H9 H 0 1 N N N -3.990 7.002 26.348 11.379 -0.994 -0.118 H9 T3D 66 T3D H10 H10 H 0 1 N N N -2.318 5.347 25.538 10.380 -2.253 1.769 H10 T3D 67 T3D H11 H11 H 0 1 N N N -1.400 5.537 27.070 9.490 -0.796 2.271 H11 T3D 68 T3D H12 H12 H 0 1 N N N -3.867 4.007 26.682 8.884 -1.321 -0.437 H12 T3D 69 T3D H13 H13 H 0 1 N N N -5.083 3.511 29.562 6.239 -1.839 -0.465 H13 T3D 70 T3D H14 H14 H 0 1 N N N -4.426 2.523 28.214 7.129 -3.297 -0.966 H14 T3D 71 T3D H15 H15 H 0 1 N N N -2.317 2.169 29.536 6.130 -4.557 0.921 H15 T3D 72 T3D H16 H16 H 0 1 N N N -3.035 3.098 30.896 5.240 -3.099 1.423 H16 T3D 73 T3D H17 H17 H 0 1 N N N -3.679 0.337 30.118 4.634 -3.624 -1.285 H17 T3D 74 T3D H18 H18 H 0 1 N N N -5.795 -0.296 32.711 2.173 -6.033 -0.957 H18 T3D 75 T3D H19 H19 H 0 1 N N N -4.480 -1.830 31.942 2.971 -3.578 -2.286 H19 T3D 76 T3D H20 H20 H 0 1 N N N -6.331 0.952 29.214 0.524 -5.844 0.789 H20 T3D 77 T3D H21 H21 H 0 1 N N N -5.883 -0.765 28.934 1.483 -4.620 1.655 H21 T3D 78 T3D H22 H22 H 0 1 N N N -7.595 -0.246 28.776 -0.208 -4.278 1.214 H22 T3D 79 T3D H23 H23 H 0 1 N N N -8.228 0.309 32.408 0.669 -2.171 0.099 H23 T3D 80 T3D H24 H24 H 0 1 N N N -7.757 1.557 31.205 2.344 -2.635 0.482 H24 T3D 81 T3D H25 H25 H 0 1 N N N -8.948 0.287 30.763 1.874 -2.308 -1.203 H25 T3D 82 T3D H26 H26 H 0 1 N N N -8.368 -1.936 30.554 0.383 -3.904 -2.417 H26 T3D 83 T3D H27 H27 H 0 1 N N N -6.669 -2.474 30.330 -0.210 -5.367 -1.595 H27 T3D 84 T3D H28 H28 H 0 1 N N N -8.324 -4.801 34.004 -1.893 -1.806 -3.091 H28 T3D 85 T3D H29 H29 H 0 1 N N N -4.278 -4.750 34.758 -5.545 -4.059 0.631 H29 T3D 86 T3D H30 H30 H 0 1 N N N -4.213 -6.116 30.600 -7.416 -0.762 -1.209 H30 T3D 87 T3D H31 H31 H 0 1 N N N -3.241 -6.573 32.039 -7.647 -1.715 0.276 H31 T3D 88 T3D H32 H32 H 0 1 N N N -1.892 -6.915 29.994 -6.702 0.243 1.588 H32 T3D 89 T3D H33 H33 H 0 1 N N N -0.976 -5.515 32.232 -9.264 0.315 -0.015 H33 T3D 90 T3D H34 H34 H 0 1 N N N 0.294 -9.110 30.624 -11.972 0.788 2.117 H34 T3D 91 T3D H35 H35 H 0 1 N N N 2.002 -6.851 33.037 -11.285 -1.670 3.975 H35 T3D 92 T3D H36 H36 H 0 1 N N N -1.547 -3.377 31.174 -9.264 2.619 -0.161 H36 T3D 93 T3D H37 H37 H 0 1 N N N 0.710 -3.191 31.775 -9.165 3.836 1.892 H37 T3D 94 T3D H38 H38 H 0 1 N N N -0.147 -4.347 28.644 -6.699 2.888 1.420 H38 T3D 95 T3D H39 H39 H 0 1 N N N -3.557 -2.499 29.598 -6.861 2.781 -2.376 H39 T3D 96 T3D H40 H40 H 0 1 N N N 2.083 -1.351 26.377 -7.260 7.629 1.950 H40 T3D 97 T3D H41 H41 H 0 1 N N N -1.048 1.817 26.086 -6.746 8.935 -2.389 H41 T3D 98 T3D H42 H42 H 0 1 N N N -2.453 0.985 26.110 -6.684 7.521 -3.295 H42 T3D 99 # # 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 T3D O2 C1 DOUB N N 1 T3D C3 C2 SING N N 2 T3D C3 C4 DOUB N E 3 T3D C1 C2 SING N N 4 T3D C1 O1 SING N N 5 T3D C5 C4 SING N N 6 T3D C5 C6 SING N N 7 T3D O3 C6 DOUB N N 8 T3D C6 S1 SING N N 9 T3D S1 C7 SING N N 10 T3D N6 C26 DOUB Y N 11 T3D N6 C27 SING Y N 12 T3D C8 C7 SING N N 13 T3D C8 N1 SING N N 14 T3D N7 C27 SING N N 15 T3D C26 N5 SING Y N 16 T3D C27 C24 DOUB Y N 17 T3D N1 C9 SING N N 18 T3D N5 C25 DOUB Y N 19 T3D C24 C25 SING Y N 20 T3D C24 N4 SING Y N 21 T3D C25 N3 SING Y N 22 T3D N4 C23 DOUB Y N 23 T3D C9 C10 SING N N 24 T3D C9 O4 DOUB N N 25 T3D N3 C23 SING Y N 26 T3D N3 C22 SING N N 27 T3D C10 C11 SING N N 28 T3D O14 C22 SING N N 29 T3D O14 C19 SING N N 30 T3D C22 C21 SING N N 31 T3D C15 C14 SING N N 32 T3D C11 N2 SING N N 33 T3D C19 C20 SING N N 34 T3D C19 C18 SING N N 35 T3D N2 C12 SING N N 36 T3D O15 C20 SING N N 37 T3D O15 P3 SING N N 38 T3D C21 O19 SING N N 39 T3D C21 C20 SING N N 40 T3D O17 P3 DOUB N N 41 T3D C14 C17 SING N N 42 T3D C14 C16 SING N N 43 T3D C14 C13 SING N N 44 T3D C17 O7 SING N N 45 T3D O16 P3 SING N N 46 T3D C18 O13 SING N N 47 T3D O6 C13 SING N N 48 T3D C12 C13 SING N N 49 T3D C12 O5 DOUB N N 50 T3D P3 O18 SING N N 51 T3D O9 P1 DOUB N N 52 T3D O13 P2 SING N N 53 T3D O10 P1 SING N N 54 T3D O10 P2 SING N N 55 T3D O7 P1 SING N N 56 T3D P1 O8 SING N N 57 T3D P2 O12 DOUB N N 58 T3D P2 O11 SING N N 59 T3D O1 H1 SING N N 60 T3D C2 H2 SING N N 61 T3D C2 H3 SING N N 62 T3D C3 H4 SING N N 63 T3D C4 H5 SING N N 64 T3D C5 H6 SING N N 65 T3D C5 H7 SING N N 66 T3D C7 H8 SING N N 67 T3D C7 H9 SING N N 68 T3D C8 H10 SING N N 69 T3D C8 H11 SING N N 70 T3D N1 H12 SING N N 71 T3D C10 H13 SING N N 72 T3D C10 H14 SING N N 73 T3D C11 H15 SING N N 74 T3D C11 H16 SING N N 75 T3D N2 H17 SING N N 76 T3D C13 H18 SING N N 77 T3D O6 H19 SING N N 78 T3D C15 H20 SING N N 79 T3D C15 H21 SING N N 80 T3D C15 H22 SING N N 81 T3D C16 H23 SING N N 82 T3D C16 H24 SING N N 83 T3D C16 H25 SING N N 84 T3D C17 H26 SING N N 85 T3D C17 H27 SING N N 86 T3D O8 H28 SING N N 87 T3D O11 H29 SING N N 88 T3D C18 H30 SING N N 89 T3D C18 H31 SING N N 90 T3D C19 H32 SING N N 91 T3D C20 H33 SING N N 92 T3D O16 H34 SING N N 93 T3D O18 H35 SING N N 94 T3D C21 H36 SING N N 95 T3D O19 H37 SING N N 96 T3D C22 H38 SING N N 97 T3D C23 H39 SING N N 98 T3D C26 H40 SING N N 99 T3D N7 H41 SING N N 100 T3D N7 H42 SING N N 101 # # 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 T3D InChI InChI 1.03 "InChI=1S/C27H42N7O19P3S/c1-27(2,22(40)25(41)30-8-7-16(35)29-9-10-57-18(38)6-4-3-5-17(36)37)12-50-56(47,48)53-55(45,46)49-11-15-21(52-54(42,43)44)20(39)26(51-15)34-14-33-19-23(28)31-13-32-24(19)34/h3-4,13-15,20-22,26,39-40H,5-12H2,1-2H3,(H,29,35)(H,30,41)(H,36,37)(H,45,46)(H,47,48)(H2,28,31,32)(H2,42,43,44)/b4-3+/t15-,20-,21-,22+,26-/m1/s1" T3D InChIKey InChI 1.03 VYSXESTVCZRDBA-ZPJAMBCCSA-N T3D SMILES_CANONICAL CACTVS 3.385 "CC(C)(CO[P](O)(=O)O[P](O)(=O)OC[C@H]1O[C@H]([C@H](O)[C@@H]1O[P](O)(O)=O)n2cnc3c(N)ncnc23)[C@@H](O)C(=O)NCCC(=O)NCCSC(=O)C/C=C/CC(O)=O" T3D SMILES CACTVS 3.385 "CC(C)(CO[P](O)(=O)O[P](O)(=O)OC[CH]1O[CH]([CH](O)[CH]1O[P](O)(O)=O)n2cnc3c(N)ncnc23)[CH](O)C(=O)NCCC(=O)NCCSC(=O)CC=CCC(O)=O" T3D SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "CC(C)(COP(=O)(O)OP(=O)(O)OC[C@@H]1[C@H]([C@H]([C@@H](O1)n2cnc3c2ncnc3N)O)OP(=O)(O)O)[C@H](C(=O)NCCC(=O)NCCSC(=O)C/C=C/CC(=O)O)O" T3D SMILES "OpenEye OEToolkits" 2.0.7 "CC(C)(COP(=O)(O)OP(=O)(O)OCC1C(C(C(O1)n2cnc3c2ncnc3N)O)OP(=O)(O)O)C(C(=O)NCCC(=O)NCCSC(=O)CC=CCC(=O)O)O" # _pdbx_chem_comp_identifier.comp_id T3D _pdbx_chem_comp_identifier.type "SYSTEMATIC NAME" _pdbx_chem_comp_identifier.program "OpenEye OEToolkits" _pdbx_chem_comp_identifier.program_version 2.0.7 _pdbx_chem_comp_identifier.identifier "(~{E})-6-[2-[3-[[(2~{R})-4-[[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-4-oxidanyl-3-phosphonooxy-oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-3,3-dimethyl-2-oxidanyl-butanoyl]amino]propanoylamino]ethylsulfanyl]-6-oxidanylidene-hex-3-enoic acid" # # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site T3D "Create component" 2019-08-19 EBI T3D "Initial release" 2019-12-11 RCSB ##