data_R5I # _chem_comp.id R5I _chem_comp.name "inosine diphosphate ribose" _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C15 H22 N4 O15 P2" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2018-09-18 _chem_comp.pdbx_modified_date 2018-11-23 _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 560.301 _chem_comp.one_letter_code ? _chem_comp.three_letter_code R5I _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 6HOZ _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 R5I O1 O1 O 0 1 N N N 19.520 6.945 -3.299 8.227 2.884 2.477 O1 R5I 1 R5I C6 C1 C 0 1 N N N 18.284 7.027 -3.421 7.724 2.643 1.393 C6 R5I 2 R5I N1 N1 N 0 1 N N N 17.536 8.043 -2.808 8.161 3.261 0.272 N1 R5I 3 R5I C2 C2 C 0 1 N N N 16.203 8.221 -2.906 7.593 2.986 -0.929 C2 R5I 4 R5I N3 N2 N 0 1 N N N 15.400 7.444 -3.590 6.619 2.128 -1.056 N3 R5I 5 R5I C4 C3 C 0 1 Y N N 16.074 6.433 -4.209 6.127 1.472 0.004 C4 R5I 6 R5I C5 C4 C 0 1 Y N N 17.429 6.181 -4.179 6.670 1.704 1.271 C5 R5I 7 R5I N7 N3 N 0 1 Y N N 17.738 5.071 -4.951 5.996 0.922 2.147 N7 R5I 8 R5I C8 C5 C 0 1 Y N N 16.580 4.673 -5.440 5.092 0.239 1.505 C8 R5I 9 R5I N9 N4 N 0 1 Y N N 15.531 5.471 -5.015 5.144 0.537 0.177 N9 R5I 10 R5I "C1'" C6 C 0 1 N N R 14.118 5.326 -5.306 4.289 -0.025 -0.872 "C1'" R5I 11 R5I "O4'" O2 O 0 1 N N N 13.926 4.084 -5.946 3.064 -0.535 -0.302 "O4'" R5I 12 R5I "C4'" C7 C 0 1 N N R 13.268 4.290 -7.213 2.552 -1.471 -1.276 "C4'" R5I 13 R5I "C5'" C8 C 0 1 N N N 13.697 3.210 -8.172 1.571 -2.442 -0.616 "C5'" R5I 14 R5I "O5'" O3 O 0 1 N N N 15.114 3.330 -8.438 0.409 -1.728 -0.189 "O5'" R5I 15 R5I PA P1 P 0 1 N N N 15.633 3.529 -9.939 -0.835 -2.438 0.547 PA R5I 16 R5I O2A O4 O 0 1 N N N 14.925 4.680 -10.575 -1.332 -3.553 -0.289 O2A R5I 17 R5I O1A O5 O 0 1 N N N 17.156 3.513 -9.928 -0.358 -3.009 1.975 O1A R5I 18 R5I O3A O6 O 0 1 N N N 15.043 2.249 -10.703 -2.014 -1.363 0.765 O3A R5I 19 R5I PB P2 P 0 1 N N N 15.320 0.670 -10.613 -3.576 -1.476 1.139 PB R5I 20 R5I O2B O7 O 0 1 N N N 16.118 0.371 -9.400 -3.733 -1.696 2.727 O2B R5I 21 R5I O1B O8 O 0 1 N N N 15.734 0.211 -11.966 -4.173 -2.624 0.421 O1B R5I 22 R5I O5D O9 O 0 1 N N N 13.831 0.188 -10.375 -4.331 -0.122 0.708 O5D R5I 23 R5I C5D C9 C 0 1 N N N 13.591 -1.204 -10.406 -5.746 0.048 0.813 C5D R5I 24 R5I C4D C10 C 0 1 N N R 12.139 -1.343 -10.041 -6.130 1.445 0.320 C4D R5I 25 R5I O4D O10 O 0 1 N N N 11.387 -0.566 -11.015 -5.877 1.553 -1.090 O4D R5I 26 R5I C1D C11 C 0 1 N N R 10.403 -1.436 -11.556 -6.898 2.415 -1.637 C1D R5I 27 R5I O1D O11 O 0 1 N N N 10.282 -1.270 -12.845 -7.040 2.195 -3.042 O1D R5I 28 R5I C2D C12 C 0 1 N N R 10.984 -2.838 -11.477 -8.180 1.979 -0.884 C2D R5I 29 R5I O2D O12 O 0 1 N N N 10.031 -3.882 -11.650 -9.137 3.039 -0.850 O2D R5I 30 R5I C3D C13 C 0 1 N N S 11.584 -2.764 -10.075 -7.637 1.681 0.538 C3D R5I 31 R5I O3D O13 O 0 1 N N N 10.614 -2.917 -9.036 -7.852 2.801 1.400 O3D R5I 32 R5I "C3'" C14 C 0 1 N N S 13.606 5.732 -7.584 3.797 -2.227 -1.789 "C3'" R5I 33 R5I "O3'" O14 O 0 1 N N N 12.698 6.304 -8.526 3.681 -2.491 -3.188 "O3'" R5I 34 R5I "C2'" C15 C 0 1 N N R 13.522 6.398 -6.208 4.968 -1.252 -1.519 "C2'" R5I 35 R5I "O2'" O15 O 0 1 N N N 12.194 6.627 -5.795 5.607 -0.887 -2.744 "O2'" R5I 36 R5I H1 H1 H 0 1 N N N 18.039 8.698 -2.244 8.884 3.905 0.328 H1 R5I 37 R5I H2 H2 H 0 1 N N N 15.768 9.061 -2.385 7.960 3.493 -1.809 H2 R5I 38 R5I H3 H3 H 0 1 N N N 16.463 3.823 -6.096 4.413 -0.470 1.957 H3 R5I 39 R5I H4 H4 H 0 1 N N N 13.560 5.336 -4.358 4.070 0.730 -1.627 H4 R5I 40 R5I H5 H5 H 0 1 N N N 12.179 4.218 -7.073 2.067 -0.939 -2.094 H5 R5I 41 R5I H6 H6 H 0 1 N N N 13.138 3.314 -9.114 1.282 -3.210 -1.334 H6 R5I 42 R5I H7 H7 H 0 1 N N N 13.490 2.224 -7.729 2.046 -2.911 0.245 H7 R5I 43 R5I H8 H8 H 0 1 N N N 17.484 4.294 -10.358 -0.019 -2.331 2.576 H8 R5I 44 R5I H9 H9 H 0 1 N N N 16.886 -0.133 -9.642 -3.362 -0.981 3.261 H9 R5I 45 R5I H10 H10 H 0 1 N N N 13.780 -1.609 -11.411 -6.248 -0.703 0.203 H10 R5I 46 R5I H11 H11 H 0 1 N N N 14.227 -1.725 -9.675 -6.049 -0.067 1.853 H11 R5I 47 R5I H12 H12 H 0 1 N N N 11.981 -0.927 -9.035 -5.555 2.198 0.859 H12 R5I 48 R5I H13 H13 H 0 1 N N N 9.453 -1.380 -11.004 -6.669 3.461 -1.432 H13 R5I 49 R5I H14 H14 H 0 1 N N N 9.920 -0.409 -13.021 -6.265 2.451 -3.560 H14 R5I 50 R5I H15 H15 H 0 1 N N N 11.797 -2.933 -12.211 -8.610 1.083 -1.333 H15 R5I 51 R5I H16 H16 H 0 1 N N N 10.468 -4.723 -11.588 -9.440 3.324 -1.724 H16 R5I 52 R5I H17 H17 H 0 1 N N N 12.402 -3.492 -9.975 -8.107 0.787 0.947 H17 R5I 53 R5I H18 H18 H 0 1 N N N 11.044 -2.862 -8.190 -8.784 3.029 1.523 H18 R5I 54 R5I H19 H19 H 0 1 N N N 14.641 5.784 -7.954 3.936 -3.155 -1.234 H19 R5I 55 R5I H20 H20 H 0 1 N N N 12.959 7.197 -8.716 4.436 -2.965 -3.563 H20 R5I 56 R5I H21 H21 H 0 1 N N N 14.134 7.312 -6.183 5.686 -1.699 -0.832 H21 R5I 57 R5I H22 H22 H 0 1 N N N 12.195 7.040 -4.939 5.998 -1.632 -3.221 H22 R5I 58 # 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 R5I O1D C1D SING N N 1 R5I O1B PB DOUB N N 2 R5I O2D C2D SING N N 3 R5I C1D C2D SING N N 4 R5I C1D O4D SING N N 5 R5I C2D C3D SING N N 6 R5I O4D C4D SING N N 7 R5I O3A PB SING N N 8 R5I O3A PA SING N N 9 R5I PB O5D SING N N 10 R5I PB O2B SING N N 11 R5I O2A PA DOUB N N 12 R5I C5D O5D SING N N 13 R5I C5D C4D SING N N 14 R5I C3D C4D SING N N 15 R5I C3D O3D SING N N 16 R5I PA O1A SING N N 17 R5I PA "O5'" SING N N 18 R5I "O3'" "C3'" SING N N 19 R5I "O5'" "C5'" SING N N 20 R5I "C5'" "C4'" SING N N 21 R5I "C3'" "C4'" SING N N 22 R5I "C3'" "C2'" SING N N 23 R5I "C4'" "O4'" SING N N 24 R5I "C2'" "O2'" SING N N 25 R5I "C2'" "C1'" SING N N 26 R5I "O4'" "C1'" SING N N 27 R5I C8 N9 SING Y N 28 R5I C8 N7 DOUB Y N 29 R5I "C1'" N9 SING N N 30 R5I N9 C4 SING Y N 31 R5I N7 C5 SING Y N 32 R5I C4 C5 DOUB Y N 33 R5I C4 N3 SING N N 34 R5I C5 C6 SING N N 35 R5I N3 C2 DOUB N N 36 R5I C6 O1 DOUB N N 37 R5I C6 N1 SING N N 38 R5I C2 N1 SING N N 39 R5I N1 H1 SING N N 40 R5I C2 H2 SING N N 41 R5I C8 H3 SING N N 42 R5I "C1'" H4 SING N N 43 R5I "C4'" H5 SING N N 44 R5I "C5'" H6 SING N N 45 R5I "C5'" H7 SING N N 46 R5I O1A H8 SING N N 47 R5I O2B H9 SING N N 48 R5I C5D H10 SING N N 49 R5I C5D H11 SING N N 50 R5I C4D H12 SING N N 51 R5I C1D H13 SING N N 52 R5I O1D H14 SING N N 53 R5I C2D H15 SING N N 54 R5I O2D H16 SING N N 55 R5I C3D H17 SING N N 56 R5I O3D H18 SING N N 57 R5I "C3'" H19 SING N N 58 R5I "O3'" H20 SING N N 59 R5I "C2'" H21 SING N N 60 R5I "O2'" H22 SING N N 61 # 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 R5I InChI InChI 1.03 "InChI=1S/C15H22N4O15P2/c20-8-5(32-14(10(8)22)19-4-18-7-12(19)16-3-17-13(7)24)1-30-35(26,27)34-36(28,29)31-2-6-9(21)11(23)15(25)33-6/h3-6,8-11,14-15,20-23,25H,1-2H2,(H,26,27)(H,28,29)(H,16,17,24)/t5-,6-,8-,9-,10-,11-,14-,15-/m1/s1" R5I InChIKey InChI 1.03 GKBLKKRZILWFNP-KEOHHSTQSA-N R5I SMILES_CANONICAL CACTVS 3.385 "O[C@@H]1O[C@H](CO[P](O)(=O)O[P](O)(=O)OC[C@H]2O[C@H]([C@H](O)[C@@H]2O)n3cnc4C(=O)NC=Nc34)[C@@H](O)[C@H]1O" R5I SMILES CACTVS 3.385 "O[CH]1O[CH](CO[P](O)(=O)O[P](O)(=O)OC[CH]2O[CH]([CH](O)[CH]2O)n3cnc4C(=O)NC=Nc34)[CH](O)[CH]1O" R5I SMILES_CANONICAL "OpenEye OEToolkits" 2.0.6 "c1nc2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)COP(=O)(O)OP(=O)(O)OC[C@@H]4[C@H]([C@H]([C@@H](O4)O)O)O)O)O)N=CNC2=O" R5I SMILES "OpenEye OEToolkits" 2.0.6 "c1nc2c(n1C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OCC4C(C(C(O4)O)O)O)O)O)N=CNC2=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 R5I "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.6 "[[(2~{R},3~{S},4~{R},5~{R})-3,4-bis(oxidanyl)-5-(6-oxidanylidene-1~{H}-purin-9-yl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2~{R},3~{S},4~{R},5~{R})-3,4,5-tris(oxidanyl)oxolan-2-yl]methyl hydrogen phosphate" # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site R5I "Create component" 2018-09-18 EBI R5I "Initial release" 2018-11-28 RCSB #