data_RK3 # _chem_comp.id RK3 _chem_comp.name "(1S,3S,4R,5R,7R,15R,16S,17R)-5-imidazo[2,1-f]purin-3-yl-10,12-bis(oxidanyl)-10,12-bis(oxidanylidene)-2,6,9,11,13,18-hexaoxa-10$l^{5},12$l^{5}-diphosphatricyclo[13.2.1.0^{3,7}]octadecane-4,16,17-triol" _chem_comp.type non-polymer _chem_comp.pdbx_type HETAIN _chem_comp.formula "C17 H21 N5 O13 P2" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms "1''-3'gc(etheno)ADPR" _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2022-11-30 _chem_comp.pdbx_modified_date 2024-02-16 _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 565.322 _chem_comp.one_letter_code ? _chem_comp.three_letter_code RK3 _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 8BTP _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site PDBE # 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.pdbx_backbone_atom_flag _chem_comp_atom.pdbx_n_terminal_atom_flag _chem_comp_atom.pdbx_c_terminal_atom_flag _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 RK3 C28 C1 C 0 1 N N N N N N 238.345 196.032 159.466 0.947 1.254 0.130 C28 RK3 1 RK3 C36 C2 C 0 1 N N S N N N 237.183 193.212 154.480 3.821 -3.283 -0.094 C36 RK3 2 RK3 O37 O1 O 0 1 N N N N N N 236.625 192.059 153.873 4.702 -3.843 0.881 O37 RK3 3 RK3 C05 C3 C 0 1 N N N N N N 239.593 192.990 155.290 4.859 -1.400 -1.394 C05 RK3 4 RK3 C06 C4 C 0 1 N N R N N N 238.132 192.814 155.615 4.007 -1.757 -0.177 C06 RK3 5 RK3 C08 C5 C 0 1 N N S N N N 236.808 194.617 156.384 1.732 -2.053 0.264 C08 RK3 6 RK3 C10 C6 C 0 1 N N S N N N 238.404 196.354 156.908 -0.136 -0.856 -0.677 C10 RK3 7 RK3 C11 C7 C 0 1 N N R N N N 239.248 197.528 156.392 -1.655 -1.103 -0.690 C11 RK3 8 RK3 C13 C8 C 0 1 N N R N N N 238.569 198.685 157.099 -2.184 -0.400 0.568 C13 RK3 9 RK3 C15 C9 C 0 1 Y N N N N N 239.217 200.957 156.228 -3.427 1.697 -0.076 C15 RK3 10 RK3 C17 C10 C 0 1 Y N N N N N 240.758 201.550 157.608 -5.470 0.986 -0.163 C17 RK3 11 RK3 C18 C11 C 0 1 Y N N N N N 240.324 200.284 158.004 -4.669 -0.103 0.191 C18 RK3 12 RK3 C20 C12 C 0 1 Y N N N N N 241.780 200.193 159.752 -6.512 -1.500 0.289 C20 RK3 13 RK3 C22 C13 C 0 1 Y N N N N N 243.257 202.241 160.022 -8.739 -0.465 -0.228 C22 RK3 14 RK3 C23 C14 C 0 1 Y N N N N N 243.342 203.397 159.302 -9.056 0.802 -0.565 C23 RK3 15 RK3 C25 C15 C 0 1 Y N N N N N 241.763 202.145 158.351 -6.910 0.762 -0.289 C25 RK3 16 RK3 C27 C16 C 0 1 N N R N N N 237.915 196.848 158.275 0.113 0.039 0.546 C27 RK3 17 RK3 C34 C17 C 0 1 N N R N N N 236.094 194.034 155.166 2.353 -3.455 0.341 C34 RK3 18 RK3 N14 N1 N 0 1 Y N N N N N 239.341 199.918 157.115 -3.383 0.374 0.239 N14 RK3 19 RK3 N16 N2 N 0 1 Y N N N N N 240.036 201.946 156.489 -4.658 2.054 -0.312 N16 RK3 20 RK3 N19 N3 N 0 1 Y N N N N N 240.829 199.616 159.057 -5.231 -1.301 0.401 N19 RK3 21 RK3 N21 N4 N 0 1 Y N N N N N 242.270 201.451 159.436 -7.381 -0.508 -0.050 N21 RK3 22 RK3 N24 N5 N 0 1 Y N N N N N 242.432 203.344 158.279 -7.934 1.531 -0.596 N24 RK3 23 RK3 O01 O2 O 0 1 N N N N N N 242.017 194.404 155.575 3.261 1.053 -1.908 O01 RK3 24 RK3 O03 O3 O 0 1 N N N N N N 242.621 192.968 157.612 5.313 2.501 -1.663 O03 RK3 25 RK3 O04 O4 O 0 1 N N N N N N 240.415 192.665 156.428 5.406 -0.089 -1.224 O04 RK3 26 RK3 O07 O5 O 0 1 N N N N N N 237.808 193.666 156.734 2.705 -1.175 -0.303 O07 RK3 27 RK3 O09 O6 O 0 1 N N N N N N 237.356 195.872 156.063 0.566 -2.092 -0.557 O09 RK3 28 RK3 O12 O7 O 0 1 N N N N N N 239.330 197.628 154.991 -1.931 -2.504 -0.630 O12 RK3 29 RK3 O26 O8 O 0 1 N N N N N N 238.436 198.192 158.402 -1.155 0.474 1.034 O26 RK3 30 RK3 O29 O9 O 0 1 N N N N N N 239.788 196.021 159.572 1.626 1.781 1.271 O29 RK3 31 RK3 O31 O10 O 0 1 N N N N N N 241.736 194.519 160.154 2.965 3.851 0.355 O31 RK3 32 RK3 O32 O11 O 0 1 N N N N N N 239.461 193.536 159.499 3.574 2.756 2.547 O32 RK3 33 RK3 O33 O12 O 0 1 N N N N N N 240.907 194.710 157.800 4.100 1.480 0.433 O33 RK3 34 RK3 O35 O13 O 0 1 N N N N N N 234.960 193.246 155.455 2.289 -3.952 1.679 O35 RK3 35 RK3 P02 P1 P 0 1 N N N N N N 241.596 193.674 156.798 4.493 1.232 -1.107 P02 RK3 36 RK3 P30 P2 P 0 1 N N N N N N 240.490 194.603 159.341 3.077 2.473 1.182 P30 RK3 37 RK3 H1 H1 H 0 1 N N N N N N 237.917 196.470 160.380 1.679 0.953 -0.621 H1 RK3 38 RK3 H2 H2 H 0 1 N N N N N N 237.982 195.000 159.349 0.292 2.018 -0.288 H2 RK3 39 RK3 H3 H3 H 0 1 N N N N N N 237.717 193.835 153.748 3.988 -3.742 -1.069 H3 RK3 40 RK3 H4 H4 H 0 1 N N N N N N 237.313 191.558 153.451 4.584 -4.793 1.018 H4 RK3 41 RK3 H5 H5 H 0 1 N N N N N N 239.858 192.327 154.453 5.670 -2.122 -1.494 H5 RK3 42 RK3 H6 H6 H 0 1 N N N N N N 239.774 194.036 155.001 4.240 -1.422 -2.291 H6 RK3 43 RK3 H7 H7 H 0 1 N N N N N N 237.947 191.762 155.878 4.486 -1.398 0.733 H7 RK3 44 RK3 H8 H8 H 0 1 N N N N N N 236.080 194.717 157.203 1.469 -1.712 1.266 H8 RK3 45 RK3 H9 H9 H 0 1 N N N N N N 239.098 195.523 157.099 0.167 -0.338 -1.589 H9 RK3 46 RK3 H10 H10 H 0 1 N N N N N N 240.260 197.422 156.810 -2.102 -0.668 -1.584 H10 RK3 47 RK3 H11 H11 H 0 1 N N N N N N 237.584 198.861 156.643 -2.418 -1.139 1.334 H11 RK3 48 RK3 H12 H12 H 0 1 N N N N N N 238.520 200.960 155.403 -2.570 2.354 -0.119 H12 RK3 49 RK3 H13 H13 H 0 1 N N N N N N 242.196 199.670 160.600 -6.901 -2.491 0.472 H13 RK3 50 RK3 H14 H14 H 0 1 N N N N N N 243.848 201.985 160.889 -9.426 -1.291 -0.120 H14 RK3 51 RK3 H15 H15 H 0 1 N N N N N N 244.015 204.217 159.505 -10.051 1.168 -0.775 H15 RK3 52 RK3 H16 H16 H 0 1 N N N N N N 236.816 196.884 158.254 0.637 -0.522 1.319 H16 RK3 53 RK3 H17 H17 H 0 1 N N N N N N 235.814 194.863 154.499 1.836 -4.135 -0.337 H17 RK3 54 RK3 H18 H18 H 0 1 N N N N N N 243.476 193.084 157.215 4.823 3.334 -1.623 H18 RK3 55 RK3 H19 H19 H 0 1 N N N N N N 239.867 198.376 154.757 -2.873 -2.720 -0.635 H19 RK3 56 RK3 H20 H20 H 0 1 N N N N N N 241.706 193.743 160.702 3.804 4.322 0.262 H20 RK3 57 RK3 H21 H21 H 0 1 N N N N N N 234.301 193.782 155.880 1.389 -4.081 2.008 H21 RK3 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 RK3 O37 C36 SING N N 1 RK3 C36 C34 SING N N 2 RK3 C36 C06 SING N N 3 RK3 O12 C11 SING N N 4 RK3 C34 O35 SING N N 5 RK3 C34 C08 SING N N 6 RK3 C05 C06 SING N N 7 RK3 C05 O04 SING N N 8 RK3 O01 P02 DOUB N N 9 RK3 C06 O07 SING N N 10 RK3 O09 C08 SING N N 11 RK3 O09 C10 SING N N 12 RK3 C15 N16 DOUB Y N 13 RK3 C15 N14 SING Y N 14 RK3 C08 O07 SING N N 15 RK3 C11 C10 SING N N 16 RK3 C11 C13 SING N N 17 RK3 O04 P02 SING N N 18 RK3 N16 C17 SING Y N 19 RK3 P02 O03 SING N N 20 RK3 P02 O33 SING N N 21 RK3 C10 C27 SING N N 22 RK3 C13 N14 SING N N 23 RK3 C13 O26 SING N N 24 RK3 N14 C18 SING Y N 25 RK3 C17 C18 DOUB Y N 26 RK3 C17 C25 SING Y N 27 RK3 O33 P30 SING N N 28 RK3 C18 N19 SING Y N 29 RK3 C27 O26 SING N N 30 RK3 C27 C28 SING N N 31 RK3 N24 C25 DOUB Y N 32 RK3 N24 C23 SING Y N 33 RK3 C25 N21 SING Y N 34 RK3 N19 C20 DOUB Y N 35 RK3 C23 C22 DOUB Y N 36 RK3 P30 O32 DOUB N N 37 RK3 P30 O29 SING N N 38 RK3 P30 O31 SING N N 39 RK3 N21 C20 SING Y N 40 RK3 N21 C22 SING Y N 41 RK3 C28 O29 SING N N 42 RK3 C28 H1 SING N N 43 RK3 C28 H2 SING N N 44 RK3 C36 H3 SING N N 45 RK3 O37 H4 SING N N 46 RK3 C05 H5 SING N N 47 RK3 C05 H6 SING N N 48 RK3 C06 H7 SING N N 49 RK3 C08 H8 SING N N 50 RK3 C10 H9 SING N N 51 RK3 C11 H10 SING N N 52 RK3 C13 H11 SING N N 53 RK3 C15 H12 SING N N 54 RK3 C20 H13 SING N N 55 RK3 C22 H14 SING N N 56 RK3 C23 H15 SING N N 57 RK3 C27 H16 SING N N 58 RK3 C34 H17 SING N N 59 RK3 O03 H18 SING N N 60 RK3 O12 H19 SING N N 61 RK3 O31 H20 SING N N 62 RK3 O35 H21 SING N N 63 # 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 RK3 InChI InChI 1.06 "InChI=1S/C17H21N5O13P2/c23-10-7-3-30-36(26,27)35-37(28,29)31-4-8-13(34-17(33-7)11(10)24)12(25)16(32-8)22-6-19-9-14-18-1-2-21(14)5-20-15(9)22/h1-2,5-8,10-13,16-17,23-25H,3-4H2,(H,26,27)(H,28,29)/t7-,8-,10-,11-,12-,13-,16-,17+/m1/s1" RK3 InChIKey InChI 1.06 LFJBQYHLOPJAJZ-DLFWLGJNSA-N RK3 SMILES_CANONICAL CACTVS 3.385 "O[C@H]1[C@@H](O)[C@H]2O[C@@H]1CO[P](O)(=O)O[P](O)(=O)OC[C@H]3O[C@H]([C@H](O)[C@@H]3O2)n4cnc5c6nccn6cnc45" RK3 SMILES CACTVS 3.385 "O[CH]1[CH](O)[CH]2O[CH]1CO[P](O)(=O)O[P](O)(=O)OC[CH]3O[CH]([CH](O)[CH]3O2)n4cnc5c6nccn6cnc45" RK3 SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "c1cn2cnc3c(c2n1)ncn3[C@H]4[C@@H]([C@H]5[C@H](O4)COP(=O)(OP(=O)(OC[C@@H]6[C@H]([C@H]([C@@H](O6)O5)O)O)O)O)O" RK3 SMILES "OpenEye OEToolkits" 2.0.7 "c1cn2cnc3c(c2n1)ncn3C4C(C5C(O4)COP(=O)(OP(=O)(OCC6C(C(C(O6)O5)O)O)O)O)O" # _pdbx_chem_comp_identifier.comp_id RK3 _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 "(1~{S},3~{S},4~{R},5~{R},7~{R},15~{R},16~{S},17~{R})-5-imidazo[2,1-f]purin-3-yl-10,12-bis(oxidanyl)-10,12-bis(oxidanylidene)-2,6,9,11,13,18-hexaoxa-10$l^{5},12$l^{5}-diphosphatricyclo[13.2.1.0^{3,7}]octadecane-4,16,17-triol" # _pdbx_chem_comp_synonyms.ordinal 1 _pdbx_chem_comp_synonyms.comp_id RK3 _pdbx_chem_comp_synonyms.name "1''-3'gc(etheno)ADPR" _pdbx_chem_comp_synonyms.provenance AUTHOR _pdbx_chem_comp_synonyms.type ? # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site RK3 "Create component" 2022-11-30 PDBE RK3 "Modify synonyms" 2023-02-06 PDBE RK3 "Initial release" 2024-02-21 RCSB #