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 
# 
