data_OI3 # _chem_comp.id OI3 _chem_comp.name ;2'-deoxyadenosine 5'-fluoro-diphosphoribose ; _chem_comp.type non-polymer _chem_comp.pdbx_type HETAIN _chem_comp.formula "C15 H22 F N5 O13 P2" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ;[[(2~{R},3~{R},4~{R},5~{R})-5-(6-aminopurin-9-yl)-4-fluoranyl-3-oxidanyl-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; [[(2R,3R,4R,5R)-5-(6-aminopurin-9-yl)-4-fluoranyl-3-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2R,3S,4R,5R)-3,4,5-tris(oxidanyl)oxolan-2-yl]methyl hydrogen phosphate; 2'-deoxy-2'-fluoro-ADPR ; _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2022-09-07 _chem_comp.pdbx_modified_date 2024-03-15 _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 561.307 _chem_comp.one_letter_code ? _chem_comp.three_letter_code OI3 _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 8AZL _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 OI3 "C4'" C1 C 0 1 N N R N N N 19.869 -6.555 -8.155 2.726 1.873 0.777 "C4'" OI3 1 OI3 "C1'" C2 C 0 1 N N R N N N 21.695 -5.094 -8.153 4.435 0.340 0.823 "C1'" OI3 2 OI3 C5 C3 C 0 1 Y N N N N N 22.524 -2.271 -6.083 6.635 -2.153 -0.678 C5 OI3 3 OI3 C6 C4 C 0 1 Y N N N N N 22.400 -0.880 -5.904 7.707 -3.048 -0.523 C6 OI3 4 OI3 "C2'" C5 C 0 1 N N R N N N 22.256 -6.270 -8.111 5.156 1.707 0.844 "C2'" OI3 5 OI3 C3D C6 C 0 1 N N S N N N 18.585 -10.718 0.409 -7.596 -2.022 -0.164 C3D OI3 6 OI3 C4D C7 C 0 1 N N R N N N 19.184 -10.886 -0.734 -6.241 -1.442 0.286 C4D OI3 7 OI3 C5D C8 C 0 1 N N N N N N 18.251 -10.684 -1.884 -5.596 -0.672 -0.868 C5D OI3 8 OI3 "C5'" C9 C 0 1 N N N N N N 19.342 -7.349 -6.916 1.669 2.522 -0.118 "C5'" OI3 9 OI3 C8 C10 C 0 1 Y N N N N N 22.900 -4.417 -6.084 4.975 -0.906 -1.304 C8 OI3 10 OI3 C2 C11 C 0 1 Y N N N N N 21.145 -0.748 -7.805 7.881 -2.403 1.687 C2 OI3 11 OI3 C4 C12 C 0 1 Y N N N N N 21.916 -2.834 -7.181 6.236 -1.396 0.437 C4 OI3 12 OI3 "C3'" C13 C 0 1 N N R N N N 21.189 -7.178 -8.680 4.005 2.738 0.813 "C3'" OI3 13 OI3 C1D C14 C 0 1 N N R N N N 20.517 -9.295 0.367 -7.715 -1.006 2.017 C1D OI3 14 OI3 C2D C15 C 0 1 N N R N N N 19.031 -9.294 0.861 -8.618 -1.407 0.823 C2D OI3 15 OI3 F1 F1 F 0 1 N N N N N N 23.398 -6.367 -9.022 5.908 1.846 2.014 F1 OI3 16 OI3 N9 N1 N 0 1 Y N N N N N 22.176 -4.155 -7.161 5.188 -0.620 0.012 N9 OI3 17 OI3 N7 N2 N 0 1 Y N N N N N 23.114 -3.283 -5.425 5.828 -1.802 -1.708 N7 OI3 18 OI3 N6 N3 N 0 1 N N N N N N 23.002 -0.208 -4.774 8.145 -3.819 -1.585 N6 OI3 19 OI3 N1 N4 N 0 1 Y N N N N N 21.709 -0.157 -6.758 8.291 -3.136 0.668 N1 OI3 20 OI3 N3 N5 N 0 1 Y N N N N N 21.227 -2.051 -8.017 6.881 -1.553 1.588 N3 OI3 21 OI3 O3D O1 O 0 1 N N N N N N 19.119 -11.755 1.331 -7.591 -3.447 -0.056 O3D OI3 22 OI3 O5D O2 O 0 1 N N N N N N 18.922 -11.132 -3.027 -4.291 -0.238 -0.481 O5D OI3 23 OI3 O1B O3 O 0 1 N N N N N N 17.138 -10.433 -4.737 -4.027 1.818 -1.921 O1B OI3 24 OI3 O2B O4 O 0 1 N N N N N N 19.417 -11.096 -5.518 -2.913 -0.301 -2.719 O2B OI3 25 OI3 O3A O5 O 0 1 N N N N N N 19.044 -8.812 -4.313 -1.994 1.032 -0.648 O3A OI3 26 OI3 O1A O6 O 0 1 N N N N N N 20.587 -6.783 -4.182 -0.551 2.274 -2.304 O1A OI3 27 OI3 O2A O7 O 0 1 N N N N N N 21.638 -9.066 -4.368 -1.428 3.580 -0.331 O2A OI3 28 OI3 "O5'" O8 O 0 1 N N N N N N 20.424 -8.058 -6.394 0.456 1.769 -0.046 "O5'" OI3 29 OI3 "O4'" O9 O 0 1 N N N N N N 20.139 -5.345 -7.819 3.151 0.610 0.220 "O4'" OI3 30 OI3 "O3'" O10 O 0 1 N N N N N N 21.201 -7.103 -10.049 4.029 3.549 1.990 "O3'" OI3 31 OI3 O4D O11 O 0 1 N N N N N N 20.414 -9.767 -0.826 -6.500 -0.551 1.383 O4D OI3 32 OI3 O1D O12 O 0 1 N N N N N N 21.001 -7.968 0.309 -8.315 0.050 2.770 O1D OI3 33 OI3 O2D O13 O 0 1 N N N N N N 18.981 -9.116 2.178 -9.589 -2.376 1.221 O2D OI3 34 OI3 PB P1 P 0 1 N N N N N N 18.615 -10.387 -4.466 -3.322 0.604 -1.452 PB OI3 35 OI3 PA P2 P 0 1 N N N N N N 20.486 -8.174 -4.775 -0.872 2.166 -0.864 PA OI3 36 OI3 "H'4" H1 H 0 1 N N N N N N 19.113 -6.614 -8.952 2.335 1.732 1.785 "H'4" OI3 37 OI3 "H'1" H2 H 0 1 N N N N N N 21.754 -4.642 -9.154 4.309 -0.037 1.837 "H'1" OI3 38 OI3 "H'2" H3 H 0 1 N N N N N N 22.532 -6.594 -7.096 5.791 1.817 -0.035 "H'2" OI3 39 OI3 "HR'3" H4 H 0 0 N N N N N N 17.488 -10.768 0.353 -7.821 -1.717 -1.186 "HR'3" OI3 40 OI3 "HR'4" H5 H 0 0 N N N N N N 19.646 -11.881 -0.816 -5.581 -2.248 0.608 "HR'4" OI3 41 OI3 H5R1 H7 H 0 0 N N N N N N 17.330 -11.266 -1.732 -5.518 -1.321 -1.740 H5R1 OI3 42 OI3 H5R2 H8 H 0 0 N N N N N N 17.999 -9.618 -1.985 -6.209 0.195 -1.114 H5R2 OI3 43 OI3 "H5'1" H9 H 0 0 N N N N N N 18.947 -6.653 -6.161 1.484 3.542 0.219 "H5'1" OI3 44 OI3 "H5'2" H10 H 0 0 N N N N N N 18.548 -8.045 -7.224 2.026 2.538 -1.148 "H5'2" OI3 45 OI3 H8 H11 H 0 1 N N N N N N 23.258 -5.392 -5.789 4.213 -0.454 -1.921 H8 OI3 46 OI3 H2 H12 H 0 1 N N N N N N 20.598 -0.141 -8.511 8.384 -2.506 2.637 H2 OI3 47 OI3 "H'3" H13 H 0 1 N N N N N N 21.305 -8.204 -8.302 4.072 3.358 -0.081 "H'3" OI3 48 OI3 "HR'2" H14 H 0 0 N N N N N N 18.461 -8.537 0.303 -9.099 -0.531 0.388 "HR'2" OI3 49 OI3 H61 H15 H 0 1 N N N N N N 22.789 0.768 -4.814 7.711 -3.745 -2.449 H61 OI3 50 OI3 H62 H16 H 0 1 N N N N N N 22.640 -0.594 -3.925 8.886 -4.433 -1.465 H62 OI3 51 OI3 HOR3 H17 H 0 0 N N N N N N 18.705 -11.667 2.182 -8.420 -3.864 -0.326 HOR3 OI3 52 OI3 HOB2 H18 H 0 0 N N N N N N 18.832 -11.452 -6.177 -2.446 -1.115 -2.487 HOB2 OI3 53 OI3 HOA2 H19 H 0 0 N N N N N N 22.229 -8.583 -3.802 -1.660 3.583 0.608 HOA2 OI3 54 OI3 "HO'3" H20 H 0 0 N N N N N N 22.006 -7.482 -10.380 4.811 4.113 2.063 "HO'3" OI3 55 OI3 HOR1 H22 H 0 0 N N N N N N 21.902 -7.972 0.009 -7.791 0.340 3.529 HOR1 OI3 56 OI3 HOR2 H23 H 0 0 N N N N N N 19.263 -8.234 2.390 -10.252 -2.038 1.839 HOR2 OI3 57 OI3 "HR'1" H6 H 0 0 N N N N N N 21.125 -9.918 1.040 -7.516 -1.867 2.655 "HR'1" OI3 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 OI3 "C4'" "C5'" SING N N 1 OI3 "C4'" "C3'" SING N N 2 OI3 "C4'" "O4'" SING N N 3 OI3 "C1'" "C2'" SING N N 4 OI3 "C1'" N9 SING N N 5 OI3 "C1'" "O4'" SING N N 6 OI3 C5 C6 DOUB Y N 7 OI3 C5 C4 SING Y N 8 OI3 C5 N7 SING Y N 9 OI3 C6 N6 SING N N 10 OI3 C6 N1 SING Y N 11 OI3 "C2'" "C3'" SING N N 12 OI3 "C2'" F1 SING N N 13 OI3 C3D C4D SING N N 14 OI3 C3D C2D SING N N 15 OI3 C3D O3D SING N N 16 OI3 C4D C5D SING N N 17 OI3 C5D O5D SING N N 18 OI3 "C5'" "O5'" SING N N 19 OI3 C8 N9 SING Y N 20 OI3 C8 N7 DOUB Y N 21 OI3 C2 N1 DOUB Y N 22 OI3 C2 N3 SING Y N 23 OI3 C4 N9 SING Y N 24 OI3 C4 N3 DOUB Y N 25 OI3 "C3'" "O3'" SING N N 26 OI3 C1D C2D SING N N 27 OI3 C1D O4D SING N N 28 OI3 C1D O1D SING N N 29 OI3 C2D O2D SING N N 30 OI3 O5D PB SING N N 31 OI3 O1B PB DOUB N N 32 OI3 O2B PB SING N N 33 OI3 O3A PB SING N N 34 OI3 O3A PA SING N N 35 OI3 O1A PA DOUB N N 36 OI3 O2A PA SING N N 37 OI3 "O5'" PA SING N N 38 OI3 "C4'" "H'4" SING N N 39 OI3 "C1'" "H'1" SING N N 40 OI3 "C2'" "H'2" SING N N 41 OI3 C3D "HR'3" SING N N 42 OI3 C4D "HR'4" SING N N 43 OI3 C5D H5R1 SING N N 44 OI3 C5D H5R2 SING N N 45 OI3 "C5'" "H5'1" SING N N 46 OI3 "C5'" "H5'2" SING N N 47 OI3 C8 H8 SING N N 48 OI3 C2 H2 SING N N 49 OI3 "C3'" "H'3" SING N N 50 OI3 C2D "HR'2" SING N N 51 OI3 N6 H61 SING N N 52 OI3 N6 H62 SING N N 53 OI3 O3D HOR3 SING N N 54 OI3 O2B HOB2 SING N N 55 OI3 O2A HOA2 SING N N 56 OI3 "O3'" "HO'3" SING N N 57 OI3 O1D HOR1 SING N N 58 OI3 O2D HOR2 SING N N 59 OI3 C4D O4D SING N N 60 OI3 C1D "HR'1" 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 OI3 InChI InChI 1.06 "InChI=1S/C15H22FN5O13P2/c16-7-9(22)5(32-14(7)21-4-20-8-12(17)18-3-19-13(8)21)1-30-35(26,27)34-36(28,29)31-2-6-10(23)11(24)15(25)33-6/h3-7,9-11,14-15,22-25H,1-2H2,(H,26,27)(H,28,29)(H2,17,18,19)/t5-,6-,7-,9-,10-,11-,14-,15-/m1/s1" OI3 InChIKey InChI 1.06 DGMUNKKEZYJBEL-IUNVFAKASA-N OI3 SMILES_CANONICAL CACTVS 3.385 "Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P](O)(=O)O[P](O)(=O)OC[C@H]4O[C@@H](O)[C@H](O)[C@@H]4O)[C@@H](O)[C@H]3F" OI3 SMILES CACTVS 3.385 "Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(=O)OC[CH]4O[CH](O)[CH](O)[CH]4O)[CH](O)[CH]3F" OI3 SMILES_CANONICAL "OpenEye OEToolkits" 3.1.0.0 "c1nc(c2c(n1)n(cn2)[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)F)N" OI3 SMILES "OpenEye OEToolkits" 3.1.0.0 "c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OCC4C(C(C(O4)O)O)O)O)F)N" # _pdbx_chem_comp_identifier.comp_id OI3 _pdbx_chem_comp_identifier.type "SYSTEMATIC NAME" _pdbx_chem_comp_identifier.program "OpenEye OEToolkits" _pdbx_chem_comp_identifier.program_version 3.1.0.0 _pdbx_chem_comp_identifier.identifier "[[(2~{R},3~{R},4~{R},5~{R})-5-(6-aminopurin-9-yl)-4-fluoranyl-3-oxidanyl-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_synonyms.ordinal _pdbx_chem_comp_synonyms.comp_id _pdbx_chem_comp_synonyms.name _pdbx_chem_comp_synonyms.provenance _pdbx_chem_comp_synonyms.type 1 OI3 "[[(2~{R},3~{R},4~{R},5~{R})-5-(6-aminopurin-9-yl)-4-fluoranyl-3-oxidanyl-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" PDB ? 2 OI3 "[[(2R,3R,4R,5R)-5-(6-aminopurin-9-yl)-4-fluoranyl-3-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2R,3S,4R,5R)-3,4,5-tris(oxidanyl)oxolan-2-yl]methyl hydrogen phosphate" PDB ? 3 OI3 "2'-deoxy-2'-fluoro-ADPR" AUTHOR ? # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site OI3 "Create component" 2022-09-08 PDBE OI3 "Initial release" 2024-03-20 RCSB #