data_RDG # _chem_comp.id RDG _chem_comp.name "2'-deoxy-N-(furan-2-ylmethyl)guanosine 5'-(dihydrogen phosphate)" _chem_comp.type "DNA LINKING" _chem_comp.pdbx_type ATOMN _chem_comp.formula "C15 H18 N5 O8 P" _chem_comp.mon_nstd_parent_comp_id DG _chem_comp.pdbx_synonyms "N2-furfuryl-deoxyguanosine-5'-monophosphate" _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2013-04-22 _chem_comp.pdbx_modified_date 2020-06-17 _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 427.306 _chem_comp.one_letter_code ? _chem_comp.three_letter_code RDG _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 4K2Q _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site PDBJ # # 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 RDG OP3 OP3 O 0 1 N Y N 5.527 -26.897 26.901 6.731 0.748 -2.391 OP3 RDG 1 RDG OP2 OP2 O 0 1 N N N 5.086 -24.742 28.409 6.805 -0.891 -0.337 OP2 RDG 2 RDG P P P 0 1 N N N 5.787 -25.334 27.162 6.402 0.590 -0.823 P RDG 3 RDG OP1 OP1 O 0 1 N N N 5.333 -24.613 25.921 7.175 1.589 -0.053 OP1 RDG 4 RDG "O5'" "O5'" O 0 1 N N N 7.333 -25.252 27.458 4.828 0.825 -0.579 "O5'" RDG 5 RDG "C5'" "C5'" C 0 1 N N N 8.286 -25.900 26.708 4.238 0.854 0.723 "C5'" RDG 6 RDG "C4'" "C4'" C 0 1 N N R 9.638 -25.293 26.690 2.733 1.097 0.595 "C4'" RDG 7 RDG "C3'" "C3'" C 0 1 N N S 9.703 -23.870 27.120 2.094 1.258 1.993 "C3'" RDG 8 RDG "O3'" "O3'" O 0 1 N N N 11.014 -23.482 27.322 1.923 2.641 2.309 "O3'" RDG 9 RDG "C2'" "C2'" C 0 1 N N N 9.140 -23.155 25.982 0.722 0.559 1.860 "C2'" RDG 10 RDG "C1'" "C1'" C 0 1 N N R 9.557 -23.984 24.772 0.694 0.059 0.399 "C1'" RDG 11 RDG "O4'" "O4'" O 0 1 N N N 10.071 -25.245 25.383 2.084 -0.060 0.023 "O4'" RDG 12 RDG N9 N9 N 0 1 Y N N 8.621 -24.133 23.553 0.031 -1.244 0.319 N9 RDG 13 RDG C4 C4 C 0 1 Y N N 9.053 -24.110 22.241 -1.310 -1.461 0.150 C4 RDG 14 RDG N3 N3 N 0 1 N N N 10.310 -23.955 21.665 -2.375 -0.662 0.018 N3 RDG 15 RDG C2 C2 C 0 1 N N N 10.425 -23.978 20.320 -3.582 -1.158 -0.135 C2 RDG 16 RDG N1 N1 N 0 1 N N N 9.342 -24.150 19.535 -3.810 -2.502 -0.167 N1 RDG 17 RDG C6 C6 C 0 1 N N N 8.094 -24.308 20.056 -2.783 -3.371 -0.040 C6 RDG 18 RDG O6 O6 O 0 1 N N N 7.001 -24.474 19.284 -2.976 -4.575 -0.068 O6 RDG 19 RDG C5 C5 C 0 1 Y N N 7.931 -24.286 21.471 -1.478 -2.850 0.125 C5 RDG 20 RDG N7 N7 N 0 1 Y N N 6.832 -24.413 22.320 -0.252 -3.407 0.278 N7 RDG 21 RDG C8 C8 C 0 1 Y N N 7.282 -24.321 23.576 0.638 -2.465 0.392 C8 RDG 22 RDG N2 N2 N 0 1 N N N 11.717 -23.804 19.738 -4.644 -0.299 -0.266 N2 RDG 23 RDG C11 C11 C 0 1 N N N 12.840 -23.435 20.554 -4.423 1.149 -0.235 C11 RDG 24 RDG C10 C10 C 0 1 Y N N 13.723 -24.588 21.004 -5.741 1.862 -0.398 C10 RDG 25 RDG C9 C9 C 0 1 Y N N 13.777 -25.124 22.296 -6.564 2.231 0.599 C9 RDG 26 RDG O7 O7 O 0 1 Y N N 14.561 -25.265 20.234 -6.289 2.241 -1.564 O7 RDG 27 RDG C12 C12 C 0 1 Y N N 15.181 -26.220 20.922 -7.464 2.848 -1.330 C12 RDG 28 RDG C7 C7 C 0 1 Y N N 14.748 -26.208 22.246 -7.676 2.865 -0.002 C7 RDG 29 RDG H1 H1 H 0 1 N N N 5.151 -27.016 26.037 7.663 0.619 -2.612 H1 RDG 30 RDG H2 H2 H 0 1 N N N 4.506 -24.038 28.143 6.335 -1.599 -0.800 H2 RDG 31 RDG H3 H3 H 0 1 N N N 7.924 -25.941 25.670 4.412 -0.099 1.222 H3 RDG 32 RDG H4 H4 H 0 1 N N N 8.384 -26.922 27.102 4.688 1.658 1.307 H4 RDG 33 RDG H5 H5 H 0 1 N N N 10.319 -25.894 27.310 2.542 1.981 -0.013 H5 RDG 34 RDG H6 H6 H 0 1 N N N 9.087 -23.716 28.019 2.704 0.766 2.750 H6 RDG 35 RDG "HO3'" "HO3'" H 0 0 N Y N 11.373 -23.953 28.065 1.526 2.799 3.176 "HO3'" RDG 36 RDG H8 H8 H 0 1 N N N 9.553 -22.137 25.918 0.652 -0.280 2.553 H8 RDG 37 RDG H9 H9 H 0 1 N N N 8.044 -23.102 26.059 -0.086 1.268 2.039 H9 RDG 38 RDG H10 H10 H 0 1 N N N 10.448 -23.474 24.376 0.189 0.784 -0.240 H10 RDG 39 RDG H12 H12 H 0 1 N N N 6.674 -24.386 24.466 1.698 -2.624 0.521 H12 RDG 40 RDG H13 H13 H 0 1 N N N 11.841 -23.940 18.755 -5.541 -0.650 -0.380 H13 RDG 41 RDG H14 H14 H 0 1 N N N 13.463 -22.735 19.978 -3.975 1.428 0.719 H14 RDG 42 RDG H15 H15 H 0 1 N N N 12.456 -22.930 21.453 -3.754 1.432 -1.047 H15 RDG 43 RDG H16 H16 H 0 1 N N N 13.212 -24.799 23.157 -6.406 2.074 1.656 H16 RDG 44 RDG H17 H17 H 0 1 N N N 15.912 -26.903 20.515 -8.125 3.256 -2.080 H17 RDG 45 RDG H18 H18 H 0 1 N N N 15.061 -26.855 23.052 -8.533 3.282 0.508 H18 RDG 46 RDG H11 H11 H 0 1 N N N 9.459 -24.162 18.542 -4.713 -2.835 -0.281 H11 RDG 47 # # 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 RDG O6 C6 DOUB N N 1 RDG N1 C6 SING N N 2 RDG N1 C2 SING N N 3 RDG N2 C2 SING N N 4 RDG N2 C11 SING N N 5 RDG C6 C5 SING N N 6 RDG O7 C12 SING Y N 7 RDG O7 C10 SING Y N 8 RDG C2 N3 DOUB N N 9 RDG C11 C10 SING N N 10 RDG C12 C7 DOUB Y N 11 RDG C10 C9 DOUB Y N 12 RDG C5 C4 DOUB Y N 13 RDG C5 N7 SING Y N 14 RDG N3 C4 SING N N 15 RDG C4 N9 SING Y N 16 RDG C7 C9 SING Y N 17 RDG N7 C8 DOUB Y N 18 RDG N9 C8 SING Y N 19 RDG N9 "C1'" SING N N 20 RDG "C1'" "O4'" SING N N 21 RDG "C1'" "C2'" SING N N 22 RDG "O4'" "C4'" SING N N 23 RDG OP1 P DOUB N N 24 RDG "C2'" "C3'" SING N N 25 RDG "C4'" "C5'" SING N N 26 RDG "C4'" "C3'" SING N N 27 RDG "C5'" "O5'" SING N N 28 RDG OP3 P SING N N 29 RDG "C3'" "O3'" SING N N 30 RDG P "O5'" SING N N 31 RDG P OP2 SING N N 32 RDG OP3 H1 SING N N 33 RDG OP2 H2 SING N N 34 RDG "C5'" H3 SING N N 35 RDG "C5'" H4 SING N N 36 RDG "C4'" H5 SING N N 37 RDG "C3'" H6 SING N N 38 RDG "O3'" "HO3'" SING N N 39 RDG "C2'" H8 SING N N 40 RDG "C2'" H9 SING N N 41 RDG "C1'" H10 SING N N 42 RDG C8 H12 SING N N 43 RDG N2 H13 SING N N 44 RDG C11 H14 SING N N 45 RDG C11 H15 SING N N 46 RDG C9 H16 SING N N 47 RDG C12 H17 SING N N 48 RDG C7 H18 SING N N 49 RDG N1 H11 SING N N 50 # # 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 RDG SMILES ACDLabs 12.01 "O=P(O)(O)OCC4OC(n3cnc2c3N=C(NCc1occc1)NC2=O)CC4O" RDG InChI InChI 1.03 "InChI=1S/C15H18N5O8P/c21-9-4-11(28-10(9)6-27-29(23,24)25)20-7-17-12-13(20)18-15(19-14(12)22)16-5-8-2-1-3-26-8/h1-3,7,9-11,21H,4-6H2,(H2,23,24,25)(H2,16,18,19,22)/t9-,10+,11+/m0/s1" RDG InChIKey InChI 1.03 DBFJIGOYTNZKTK-HBNTYKKESA-N RDG SMILES_CANONICAL CACTVS 3.370 "O[C@H]1C[C@@H](O[C@@H]1CO[P](O)(O)=O)n2cnc3C(=O)NC(=Nc23)NCc4occc4" RDG SMILES CACTVS 3.370 "O[CH]1C[CH](O[CH]1CO[P](O)(O)=O)n2cnc3C(=O)NC(=Nc23)NCc4occc4" RDG SMILES_CANONICAL "OpenEye OEToolkits" 1.7.6 "c1cc(oc1)CNC2=Nc3c(ncn3[C@H]4C[C@@H]([C@H](O4)COP(=O)(O)O)O)C(=O)N2" RDG SMILES "OpenEye OEToolkits" 1.7.6 "c1cc(oc1)CNC2=Nc3c(ncn3C4CC(C(O4)COP(=O)(O)O)O)C(=O)N2" # # 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 RDG "SYSTEMATIC NAME" ACDLabs 12.01 "2'-deoxy-N-(furan-2-ylmethyl)guanosine 5'-(dihydrogen phosphate)" RDG "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.7.6 "[(2R,3S,5R)-5-[2-(furan-2-ylmethylamino)-6-oxidanylidene-1H-purin-9-yl]-3-oxidanyl-oxolan-2-yl]methyl dihydrogen 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 RDG "Create component" 2013-04-22 PDBJ RDG "Initial release" 2015-05-06 RCSB RDG "Modify synonyms" 2020-06-05 PDBE # _pdbx_chem_comp_synonyms.ordinal 1 _pdbx_chem_comp_synonyms.comp_id RDG _pdbx_chem_comp_synonyms.name "N2-furfuryl-deoxyguanosine-5'-monophosphate" _pdbx_chem_comp_synonyms.provenance ? _pdbx_chem_comp_synonyms.type ? ##