data_D3N # _chem_comp.id D3N _chem_comp.name "1-(2-deoxy-5-O-phosphono-beta-D-erythro-pentofuranosyl)-1H-perimidin-2(3H)-one" _chem_comp.type "DNA LINKING" _chem_comp.pdbx_type ATOMN _chem_comp.formula "C16 H17 N2 O7 P" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2012-11-02 _chem_comp.pdbx_modified_date 2013-06-07 _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 380.289 _chem_comp.one_letter_code ? _chem_comp.three_letter_code D3N _chem_comp.pdbx_model_coordinates_details ? _chem_comp.pdbx_model_coordinates_missing_flag Y _chem_comp.pdbx_ideal_coordinates_details Corina _chem_comp.pdbx_ideal_coordinates_missing_flag N _chem_comp.pdbx_model_coordinates_db_code 4HQI _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site RCSB # 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 D3N O1P O1P O 0 1 N N N 9.151 11.502 5.034 -6.295 -0.278 0.125 O1P D3N 1 D3N P P P 0 1 N N N 10.467 10.803 4.830 -4.990 -1.154 0.474 P D3N 2 D3N O2P O2P O 0 1 N N N 11.529 11.563 4.178 -4.745 -2.129 -0.612 O2P D3N 3 D3N "O5'" "O5'" O 0 1 N N N 10.132 9.407 4.099 -3.714 -0.183 0.621 "O5'" D3N 4 D3N "C5'" "C5'" C 0 1 N N N 9.339 9.445 2.962 -3.183 0.574 -0.468 "C5'" D3N 5 D3N "C4'" "C4'" C 0 1 N N R 9.661 8.312 2.011 -1.979 1.386 0.014 "C4'" D3N 6 D3N "O4'" "O4'" O 0 1 N N N 8.863 7.224 2.387 -0.891 0.511 0.382 "O4'" D3N 7 D3N "C3'" "C3'" C 0 1 N N S 9.320 8.677 0.601 -1.390 2.229 -1.145 "C3'" D3N 8 D3N "O3'" "O3'" O 0 1 N N N 10.640 8.976 -0.003 -2.065 3.483 -1.258 "O3'" D3N 9 D3N "C2'" "C2'" C 0 1 N N N 8.658 7.422 0.042 0.076 2.429 -0.687 "C2'" D3N 10 D3N "C1'" "C1'" C 0 1 N N R 8.417 6.534 1.230 0.313 1.294 0.327 "C1'" D3N 11 D3N N1 N1 N 0 1 N N N 7.078 6.124 1.580 1.431 0.457 -0.115 N1 D3N 12 D3N C2 C2 C 0 1 N N N 6.110 7.057 1.685 1.299 -0.310 -1.214 C2 D3N 13 D3N O2 O2 O 0 1 N N N 6.297 8.251 1.417 0.245 -0.290 -1.820 O2 D3N 14 D3N N3 N3 N 0 1 N N N 4.887 6.635 2.099 2.293 -1.098 -1.667 N3 D3N 15 D3N C4 C4 C 0 1 Y N N 4.594 5.301 2.451 3.514 -1.147 -0.999 C4 D3N 16 D3N C5 C5 C 0 1 Y N N 5.607 4.371 2.331 3.685 -0.356 0.155 C5 D3N 17 D3N C6 C6 C 0 1 Y N N 6.891 4.763 1.888 2.627 0.463 0.600 C6 D3N 18 D3N C7 C7 C 0 1 Y N N 7.850 3.823 1.781 2.804 1.236 1.724 C7 D3N 19 D3N C8 C8 C 0 1 Y N N 7.548 2.482 2.091 4.017 1.213 2.411 C8 D3N 20 D3N C9 C9 C 0 1 Y N N 6.313 2.075 2.503 5.055 0.433 1.996 C9 D3N 21 D3N C10 C10 C 0 1 Y N N 5.329 3.022 2.649 4.909 -0.380 0.859 C10 D3N 22 D3N C11 C11 C 0 1 Y N N 4.040 2.682 3.115 5.947 -1.202 0.389 C11 D3N 23 D3N C12 C12 C 0 1 Y N N 3.039 3.617 3.226 5.759 -1.959 -0.730 C12 D3N 24 D3N C13 C13 C 0 1 Y N N 3.306 4.953 2.885 4.554 -1.940 -1.428 C13 D3N 25 D3N H1 H1 H 0 1 N N N 9.205 12.386 4.690 -6.515 0.383 0.796 H1 D3N 26 D3N H3 H3 H 0 1 N N N 9.505 10.401 2.445 -2.870 -0.103 -1.263 H3 D3N 27 D3N H4 H4 H 0 1 N N N 8.283 9.368 3.262 -3.949 1.251 -0.847 H4 D3N 28 D3N H5 H5 H 0 1 N N N 10.730 8.064 2.083 -2.259 2.024 0.853 H5 D3N 29 D3N H6 H6 H 0 1 N N N 8.641 9.541 0.556 -1.432 1.680 -2.086 H6 D3N 30 D3N H7 H7 H 0 1 N N N 10.996 9.766 0.387 -1.732 4.046 -1.970 H7 D3N 31 D3N H8 H8 H 0 1 N N N 7.706 7.675 -0.449 0.756 2.334 -1.533 H8 D3N 32 D3N H9 H9 H 0 1 N N N 9.323 6.926 -0.681 0.196 3.401 -0.207 H9 D3N 33 D3N H10 H10 H 0 1 N N N 9.032 5.631 1.100 0.531 1.714 1.309 H10 D3N 34 D3N H11 H11 H 0 1 N N N 4.151 7.310 2.158 2.157 -1.635 -2.463 H11 D3N 35 D3N H12 H12 H 0 1 N N N 8.844 4.096 1.460 2.000 1.864 2.077 H12 D3N 36 D3N H13 H13 H 0 1 N N N 8.330 1.743 1.998 4.137 1.827 3.291 H13 D3N 37 D3N H14 H14 H 0 1 N N N 6.114 1.034 2.709 5.985 0.433 2.545 H14 D3N 38 D3N H15 H15 H 0 1 N N N 3.835 1.658 3.392 6.891 -1.235 0.912 H15 D3N 39 D3N H16 H16 H 0 1 N N N 2.058 3.328 3.572 6.564 -2.587 -1.083 H16 D3N 40 D3N H17 H17 H 0 1 N N N 2.531 5.702 2.956 4.435 -2.550 -2.311 H17 D3N 41 D3N OP3 OP3 O 0 1 N Y N ? ? ? -5.227 -1.942 1.859 OP3 D3N 42 D3N H2 H2 H 0 1 N Y N ? ? ? -5.981 -2.547 1.842 H2 D3N 43 # 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 D3N "O3'" "C3'" SING N N 1 D3N "C2'" "C3'" SING N N 2 D3N "C2'" "C1'" SING N N 3 D3N "C3'" "C4'" SING N N 4 D3N "C1'" N1 SING N N 5 D3N "C1'" "O4'" SING N N 6 D3N O2 C2 DOUB N N 7 D3N N1 C2 SING N N 8 D3N N1 C6 SING N N 9 D3N C2 N3 SING N N 10 D3N C7 C6 DOUB Y N 11 D3N C7 C8 SING Y N 12 D3N C6 C5 SING Y N 13 D3N "C4'" "O4'" SING N N 14 D3N "C4'" "C5'" SING N N 15 D3N C8 C9 DOUB Y N 16 D3N N3 C4 SING N N 17 D3N C5 C4 DOUB Y N 18 D3N C5 C10 SING Y N 19 D3N C4 C13 SING Y N 20 D3N C9 C10 SING Y N 21 D3N C10 C11 DOUB Y N 22 D3N C13 C12 DOUB Y N 23 D3N "C5'" "O5'" SING N N 24 D3N C11 C12 SING Y N 25 D3N "O5'" P SING N N 26 D3N O2P P DOUB N N 27 D3N P O1P SING N N 28 D3N O1P H1 SING N N 29 D3N "C5'" H3 SING N N 30 D3N "C5'" H4 SING N N 31 D3N "C4'" H5 SING N N 32 D3N "C3'" H6 SING N N 33 D3N "O3'" H7 SING N N 34 D3N "C2'" H8 SING N N 35 D3N "C2'" H9 SING N N 36 D3N "C1'" H10 SING N N 37 D3N N3 H11 SING N N 38 D3N C7 H12 SING N N 39 D3N C8 H13 SING N N 40 D3N C9 H14 SING N N 41 D3N C11 H15 SING N N 42 D3N C12 H16 SING N N 43 D3N C13 H17 SING N N 44 D3N P OP3 SING N N 45 D3N OP3 H2 SING N N 46 # 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 D3N SMILES ACDLabs 12.01 "O=P(O)(O)OCC4OC(N1C(=O)Nc3c2c1cccc2ccc3)CC4O" D3N InChI InChI 1.03 "InChI=1S/C16H17N2O7P/c19-12-7-14(25-13(12)8-24-26(21,22)23)18-11-6-2-4-9-3-1-5-10(15(9)11)17-16(18)20/h1-6,12-14,19H,7-8H2,(H,17,20)(H2,21,22,23)/t12-,13+,14+/m0/s1" D3N InChIKey InChI 1.03 SQPAXPCPGSJUFJ-BFHYXJOUSA-N D3N SMILES_CANONICAL CACTVS 3.370 "O[C@H]1C[C@@H](O[C@@H]1CO[P](O)(O)=O)N2C(=O)Nc3cccc4cccc2c34" D3N SMILES CACTVS 3.370 "O[CH]1C[CH](O[CH]1CO[P](O)(O)=O)N2C(=O)Nc3cccc4cccc2c34" D3N SMILES_CANONICAL "OpenEye OEToolkits" 1.7.6 "c1cc2cccc3c2c(c1)NC(=O)N3[C@H]4C[C@@H]([C@H](O4)COP(=O)(O)O)O" D3N SMILES "OpenEye OEToolkits" 1.7.6 "c1cc2cccc3c2c(c1)NC(=O)N3C4CC(C(O4)COP(=O)(O)O)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 D3N "SYSTEMATIC NAME" ACDLabs 12.01 "1-(2-deoxy-5-O-phosphono-beta-D-erythro-pentofuranosyl)-1H-perimidin-2(3H)-one" D3N "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.7.6 "[(2R,3S,5R)-3-oxidanyl-5-(2-oxidanylidene-3H-perimidin-1-yl)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 D3N "Create component" 2012-11-02 RCSB D3N "Initial release" 2013-06-12 RCSB #