data_DZ # _chem_comp.id DZ _chem_comp.name "[(2~{R},3~{S},5~{R})-5-(6-azanyl-5-nitro-2-oxidanylidene-1~{H}-pyridin-3-yl)-3-oxidanyl-oxolan-2-yl]methyl dihydrogen phosphate" _chem_comp.type "DNA linking" _chem_comp.pdbx_type ATOMN _chem_comp.formula "C10 H14 N3 O9 P" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2018-11-12 _chem_comp.pdbx_modified_date 2019-06-07 _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 351.207 _chem_comp.one_letter_code ? _chem_comp.three_letter_code DZ _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 6I4O _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site EBI # # 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 DZ P P1 P 0 1 N N N 40.099 20.048 20.447 4.648 1.157 0.341 P DZ 1 DZ OP1 O1 O 0 1 N N N 39.989 18.607 20.107 5.985 0.282 0.147 OP1 DZ 2 DZ OP2 O2 O 0 1 N N N 40.745 20.966 19.475 4.387 1.938 -0.888 OP2 DZ 3 DZ "O5'" O3 O 0 1 N N N 38.633 20.600 20.757 3.403 0.177 0.628 "O5'" DZ 4 DZ "C5'" C1 C 0 1 N N N 37.821 19.926 21.706 2.913 -0.761 -0.332 "C5'" DZ 5 DZ "C4'" C2 C 0 1 N N R 36.659 20.801 22.193 1.730 -1.528 0.261 "C4'" DZ 6 DZ "O4'" O4 O 0 1 N N N 37.127 22.046 22.698 0.623 -0.635 0.468 "O4'" DZ 7 DZ "C1'" C3 C 0 1 N N R 36.092 22.990 22.525 -0.582 -1.394 0.229 "C1'" DZ 8 DZ C1 C4 C 0 1 N N N 36.708 24.374 22.541 -1.732 -0.475 -0.093 C1 DZ 9 DZ C2 C5 C 0 1 N N N 36.155 25.385 23.355 -1.615 0.469 -1.119 C2 DZ 10 DZ O2 O5 O 0 1 N N N 35.152 25.238 24.053 -0.575 0.548 -1.755 O2 DZ 11 DZ N3 N1 N 0 1 N N N 36.781 26.576 23.348 -2.641 1.290 -1.408 N3 DZ 12 DZ C4 C6 C 0 1 N N N 37.863 26.856 22.642 -3.809 1.219 -0.710 C4 DZ 13 DZ C5 C7 C 0 1 N N N 38.465 25.906 21.797 -3.960 0.301 0.308 C5 DZ 14 DZ C6 C8 C 0 1 N N N 37.842 24.640 21.752 -2.911 -0.563 0.618 C6 DZ 15 DZ N N2 N 1 1 N N N 39.677 26.164 20.973 -5.231 0.228 1.062 N DZ 16 DZ ON1 O6 O -1 1 N N N 39.905 25.398 20.045 -5.324 -0.507 2.029 ON1 DZ 17 DZ ON2 O7 O 0 1 N N N 40.441 27.074 21.284 -6.183 0.905 0.717 ON2 DZ 18 DZ N4 N3 N 0 1 N N N 38.338 28.081 22.783 -4.845 2.068 -1.023 N4 DZ 19 DZ "C2'" C9 C 0 1 N N N 35.425 22.600 21.211 -0.221 -2.267 -1.000 "C2'" DZ 20 DZ "C3'" C10 C 0 1 N N S 35.608 21.085 21.107 1.262 -2.616 -0.725 "C3'" DZ 21 DZ "O3'" O8 O 0 1 N N N 34.424 20.343 21.390 1.369 -3.911 -0.130 "O3'" DZ 22 DZ OP3 O9 O 0 1 N Y N 40.835 20.174 21.881 4.838 2.161 1.585 OP3 DZ 23 DZ H1 H1 H 0 1 N N N 40.374 18.453 19.252 6.218 -0.257 0.916 H1 DZ 24 DZ "H5''" H2 H 0 0 N N N 37.411 19.018 21.241 2.590 -0.230 -1.227 "H5''" DZ 25 DZ "H5'" H3 H 0 1 N N N 38.442 19.647 22.570 3.706 -1.462 -0.593 "H5'" DZ 26 DZ "H4'" H4 H 0 1 N N N 36.154 20.256 23.004 2.020 -1.984 1.208 "H4'" DZ 27 DZ "H1'" H5 H 0 1 N N N 35.356 22.912 23.339 -0.820 -2.018 1.090 "H1'" DZ 28 DZ H3 H6 H 0 1 N N N 36.400 27.303 23.919 -2.549 1.941 -2.121 H3 DZ 29 DZ H6 H7 H 0 1 N N N 38.239 23.870 21.107 -3.016 -1.287 1.413 H6 DZ 30 DZ H42 H8 H 0 1 N N N 37.765 28.589 23.426 -4.716 2.768 -1.681 H42 DZ 31 DZ H41 H9 H 0 1 N N N 39.274 28.037 23.134 -5.704 1.967 -0.584 H41 DZ 32 DZ "H2''" H10 H 0 0 N N N 35.912 23.107 20.365 -0.833 -3.168 -1.030 "H2''" DZ 33 DZ "H2'" H11 H 0 1 N N N 34.356 22.860 21.228 -0.322 -1.699 -1.924 "H2'" DZ 34 DZ "H3'" H12 H 0 1 N N N 36.016 20.826 20.119 1.842 -2.572 -1.647 "H3'" DZ 35 DZ H2 H13 H 0 1 N N N 34.605 19.414 21.308 1.034 -4.628 -0.685 H2 DZ 36 DZ H4 H14 H 0 1 N N N 41.537 20.811 21.822 5.572 2.782 1.481 H4 DZ 37 # # 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 DZ OP2 P DOUB N N 1 DZ ON1 N SING N N 2 DZ OP1 P SING N N 3 DZ P "O5'" SING N N 4 DZ "O5'" "C5'" SING N N 5 DZ N ON2 DOUB N N 6 DZ N C5 SING N N 7 DZ "C3'" "C2'" SING N N 8 DZ "C3'" "O3'" SING N N 9 DZ "C3'" "C4'" SING N N 10 DZ "C2'" "C1'" SING N N 11 DZ "C5'" "C4'" SING N N 12 DZ C6 C5 SING N N 13 DZ C6 C1 DOUB N N 14 DZ C5 C4 DOUB N N 15 DZ "C4'" "O4'" SING N N 16 DZ "C1'" C1 SING N N 17 DZ "C1'" "O4'" SING N N 18 DZ C1 C2 SING N N 19 DZ C4 N4 SING N N 20 DZ C4 N3 SING N N 21 DZ N3 C2 SING N N 22 DZ C2 O2 DOUB N N 23 DZ P OP3 SING N N 24 DZ OP1 H1 SING N N 25 DZ "C5'" "H5''" SING N N 26 DZ "C5'" "H5'" SING N N 27 DZ "C4'" "H4'" SING N N 28 DZ "C1'" "H1'" SING N N 29 DZ N3 H3 SING N N 30 DZ C6 H6 SING N N 31 DZ N4 H42 SING N N 32 DZ N4 H41 SING N N 33 DZ "C2'" "H2''" SING N N 34 DZ "C2'" "H2'" SING N N 35 DZ "C3'" "H3'" SING N N 36 DZ "O3'" H2 SING N N 37 DZ OP3 H4 SING N N 38 # # 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 DZ InChI InChI 1.03 "InChI=1S/C10H14N3O9P/c11-9-5(13(16)17)1-4(10(15)12-9)7-2-6(14)8(22-7)3-21-23(18,19)20/h1,6-8,14H,2-3H2,(H3,11,12,15)(H2,18,19,20)/t6-,7+,8+/m0/s1" DZ InChIKey InChI 1.03 IUUXEDXPTYNSEU-XLPZGREQSA-N DZ SMILES_CANONICAL CACTVS 3.385 "NC1=C(C=C([C@H]2C[C@H](O)[C@@H](CO[P](O)(O)=O)O2)C(=O)N1)[N+]([O-])=O" DZ SMILES CACTVS 3.385 "NC1=C(C=C([CH]2C[CH](O)[CH](CO[P](O)(O)=O)O2)C(=O)N1)[N+]([O-])=O" DZ SMILES_CANONICAL "OpenEye OEToolkits" 2.0.6 "C1[C@@H]([C@H](O[C@H]1C2=CC(=C(NC2=O)N)[N+](=O)[O-])COP(=O)(O)O)O" DZ SMILES "OpenEye OEToolkits" 2.0.6 "C1C(C(OC1C2=CC(=C(NC2=O)N)[N+](=O)[O-])COP(=O)(O)O)O" # _pdbx_chem_comp_identifier.comp_id DZ _pdbx_chem_comp_identifier.type "SYSTEMATIC NAME" _pdbx_chem_comp_identifier.program "OpenEye OEToolkits" _pdbx_chem_comp_identifier.program_version 2.0.6 _pdbx_chem_comp_identifier.identifier "[(2~{R},3~{S},5~{R})-5-(6-azanyl-5-nitro-2-oxidanylidene-1~{H}-pyridin-3-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 DZ "Create component" 2018-11-12 EBI DZ "Initial release" 2019-06-12 RCSB ##