data_NDU # _chem_comp.id NDU _chem_comp.name "2'-DEOXY-5-NITROURIDINE 5'-MONOPHOSPHATE" _chem_comp.type "DNA LINKING" _chem_comp.pdbx_type ATOMN _chem_comp.formula "C9 H14 N3 O10 P" _chem_comp.mon_nstd_parent_comp_id DU _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2007-10-27 _chem_comp.pdbx_modified_date 2019-05-07 _chem_comp.pdbx_ambiguous_flag ? _chem_comp.pdbx_release_status REL _chem_comp.pdbx_replaced_by ? _chem_comp.pdbx_replaces ? _chem_comp.formula_weight 355.195 _chem_comp.one_letter_code U _chem_comp.three_letter_code NDU _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 2VF0 _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 NDU P P P 0 1 N N N 15.190 24.243 25.855 -4.291 1.194 0.147 P NDU 1 NDU OP1 OP1 O 0 1 N N N 14.052 25.000 25.279 -5.489 0.331 0.251 OP1 NDU 2 NDU OP2 OP2 O 0 1 N N N 16.168 25.119 26.563 -4.598 2.419 -0.852 OP2 NDU 3 NDU OP3 OP3 O 0 1 N N N 15.687 23.295 24.822 -3.917 1.770 1.603 OP3 NDU 4 NDU "O5'" "O5'" O 0 1 N N N 14.758 23.340 27.090 -3.056 0.333 -0.423 "O5'" NDU 5 NDU "C5'" "C5'" C 0 1 N N N 15.423 22.370 27.854 -2.608 -0.881 0.183 "C5'" NDU 6 NDU "C4'" "C4'" C 0 1 N N R 14.865 22.227 29.256 -1.423 -1.438 -0.608 "C4'" NDU 7 NDU "C3'" "C3'" C 0 1 N N S 15.129 23.279 30.328 -1.001 -2.814 -0.046 "C3'" NDU 8 NDU "O3'" "O3'" O 0 1 N N N 14.049 23.447 31.235 -1.556 -3.868 -0.835 "O3'" NDU 9 NDU "C2'" "C2'" C 0 1 N N N 16.394 22.809 31.025 0.540 -2.808 -0.158 "C2'" NDU 10 NDU "C1'" "C1'" C 0 1 N N R 16.214 21.283 30.990 0.867 -1.430 -0.774 "C1'" NDU 11 NDU "O4'" "O4'" O 0 1 N N N 15.309 21.010 29.888 -0.262 -0.596 -0.433 "O4'" NDU 12 NDU N1 N1 N 0 1 N N N 17.535 20.612 31.200 2.096 -0.888 -0.188 N1 NDU 13 NDU C2 C2 C 0 1 N N N 18.144 20.306 32.483 2.125 -0.572 1.117 C2 NDU 14 NDU O2 O2 O 0 1 N N N 18.066 21.020 33.439 1.164 -0.838 1.812 O2 NDU 15 NDU N3 N3 N 0 1 N N N 18.862 19.104 32.614 3.189 0.030 1.672 N3 NDU 16 NDU C4 C4 C 0 1 N N N 19.339 18.261 31.574 4.165 0.555 0.908 C4 NDU 17 NDU O4 O4 O 0 1 N N N 20.254 17.484 31.735 5.156 1.023 1.426 O4 NDU 18 NDU C5 C5 C 0 1 N N R 18.607 18.369 30.165 4.024 0.561 -0.594 C5 NDU 19 NDU C6 C6 C 0 1 N N N 17.814 19.765 29.851 3.278 -0.705 -1.033 C6 NDU 20 NDU N5 N5 N 1 1 N N N 18.831 17.494 29.096 3.273 1.747 -1.010 N5 NDU 21 NDU O51 O51 O -1 1 N N N 19.445 16.416 29.225 3.784 2.561 -1.759 O51 NDU 22 NDU O52 O52 O 0 1 N N N 18.472 17.650 27.908 2.136 1.920 -0.609 O52 NDU 23 NDU HP2 HP2 H 0 1 N N N 16.901 25.305 25.988 -5.332 2.982 -0.570 HP2 NDU 24 NDU HP3 HP3 H 0 1 N N N 15.793 23.753 23.996 -3.140 2.346 1.611 HP3 NDU 25 NDU "H51'" "1H5'" H 0 0 N N N 15.323 21.401 27.343 -2.300 -0.682 1.209 "H51'" NDU 26 NDU "H52'" "2H5'" H 0 0 N N N 16.472 22.688 27.949 -3.420 -1.609 0.182 "H52'" NDU 27 NDU "H4'" "H4'" H 0 1 N N N 13.802 22.302 28.985 -1.677 -1.521 -1.664 "H4'" NDU 28 NDU "H3'" "H3'" H 0 1 N N N 15.243 24.278 29.881 -1.310 -2.913 0.994 "H3'" NDU 29 NDU HA HA H 0 1 N N N 14.384 23.485 32.123 -1.323 -4.755 -0.526 HA NDU 30 NDU "H21'" "1H2'" H 0 0 N N N 17.304 23.133 30.499 0.995 -2.904 0.828 "H21'" NDU 31 NDU "H22'" "2H2'" H 0 0 N N N 16.523 23.219 32.037 0.878 -3.610 -0.814 "H22'" NDU 32 NDU "H1'" "H1'" H 0 1 N N N 15.690 20.787 31.820 0.966 -1.512 -1.856 "H1'" NDU 33 NDU H611 1H61 H 0 0 N N N 16.850 19.525 29.379 3.934 -1.570 -0.933 H611 NDU 34 NDU H612 2H61 H 0 0 N N N 18.443 20.375 29.186 2.969 -0.601 -2.073 H612 NDU 35 NDU H3 H3 H 0 1 N N N 19.060 18.808 33.548 3.256 0.088 2.638 H3 NDU 36 NDU H5 H5 H 0 1 N N N 17.934 17.572 30.515 5.013 0.576 -1.052 H5 NDU 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 NDU P OP1 DOUB N N 1 NDU P OP2 SING N N 2 NDU P OP3 SING N N 3 NDU P "O5'" SING N N 4 NDU "O5'" "C5'" SING N N 5 NDU "C5'" "C4'" SING N N 6 NDU "C4'" "C3'" SING N N 7 NDU "C4'" "O4'" SING N N 8 NDU "C3'" "O3'" SING N N 9 NDU "C3'" "C2'" SING N N 10 NDU "C2'" "C1'" SING N N 11 NDU "C1'" "O4'" SING N N 12 NDU "C1'" N1 SING N N 13 NDU N1 C2 SING N N 14 NDU N1 C6 SING N N 15 NDU C2 O2 DOUB N N 16 NDU C2 N3 SING N N 17 NDU N3 C4 SING N N 18 NDU C4 O4 DOUB N N 19 NDU C4 C5 SING N N 20 NDU C5 C6 SING N N 21 NDU C5 N5 SING N N 22 NDU N5 O51 SING N N 23 NDU N5 O52 DOUB N N 24 NDU OP2 HP2 SING N N 25 NDU OP3 HP3 SING N N 26 NDU "C5'" "H51'" SING N N 27 NDU "C5'" "H52'" SING N N 28 NDU "C4'" "H4'" SING N N 29 NDU "C3'" "H3'" SING N N 30 NDU "O3'" HA SING N N 31 NDU "C2'" "H21'" SING N N 32 NDU "C2'" "H22'" SING N N 33 NDU "C1'" "H1'" SING N N 34 NDU C6 H611 SING N N 35 NDU C6 H612 SING N N 36 NDU N3 H3 SING N N 37 NDU C5 H5 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 NDU SMILES ACDLabs 10.04 "[O-][N+](=O)C1C(=O)NC(=O)N(C1)C2OC(C(O)C2)COP(=O)(O)O" NDU SMILES_CANONICAL CACTVS 3.341 "O[C@H]1C[C@@H](O[C@@H]1CO[P](O)(O)=O)N2C[C@H](C(=O)NC2=O)[N+]([O-])=O" NDU SMILES CACTVS 3.341 "O[CH]1C[CH](O[CH]1CO[P](O)(O)=O)N2C[CH](C(=O)NC2=O)[N+]([O-])=O" NDU SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "C1[C@@H]([C@H](O[C@H]1N2CC(C(=O)NC2=O)[N+](=O)[O-])COP(=O)(O)O)O" NDU SMILES "OpenEye OEToolkits" 1.5.0 "C1C(C(OC1N2CC(C(=O)NC2=O)[N+](=O)[O-])COP(=O)(O)O)O" NDU InChI InChI 1.03 "InChI=1S/C9H14N3O10P/c13-5-1-7(22-6(5)3-21-23(18,19)20)11-2-4(12(16)17)8(14)10-9(11)15/h4-7,13H,1-3H2,(H,10,14,15)(H2,18,19,20)/t4-,5+,6-,7-/m1/s1" NDU InChIKey InChI 1.03 ZYBJIJYGXJSDTC-XZBKPIIZSA-N # # 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 NDU "SYSTEMATIC NAME" ACDLabs 10.04 "2'-deoxy-5-nitrouridine 5'-(dihydrogen phosphate)" NDU "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "[(2R,3S,5R)-3-hydroxy-5-(5-nitro-2,4-dioxo-1,3-diazinan-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 NDU "Create component" 2007-10-27 EBI NDU "Modify descriptor" 2011-06-04 RCSB NDU "Modify one letter code" 2019-05-07 EBI ##