data_NDN # _chem_comp.id NDN _chem_comp.name "2'-DEOXY-5-NITROURIDINE 5'-(DIHYDROGEN PHOSPHATE)" _chem_comp.type "DNA LINKING" _chem_comp.pdbx_type ATOMN _chem_comp.formula "C9 H12 N3 O10 P" _chem_comp.mon_nstd_parent_comp_id DU _chem_comp.pdbx_synonyms "[(2R,3S,5R)-3-HYDROXY-5-(5-NITRO-2,4-DIOXO-PYRIMIDIN-1-YL)OXOLAN-2-YL]METHYL DIHYDROGEN PHOSPHATE" _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2007-11-07 _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 353.179 _chem_comp.one_letter_code U _chem_comp.three_letter_code NDN _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 3B5B _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 NDN P P P 0 1 N N N 46.433 28.257 24.564 -4.772 -1.098 0.304 P NDN 1 NDN OP1 OP1 O 0 1 N N N 47.700 27.548 24.968 -5.899 -0.182 0.018 OP1 NDN 2 NDN OP2 OP2 O 0 1 N N N 45.494 28.422 25.721 -5.133 -2.010 1.581 OP2 NDN 3 NDN OP3 OP3 O 0 1 N Y N 45.849 27.841 23.248 -4.510 -2.043 -0.973 OP3 NDN 4 NDN OR5 OR5 O 0 1 N N N 46.936 29.734 24.272 -3.447 -0.237 0.616 OR5 NDN 5 NDN CR5 CR5 C 0 1 N N N 46.361 30.943 23.895 -2.930 0.747 -0.281 CR5 NDN 6 NDN CR4 CR4 C 0 1 N N R 46.859 32.042 24.811 -1.669 1.372 0.320 CR4 NDN 7 NDN CR3 CR3 C 0 1 N N S 46.554 32.079 26.296 -1.163 2.526 -0.574 CR3 NDN 8 NDN OR3 OR3 O 0 1 N N N 47.488 32.815 27.038 -1.596 3.786 -0.058 OR3 NDN 9 NDN CR2 CR2 C 0 1 N N N 45.163 32.742 26.356 0.377 2.411 -0.500 CR2 NDN 10 NDN CR1 CR1 C 0 1 N N R 45.360 33.822 25.239 0.618 1.201 0.430 CR1 NDN 11 NDN OR1 OR1 O 0 1 N N N 46.374 33.303 24.361 -0.589 0.413 0.332 OR1 NDN 12 NDN N1 N1 N 0 1 N N N 44.024 34.350 24.714 1.773 0.426 -0.030 N1 NDN 13 NDN C2 C2 C 0 1 N N N 43.216 35.326 25.294 1.724 -0.202 -1.218 C2 NDN 14 NDN O2 O2 O 0 1 N N N 43.416 35.695 26.380 0.720 -0.120 -1.899 O2 NDN 15 NDN N3 N3 N 0 1 N N N 42.162 35.840 24.534 2.772 -0.919 -1.665 N3 NDN 16 NDN C4 C4 C 0 1 N N N 42.097 35.908 23.145 3.893 -1.020 -0.923 C4 NDN 17 NDN O4 O4 O 0 1 N N N 41.389 36.685 22.533 4.841 -1.669 -1.327 O4 NDN 18 NDN C5 C5 C 0 1 N N N 43.004 34.921 22.371 3.957 -0.364 0.330 C5 NDN 19 NDN C6 C6 C 0 1 N N N 44.138 34.276 23.195 2.895 0.354 0.752 C6 NDN 20 NDN N5 N5 N 1 1 N N N 43.089 34.783 21.069 5.177 -0.459 1.164 N5 NDN 21 NDN O51 O51 O 0 1 N N N 42.206 35.225 20.299 5.224 0.108 2.241 O51 NDN 22 NDN O52 O52 O -1 1 N N N 44.027 34.233 20.465 6.133 -1.105 0.774 O52 NDN 23 NDN HOP3 HOP3 H 0 0 N N N 44.907 27.753 23.333 -3.783 -2.670 -0.856 HOP3 NDN 24 NDN HOP2 HOP2 H 0 0 N N N 45.991 28.457 26.530 -5.922 -2.556 1.464 HOP2 NDN 25 NDN HR5 HR5 H 0 1 N N N 46.641 31.175 22.857 -2.684 0.277 -1.234 HR5 NDN 26 NDN HR5A HR5A H 0 0 N N N 45.266 30.869 23.970 -3.679 1.522 -0.441 HR5A NDN 27 NDN HR4 HR4 H 0 1 N N N 47.933 31.814 24.739 -1.869 1.733 1.328 HR4 NDN 28 NDN HR3 HR3 H 0 1 N N N 46.591 31.073 26.740 -1.506 2.394 -1.600 HR3 NDN 29 NDN HOR3 HOR3 H 0 0 N Y N 48.256 32.982 26.505 -1.305 4.546 -0.581 HOR3 NDN 30 NDN HR2 HR2 H 0 1 N N N 44.341 32.043 26.142 0.794 2.221 -1.489 HR2 NDN 31 NDN HR2A HR2A H 0 0 N N N 44.871 33.133 27.342 0.807 3.316 -0.071 HR2A NDN 32 NDN HR1 HR1 H 0 1 N N N 45.764 34.790 25.569 0.770 1.535 1.456 HR1 NDN 33 NDN HN3 HN3 H 0 1 N N N 41.375 36.195 25.039 2.720 -1.366 -2.525 HN3 NDN 34 NDN H6 H6 H 0 1 N N N 44.977 33.793 22.716 2.926 0.861 1.704 H6 NDN 35 # # 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 NDN P OP1 DOUB N N 1 NDN P OP2 SING N N 2 NDN OP3 HOP3 SING N N 3 NDN OP2 HOP2 SING N N 4 NDN OP3 P SING N N 5 NDN OR5 P SING N N 6 NDN CR5 OR5 SING N N 7 NDN CR5 CR4 SING N N 8 NDN CR5 HR5 SING N N 9 NDN CR5 HR5A SING N N 10 NDN CR4 CR3 SING N N 11 NDN CR4 HR4 SING N N 12 NDN CR3 CR2 SING N N 13 NDN CR3 OR3 SING N N 14 NDN CR3 HR3 SING N N 15 NDN OR3 HOR3 SING N N 16 NDN CR2 HR2 SING N N 17 NDN CR2 HR2A SING N N 18 NDN CR1 CR2 SING N N 19 NDN CR1 HR1 SING N N 20 NDN OR1 CR4 SING N N 21 NDN OR1 CR1 SING N N 22 NDN N1 CR1 SING N N 23 NDN N1 C2 SING N N 24 NDN C2 O2 DOUB N N 25 NDN N3 C2 SING N N 26 NDN N3 HN3 SING N N 27 NDN C4 N3 SING N N 28 NDN O4 C4 DOUB N N 29 NDN C5 C4 SING N N 30 NDN C5 C6 DOUB N N 31 NDN C6 N1 SING N N 32 NDN C6 H6 SING N N 33 NDN N5 C5 SING N N 34 NDN O51 N5 DOUB N N 35 NDN O52 N5 SING N N 36 # # 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 NDN SMILES ACDLabs 10.04 "[O-][N+](=O)C=1C(=O)NC(=O)N(C=1)C2OC(C(O)C2)COP(=O)(O)O" NDN SMILES_CANONICAL CACTVS 3.341 "O[C@H]1C[C@@H](O[C@@H]1CO[P](O)(O)=O)N2C=C(C(=O)NC2=O)[N+]([O-])=O" NDN SMILES CACTVS 3.341 "O[CH]1C[CH](O[CH]1CO[P](O)(O)=O)N2C=C(C(=O)NC2=O)[N+]([O-])=O" NDN SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "C1[C@@H]([C@H](O[C@H]1N2C=C(C(=O)NC2=O)[N+](=O)[O-])COP(=O)(O)O)O" NDN SMILES "OpenEye OEToolkits" 1.5.0 "C1C(C(OC1N2C=C(C(=O)NC2=O)[N+](=O)[O-])COP(=O)(O)O)O" NDN InChI InChI 1.03 "InChI=1S/C9H12N3O10P/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/h2,5-7,13H,1,3H2,(H,10,14,15)(H2,18,19,20)/t5-,6+,7+/m0/s1" NDN InChIKey InChI 1.03 LVLPVLNNXRTCHP-RRKCRQDMSA-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 NDN "SYSTEMATIC NAME" ACDLabs 10.04 "2'-deoxy-5-nitrouridine 5'-(dihydrogen phosphate)" NDN "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "[(2R,3S,5R)-3-hydroxy-5-(5-nitro-2,4-dioxo-pyrimidin-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 NDN "Create component" 2007-11-07 RCSB NDN "Modify descriptor" 2011-06-04 RCSB NDN "Modify synonyms" 2020-06-05 PDBE # _pdbx_chem_comp_synonyms.ordinal 1 _pdbx_chem_comp_synonyms.comp_id NDN _pdbx_chem_comp_synonyms.name "[(2R,3S,5R)-3-HYDROXY-5-(5-NITRO-2,4-DIOXO-PYRIMIDIN-1-YL)OXOLAN-2-YL]METHYL DIHYDROGEN PHOSPHATE" _pdbx_chem_comp_synonyms.provenance ? _pdbx_chem_comp_synonyms.type ? ##