data_50N # _chem_comp.id 50N _chem_comp.name "(1S)-1-(6-amino-2-hydroxy-5-nitropyridin-3-yl)-1,4-anhydro-5-O-phosphono-D-ribitol" _chem_comp.type "RNA linking" _chem_comp.pdbx_type ATOMN _chem_comp.formula "C10 H14 N3 O10 P" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2015-07-08 _chem_comp.pdbx_modified_date 2015-08-07 _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 367.206 _chem_comp.one_letter_code ? _chem_comp.three_letter_code 50N _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 5C7W _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 50N P1 P1 P 0 1 N N N -7.182 -13.343 27.625 -4.484 -1.161 0.352 P1 50N 1 50N C1 C1 C 0 1 Y N N -0.364 -11.267 27.572 3.141 1.208 0.900 C1 50N 2 50N O1 O1 O 0 1 N N N 0.201 -10.159 28.154 3.219 2.453 1.434 O1 50N 3 50N N1 N1 N 0 1 Y N N 0.307 -11.997 26.674 4.235 0.468 0.803 N1 50N 4 50N C2 C2 C 0 1 Y N N -0.265 -13.069 26.091 4.201 -0.753 0.292 C2 50N 5 50N C3 C3 C 0 1 Y N N -1.565 -13.468 26.399 3.006 -1.300 -0.161 C3 50N 6 50N C4 C4 C 0 1 Y N N -2.296 -12.736 27.333 1.844 -0.552 -0.073 C4 50N 7 50N OP1 O2 O 0 1 N N N -7.009 -14.336 26.527 -5.550 -0.575 -0.491 OP1 50N 8 50N OP2 O3 O 0 1 N N N -8.455 -12.598 27.680 -3.921 -2.497 -0.348 OP2 50N 9 50N O4 O4 O 0 1 N N N -5.960 -12.299 27.743 -3.287 -0.098 0.520 O4 50N 10 50N C5 C5 C 0 1 N N N -5.975 -11.289 28.743 -2.618 0.503 -0.591 C5 50N 11 50N C6 C6 C 0 1 N N R -4.667 -10.533 28.883 -1.539 1.460 -0.080 C6 50N 12 50N O5 O5 O 0 1 N N N -3.564 -11.399 29.256 -0.491 0.730 0.594 O5 50N 13 50N C7 C7 C 0 1 N N S -4.144 -9.769 27.669 -0.804 2.137 -1.265 C7 50N 14 50N O6 O6 O 0 1 N N N -4.868 -8.574 27.404 -1.501 3.309 -1.694 O6 50N 15 50N C8 C8 C 0 1 N N R -2.679 -9.530 28.036 0.560 2.505 -0.633 C8 50N 16 50N O7 O7 O 0 1 N N N -2.532 -8.403 28.881 0.566 3.872 -0.217 O7 50N 17 50N C9 C9 C 0 1 N N S -2.342 -10.815 28.827 0.676 1.570 0.587 C9 50N 18 50N C10 C10 C 0 1 Y N N -1.676 -11.624 27.923 1.916 0.723 0.467 C10 50N 19 50N N2 N2 N 0 1 N N N 0.403 -13.798 25.198 5.373 -1.496 0.208 N2 50N 20 50N O8 O8 O -1 1 N N N -1.260 -15.261 24.740 2.249 -2.915 -1.675 O8 50N 21 50N O9 O9 O 0 1 N N N -3.209 -15.205 26.316 3.678 -3.540 -0.255 O9 50N 22 50N N3 N3 N 1 1 N N N -2.032 -14.581 25.800 2.976 -2.666 -0.731 N3 50N 23 50N H1 H1 H 0 1 N N N -3.306 -13.015 27.594 0.903 -0.953 -0.417 H1 50N 24 50N HOP2 H3 H 0 0 N N N -9.016 -12.875 26.965 -3.218 -2.936 0.151 HOP2 50N 25 50N H4 H4 H 0 1 N N N -6.766 -10.567 28.492 -2.156 -0.274 -1.200 H4 50N 26 50N H5 H5 H 0 1 N N N -6.205 -11.763 29.709 -3.339 1.056 -1.194 H5 50N 27 50N H6 H6 H 0 1 N N N -4.805 -9.797 29.689 -1.974 2.208 0.583 H6 50N 28 50N H7 H7 H 0 1 N N N -4.182 -10.434 26.793 -0.674 1.439 -2.092 H7 50N 29 50N H8 H8 H 0 1 N N N -5.766 -8.790 27.183 -1.035 3.816 -2.373 H8 50N 30 50N H9 H9 H 0 1 N N N -2.057 -9.461 27.131 1.370 2.316 -1.337 H9 50N 31 50N H10 H10 H 0 1 N N N -1.613 -8.281 29.090 0.437 4.503 -0.938 H10 50N 32 50N H11 H11 H 0 1 N N N -1.705 -10.556 29.686 0.714 2.159 1.503 H11 50N 33 50N H13 H13 H 0 1 N N N 1.318 -13.415 25.072 5.378 -2.343 -0.265 H13 50N 34 50N H14 H14 H 0 1 N N N 0.478 -14.740 25.526 6.186 -1.168 0.623 H14 50N 35 50N H15 H15 H 0 1 N N N 1.080 -10.037 27.816 3.091 2.478 2.392 H15 50N 36 50N OP3 O10 O 0 1 N Y N ? ? ? -5.085 -1.526 1.800 OP3 50N 37 50N HOP3 H16 H 0 0 N Y N ? ? ? -5.812 -2.163 1.775 HOP3 50N 38 # 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 50N O8 N3 SING N N 1 50N N2 C2 SING N N 2 50N N3 O9 DOUB N N 3 50N N3 C3 SING N N 4 50N C2 C3 SING Y N 5 50N C2 N1 DOUB Y N 6 50N C3 C4 DOUB Y N 7 50N OP1 P1 DOUB N N 8 50N N1 C1 SING Y N 9 50N C4 C10 SING Y N 10 50N O6 C7 SING N N 11 50N C1 C10 DOUB Y N 12 50N C1 O1 SING N N 13 50N P1 OP2 SING N N 14 50N P1 O4 SING N N 15 50N C7 C8 SING N N 16 50N C7 C6 SING N N 17 50N O4 C5 SING N N 18 50N C10 C9 SING N N 19 50N C8 C9 SING N N 20 50N C8 O7 SING N N 21 50N C5 C6 SING N N 22 50N C9 O5 SING N N 23 50N C6 O5 SING N N 24 50N C4 H1 SING N N 25 50N OP2 HOP2 SING N N 26 50N C5 H4 SING N N 27 50N C5 H5 SING N N 28 50N C6 H6 SING N N 29 50N C7 H7 SING N N 30 50N O6 H8 SING N N 31 50N C8 H9 SING N N 32 50N O7 H10 SING N N 33 50N C9 H11 SING N N 34 50N N2 H13 SING N N 35 50N N2 H14 SING N N 36 50N O1 H15 SING N N 37 50N P1 OP3 SING N N 38 50N OP3 HOP3 SING N N 39 # 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 50N SMILES ACDLabs 12.01 "P(O)(OCC1OC(C(C1O)O)c2c(O)nc(c(c2)[N+]([O-])=O)N)(O)=O" 50N InChI InChI 1.03 "InChI=1S/C10H14N3O10P/c11-9-4(13(17)18)1-3(10(16)12-9)8-7(15)6(14)5(23-8)2-22-24(19,20)21/h1,5-8,14-15H,2H2,(H3,11,12,16)(H2,19,20,21)/t5-,6-,7-,8+/m1/s1" 50N InChIKey InChI 1.03 NFRHBMAHQZOVIK-XUTVFYLZSA-N 50N SMILES_CANONICAL CACTVS 3.385 "Nc1nc(O)c(cc1[N+]([O-])=O)[C@@H]2O[C@H](CO[P](O)(O)=O)[C@@H](O)[C@H]2O" 50N SMILES CACTVS 3.385 "Nc1nc(O)c(cc1[N+]([O-])=O)[CH]2O[CH](CO[P](O)(O)=O)[CH](O)[CH]2O" 50N SMILES_CANONICAL "OpenEye OEToolkits" 1.9.2 "c1c(c(nc(c1[N+](=O)[O-])N)O)[C@H]2[C@@H]([C@@H]([C@H](O2)COP(=O)(O)O)O)O" 50N SMILES "OpenEye OEToolkits" 1.9.2 "c1c(c(nc(c1[N+](=O)[O-])N)O)C2C(C(C(O2)COP(=O)(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 50N "SYSTEMATIC NAME" ACDLabs 12.01 "(1S)-1-(6-amino-2-hydroxy-5-nitropyridin-3-yl)-1,4-anhydro-5-O-phosphono-D-ribitol" 50N "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.9.2 "[(2R,3S,4R,5S)-5-(6-azanyl-5-nitro-2-oxidanyl-pyridin-3-yl)-3,4-bis(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 50N "Create component" 2015-07-08 RCSB 50N "Modify name" 2015-07-17 RCSB 50N "Initial release" 2015-08-12 RCSB #