data_1W5 # _chem_comp.id 1W5 _chem_comp.name "(1R)-1-(6-amino-2-hydroxy-5-nitropyridin-3-yl)-1,4-anhydro-2-deoxy-5-O-phosphono-D-erythro-pentitol" _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 2013-06-28 _chem_comp.pdbx_modified_date 2016-05-12 _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 1W5 _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 4XNO _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 1W5 N N1 N 1 1 N N N 43.245 36.212 -15.673 3.288 -2.437 -0.666 N 1W5 1 1W5 P P1 P 0 1 N N N 47.159 39.308 -14.891 -4.484 -1.156 0.327 P 1W5 2 1W5 C1 C1 C 0 1 Y N N 46.308 34.145 -15.721 1.946 0.914 0.341 C1 1W5 3 1W5 C2 C2 C 0 1 Y N N 45.827 32.878 -16.231 3.115 1.500 0.807 C2 1W5 4 1W5 O2 O1 O 0 1 N N N 46.470 31.891 -16.434 3.084 2.768 1.286 O2 1W5 5 1W5 N3 N2 N 0 1 Y N N 44.447 32.856 -16.521 4.259 0.834 0.789 N3 1W5 6 1W5 C4 C3 C 0 1 Y N N 43.560 33.869 -16.368 4.332 -0.406 0.328 C4 1W5 7 1W5 N4 N3 N 0 1 N N N 42.290 33.603 -16.696 5.554 -1.068 0.327 N4 1W5 8 1W5 C5 C4 C 0 1 Y N N 44.058 35.066 -15.875 3.199 -1.051 -0.154 C5 1W5 9 1W5 C6 C5 C 0 1 Y N N 45.453 35.158 -15.561 1.986 -0.383 -0.148 C6 1W5 10 1W5 "C1'" C6 C 0 1 N N R 47.706 34.199 -15.380 0.647 1.677 0.371 "C1'" 1W5 11 1W5 "C2'" C7 C 0 1 N N N 48.473 34.458 -16.656 0.473 2.494 -0.928 "C2'" 1W5 12 1W5 "C3'" C8 C 0 1 N N S 49.030 35.885 -16.662 -1.040 2.400 -1.230 "C3'" 1W5 13 1W5 "O3'" O2 O 0 1 N N N 50.278 35.942 -17.382 -1.635 3.699 -1.218 "O3'" 1W5 14 1W5 "C4'" C9 C 0 1 N N R 49.197 36.087 -15.176 -1.600 1.537 -0.079 "C4'" 1W5 15 1W5 "O4'" O3 O 0 1 N N N 48.120 35.326 -14.557 -0.472 0.763 0.386 "O4'" 1W5 16 1W5 "C5'" C10 C 0 1 N N N 49.080 37.573 -14.871 -2.704 0.611 -0.595 "C5'" 1W5 17 1W5 "O5'" O4 O 0 1 N N N 47.772 37.887 -15.319 -3.287 -0.093 0.504 "O5'" 1W5 18 1W5 ON1 O5 O 0 1 N N N 42.071 36.165 -15.943 4.016 -3.244 -0.117 ON1 1W5 19 1W5 ON2 O6 O -1 1 N N N 43.774 37.199 -15.271 2.629 -2.771 -1.635 ON2 1W5 20 1W5 OP1 O7 O 0 1 N N N 48.207 40.332 -14.839 -5.800 -0.398 -0.206 OP1 1W5 21 1W5 OP2 O8 O 0 1 N N N 45.933 39.735 -15.651 -4.082 -2.194 -0.648 OP2 1W5 22 1W5 OP3 O9 O 0 1 N Y N 46.973 39.410 -13.318 -4.800 -1.847 1.747 O1 1W5 23 1W5 H1 H1 H 0 1 N N N 42.218 32.657 -17.011 6.319 -0.674 0.774 H1 1W5 24 1W5 H2 H2 H 0 1 N N N 41.705 33.733 -15.896 5.641 -1.924 -0.120 H2 1W5 25 1W5 H4 H4 H 0 1 N N N 45.832 36.093 -15.176 1.090 -0.863 -0.512 H4 1W5 26 1W5 H5 H5 H 0 1 N N N 48.037 33.250 -14.932 0.613 2.332 1.242 H5 1W5 27 1W5 H6 H6 H 0 1 N N N 47.800 34.328 -17.516 0.766 3.532 -0.768 H6 1W5 28 1W5 H7 H7 H 0 1 N N N 49.306 33.743 -16.730 1.054 2.053 -1.737 H7 1W5 29 1W5 H8 H8 H 0 1 N N N 48.288 36.587 -17.072 -1.207 1.911 -2.190 H8 1W5 30 1W5 H9 H9 H 0 1 N N N 50.608 36.833 -17.375 -1.276 4.302 -1.883 H9 1W5 31 1W5 H10 H10 H 0 1 N N N 50.179 35.713 -14.851 -1.981 2.172 0.721 H10 1W5 32 1W5 H11 H11 H 0 1 N N N 49.836 38.151 -15.422 -3.470 1.203 -1.095 H11 1W5 33 1W5 H12 H12 H 0 1 N N N 49.186 37.765 -13.793 -2.279 -0.103 -1.300 H12 1W5 34 1W5 HOP1 H13 H 0 0 N N N 47.918 41.106 -15.308 -6.121 0.297 0.384 H13 1W5 35 1W5 HOP3 H14 H 0 0 N Y N 46.100 39.730 -13.122 -5.512 -2.501 1.715 H14 1W5 36 1W5 H15 H15 H 0 1 N N N 45.905 31.210 -16.780 2.908 2.826 2.235 H15 1W5 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 1W5 "O3'" "C3'" SING N N 1 1W5 N4 C4 SING N N 2 1W5 "C3'" "C2'" SING N N 3 1W5 "C3'" "C4'" SING N N 4 1W5 "C2'" "C1'" SING N N 5 1W5 N3 C4 DOUB Y N 6 1W5 N3 C2 SING Y N 7 1W5 O2 C2 SING N N 8 1W5 C4 C5 SING Y N 9 1W5 C2 C1 DOUB Y N 10 1W5 ON1 N DOUB N N 11 1W5 C5 N SING N N 12 1W5 C5 C6 DOUB Y N 13 1W5 C1 C6 SING Y N 14 1W5 C1 "C1'" SING N N 15 1W5 N ON2 SING N N 16 1W5 OP2 P DOUB N N 17 1W5 "C1'" "O4'" SING N N 18 1W5 "O5'" P SING N N 19 1W5 "O5'" "C5'" SING N N 20 1W5 "C4'" "C5'" SING N N 21 1W5 "C4'" "O4'" SING N N 22 1W5 P OP1 SING N N 23 1W5 P OP3 SING N N 24 1W5 N4 H1 SING N N 25 1W5 N4 H2 SING N N 26 1W5 C6 H4 SING N N 27 1W5 "C1'" H5 SING N N 28 1W5 "C2'" H6 SING N N 29 1W5 "C2'" H7 SING N N 30 1W5 "C3'" H8 SING N N 31 1W5 "O3'" H9 SING N N 32 1W5 "C4'" H10 SING N N 33 1W5 "C5'" H11 SING N N 34 1W5 "C5'" H12 SING N N 35 1W5 OP1 HOP1 SING N N 36 1W5 OP3 HOP3 SING N N 37 1W5 O2 H15 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 1W5 SMILES ACDLabs 12.01 "[N+]([O-])(c1c(nc(c(c1)C2OC(C(C2)O)COP(O)(O)=O)O)N)=O" 1W5 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" 1W5 InChIKey InChI 1.03 IUUXEDXPTYNSEU-XLPZGREQSA-N 1W5 SMILES_CANONICAL CACTVS 3.385 "Nc1nc(O)c(cc1[N+]([O-])=O)[C@H]2C[C@H](O)[C@@H](CO[P](O)(O)=O)O2" 1W5 SMILES CACTVS 3.385 "Nc1nc(O)c(cc1[N+]([O-])=O)[CH]2C[CH](O)[CH](CO[P](O)(O)=O)O2" 1W5 SMILES_CANONICAL "OpenEye OEToolkits" 2.0.4 "c1c(c(nc(c1[N+](=O)[O-])N)O)[C@H]2C[C@@H]([C@H](O2)COP(=O)(O)O)O" 1W5 SMILES "OpenEye OEToolkits" 2.0.4 "c1c(c(nc(c1[N+](=O)[O-])N)O)C2CC(C(O2)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 1W5 "SYSTEMATIC NAME" ACDLabs 12.01 "(1R)-1-(6-amino-2-hydroxy-5-nitropyridin-3-yl)-1,4-anhydro-2-deoxy-5-O-phosphono-D-erythro-pentitol" 1W5 "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.4 "[(2~{R},3~{S},5~{R})-5-(6-azanyl-5-nitro-2-oxidanyl-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 1W5 "Create component" 2013-06-28 RCSB 1W5 "Modify leaving atom flag" 2014-10-17 RCSB 1W5 "Other modification" 2014-10-29 RCSB 1W5 "Initial release" 2015-05-27 RCSB 1W5 "Modify formal charge" 2016-05-09 RCSB 1W5 "Modify formula" 2016-05-12 RCSB #