data_YRJ # _chem_comp.id YRJ _chem_comp.name "3-({[(4-nitrophenyl)carbamoyl]amino}methyl)-1-(5-O-phosphono-beta-D-ribofuranosyl)pyridin-1-ium" _chem_comp.type non-polymer _chem_comp.pdbx_type HETAIN _chem_comp.formula "C18 H22 N4 O10 P" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 1 _chem_comp.pdbx_initial_date 2021-03-26 _chem_comp.pdbx_modified_date 2022-01-28 _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 485.362 _chem_comp.one_letter_code ? _chem_comp.three_letter_code YRJ _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 7M6K _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 YRJ C15 C1 C 0 1 Y N N -1.596 5.210 -14.142 2.149 -1.325 1.255 C15 YRJ 1 YRJ C17 C2 C 0 1 Y N N -1.794 3.370 -12.691 0.050 -2.462 1.281 C17 YRJ 2 YRJ C20 C3 C 0 1 N N N -0.098 1.515 -12.738 -1.769 -1.715 -0.283 C20 YRJ 3 YRJ C22 C4 C 0 1 N N N 1.664 -0.148 -13.046 -3.990 -0.820 0.166 C22 YRJ 4 YRJ C26 C5 C 0 1 Y N N 3.318 -2.624 -12.427 -6.833 -0.990 -0.087 C26 YRJ 5 YRJ C28 C6 C 0 1 Y N N 4.996 -4.099 -13.231 -8.809 0.347 -0.297 C28 YRJ 6 YRJ C02 C7 C 0 1 N N S 2.053 6.846 -16.037 4.098 2.213 0.693 C02 YRJ 7 YRJ C03 C8 C 0 1 N N R 0.862 6.607 -15.136 2.630 1.733 0.745 C03 YRJ 8 YRJ C05 C9 C 0 1 N N R 0.215 5.506 -15.677 2.597 0.522 -0.214 C05 YRJ 9 YRJ C07 C10 C 0 1 N N R 2.458 5.353 -16.364 4.778 1.234 -0.290 C07 YRJ 10 YRJ C08 C11 C 0 1 N N N 3.479 4.990 -15.263 6.201 0.916 0.174 C08 YRJ 11 YRJ C16 C12 C 0 1 Y N N -2.266 4.542 -13.160 1.338 -2.317 1.772 C16 YRJ 12 YRJ C18 C13 C 0 1 Y N N -0.615 2.900 -13.252 -0.377 -1.599 0.283 C18 YRJ 13 YRJ C19 C14 C 0 1 Y N N 0.019 3.601 -14.248 0.487 -0.623 -0.178 C19 YRJ 14 YRJ C25 C15 C 0 1 Y N N 3.740 -1.667 -13.344 -6.167 0.087 0.482 C25 YRJ 15 YRJ C27 C16 C 0 1 Y N N 3.944 -3.853 -12.391 -8.152 -0.857 -0.477 C27 YRJ 16 YRJ C29 C17 C 0 1 Y N N 5.441 -3.127 -14.103 -8.146 1.423 0.265 C29 YRJ 17 YRJ C30 C18 C 0 1 Y N N 4.822 -1.888 -14.132 -6.828 1.295 0.657 C30 YRJ 18 YRJ N14 N1 N 1 1 Y N N -0.480 4.709 -14.667 1.708 -0.518 0.309 N14 YRJ 19 YRJ N21 N2 N 0 1 N N N 1.285 1.259 -12.992 -2.683 -0.874 0.493 N21 YRJ 20 YRJ N24 N3 N 0 1 N N N 3.113 -0.364 -13.313 -4.831 -0.045 0.879 N24 YRJ 21 YRJ N31 N4 N 1 1 N N N 5.668 -5.352 -13.195 -10.222 0.486 -0.716 N31 YRJ 22 YRJ O01 O1 O 0 1 N N N 1.701 7.517 -17.241 4.170 3.552 0.202 O01 YRJ 23 YRJ O04 O2 O 0 1 N N N 0.050 7.704 -15.081 1.751 2.761 0.283 O04 YRJ 24 YRJ O06 O3 O 0 1 N N N 1.376 4.610 -16.271 3.960 0.045 -0.253 O06 YRJ 25 YRJ O09 O4 O 0 1 N N N 3.897 3.686 -15.533 6.827 0.045 -0.770 O09 YRJ 26 YRJ O11 O5 O 0 1 N N N 5.875 3.559 -13.881 8.751 -1.341 -1.905 O11 YRJ 27 YRJ O12 O6 O 0 1 N N N 4.763 1.455 -14.664 9.255 0.651 -0.439 O12 YRJ 28 YRJ O13 O7 O 0 1 N N N 3.577 3.048 -13.092 8.421 -1.440 0.701 O13 YRJ 29 YRJ O23 O8 O 0 1 N N N 0.878 -1.004 -12.932 -4.409 -1.469 -0.773 O23 YRJ 30 YRJ O32 O9 O -1 1 N N N 6.948 -5.430 -13.719 -10.802 1.546 -0.558 O32 YRJ 31 YRJ O33 O10 O 0 1 N N N 5.169 -6.273 -12.680 -10.804 -0.457 -1.220 O33 YRJ 32 YRJ P10 P1 P 0 1 N N N 4.546 2.894 -14.245 8.333 -0.496 -0.600 P10 YRJ 33 YRJ H151 H1 H 0 0 N N N -1.975 6.157 -14.498 3.154 -1.205 1.632 H151 YRJ 34 YRJ H171 H2 H 0 0 N N N -2.309 2.823 -11.915 -0.606 -3.229 1.666 H171 YRJ 35 YRJ H202 H3 H 0 0 N N N -0.260 1.471 -11.651 -1.767 -1.387 -1.323 H202 YRJ 36 YRJ H201 H4 H 0 0 N N N -0.688 0.726 -13.228 -2.097 -2.753 -0.230 H201 YRJ 37 YRJ H261 H5 H 0 0 N N N 2.506 -2.407 -11.748 -6.320 -1.930 -0.228 H261 YRJ 38 YRJ H021 H6 H 0 0 N N N 2.866 7.350 -15.495 4.557 2.144 1.680 H021 YRJ 39 YRJ H031 H7 H 0 0 N N N 1.237 6.363 -14.131 2.363 1.429 1.757 H031 YRJ 40 YRJ H051 H8 H 0 0 N N N -0.471 5.791 -16.488 2.274 0.833 -1.207 H051 YRJ 41 YRJ H071 H9 H 0 0 N N N 2.939 5.311 -17.352 4.791 1.655 -1.295 H071 YRJ 42 YRJ H082 H10 H 0 0 N N N 4.336 5.679 -15.295 6.774 1.841 0.250 H082 YRJ 43 YRJ H081 H11 H 0 0 N N N 3.005 5.041 -14.272 6.165 0.430 1.149 H081 YRJ 44 YRJ H161 H12 H 0 0 N N N -3.179 4.954 -12.756 1.704 -2.972 2.549 H161 YRJ 45 YRJ H191 H13 H 0 0 N N N 0.934 3.222 -14.678 0.160 0.058 -0.950 H191 YRJ 46 YRJ H271 H14 H 0 0 N N N 3.606 -4.615 -11.705 -8.669 -1.692 -0.924 H271 YRJ 47 YRJ H291 H15 H 0 0 N N N 6.271 -3.332 -14.763 -8.660 2.363 0.397 H291 YRJ 48 YRJ H301 H16 H 0 0 N N N 5.197 -1.106 -14.775 -6.311 2.136 1.096 H301 YRJ 49 YRJ H211 H17 H 0 0 N N N 1.948 1.996 -13.124 -2.349 -0.356 1.241 H211 YRJ 50 YRJ H241 H18 H 0 0 N N N 3.686 0.438 -13.481 -4.511 0.420 1.668 H241 YRJ 51 YRJ H011 H19 H 0 0 N N N 1.458 8.414 -17.045 3.707 4.199 0.752 H011 YRJ 52 YRJ H041 H20 H 0 0 N N N -0.687 7.525 -14.509 1.777 3.569 0.814 H041 YRJ 53 YRJ H1 H21 H 0 1 N N N 6.582 2.934 -13.990 9.649 -1.698 -1.872 H1 YRJ 54 YRJ H2 H22 H 0 1 N N N 3.265 2.192 -12.824 7.842 -2.214 0.665 H2 YRJ 55 # # 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 YRJ O01 C02 SING N N 1 YRJ C07 O06 SING N N 2 YRJ C07 C02 SING N N 3 YRJ C07 C08 SING N N 4 YRJ O06 C05 SING N N 5 YRJ C02 C03 SING N N 6 YRJ C05 C03 SING N N 7 YRJ C05 N14 SING N N 8 YRJ O09 C08 SING N N 9 YRJ O09 P10 SING N N 10 YRJ C03 O04 SING N N 11 YRJ N14 C19 DOUB Y N 12 YRJ N14 C15 SING Y N 13 YRJ O12 P10 DOUB N N 14 YRJ C19 C18 SING Y N 15 YRJ P10 O11 SING N N 16 YRJ P10 O13 SING N N 17 YRJ C15 C16 DOUB Y N 18 YRJ C30 C29 DOUB Y N 19 YRJ C30 C25 SING Y N 20 YRJ C29 C28 SING Y N 21 YRJ O32 N31 SING N N 22 YRJ C25 N24 SING N N 23 YRJ C25 C26 DOUB Y N 24 YRJ N24 C22 SING N N 25 YRJ C18 C20 SING N N 26 YRJ C18 C17 DOUB Y N 27 YRJ C28 N31 SING N N 28 YRJ C28 C27 DOUB Y N 29 YRJ N31 O33 DOUB N N 30 YRJ C16 C17 SING Y N 31 YRJ C22 N21 SING N N 32 YRJ C22 O23 DOUB N N 33 YRJ N21 C20 SING N N 34 YRJ C26 C27 SING Y N 35 YRJ C15 H151 SING N N 36 YRJ C17 H171 SING N N 37 YRJ C20 H202 SING N N 38 YRJ C20 H201 SING N N 39 YRJ C26 H261 SING N N 40 YRJ C02 H021 SING N N 41 YRJ C03 H031 SING N N 42 YRJ C05 H051 SING N N 43 YRJ C07 H071 SING N N 44 YRJ C08 H082 SING N N 45 YRJ C08 H081 SING N N 46 YRJ C16 H161 SING N N 47 YRJ C19 H191 SING N N 48 YRJ C27 H271 SING N N 49 YRJ C29 H291 SING N N 50 YRJ C30 H301 SING N N 51 YRJ N21 H211 SING N N 52 YRJ N24 H241 SING N N 53 YRJ O01 H011 SING N N 54 YRJ O04 H041 SING N N 55 YRJ O11 H1 SING N N 56 YRJ O13 H2 SING N N 57 # # 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 YRJ SMILES ACDLabs 12.01 "[O-][N+](=O)c1ccc(cc1)NC(=O)NCc1ccc[n+](c1)C1OC(COP(=O)(O)O)C(O)C1O" YRJ InChI InChI 1.03 "InChI=1S/C18H21N4O10P/c23-15-14(10-31-33(28,29)30)32-17(16(15)24)21-7-1-2-11(9-21)8-19-18(25)20-12-3-5-13(6-4-12)22(26)27/h1-7,9,14-17,23-24H,8,10H2,(H3-,19,20,25,28,29,30)/p+1/t14-,15-,16-,17-/m1/s1" YRJ InChIKey InChI 1.03 OCUAXUHZRNUDEK-QBPKDAKJSA-O YRJ SMILES_CANONICAL CACTVS 3.385 "O[C@H]1[C@@H](O)[C@@H](O[C@@H]1CO[P](O)(O)=O)[n+]2cccc(CNC(=O)Nc3ccc(cc3)[N+]([O-])=O)c2" YRJ SMILES CACTVS 3.385 "O[CH]1[CH](O)[CH](O[CH]1CO[P](O)(O)=O)[n+]2cccc(CNC(=O)Nc3ccc(cc3)[N+]([O-])=O)c2" YRJ SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "c1cc(c[n+](c1)[C@H]2[C@@H]([C@@H]([C@H](O2)COP(=O)(O)O)O)O)CNC(=O)Nc3ccc(cc3)[N+](=O)[O-]" YRJ SMILES "OpenEye OEToolkits" 2.0.7 "c1cc(c[n+](c1)C2C(C(C(O2)COP(=O)(O)O)O)O)CNC(=O)Nc3ccc(cc3)[N+](=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 YRJ "SYSTEMATIC NAME" ACDLabs 12.01 "3-({[(4-nitrophenyl)carbamoyl]amino}methyl)-1-(5-O-phosphono-beta-D-ribofuranosyl)pyridin-1-ium" YRJ "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 "[(2~{R},3~{S},4~{R},5~{R})-5-[3-[[(4-nitrophenyl)carbamoylamino]methyl]pyridin-1-ium-1-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 YRJ "Create component" 2021-03-26 RCSB YRJ "Initial release" 2022-02-02 RCSB ##