data_9L3 # _chem_comp.id 9L3 _chem_comp.name "[(2R,3S,5R)-5-(4-azanyl-5-methyl-pyrimidin-1-ium-1-yl)-3-oxidanyl-oxolan-2-yl]methyl dihydrogen phosphate" _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C10 H17 N3 O6 P" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 1 _chem_comp.pdbx_initial_date 2018-05-22 _chem_comp.pdbx_modified_date 2022-03-16 _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 306.232 _chem_comp.one_letter_code ? _chem_comp.three_letter_code 9L3 _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 5ZRI _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site PDBJ # # 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 9L3 N1 N1 N 1 1 Y N N -17.563 12.818 2.477 2.380 -0.262 -0.327 N1 9L3 1 9L3 C2 C1 C 0 1 Y N N -16.719 12.932 3.606 2.245 0.490 0.747 C2 9L3 2 9L3 N3 N2 N 0 1 Y N N -15.415 12.627 3.493 3.229 1.242 1.198 N3 9L3 3 9L3 C4 C2 C 0 1 Y N N -14.893 12.220 2.326 4.404 1.265 0.576 C4 9L3 4 9L3 C5 C3 C 0 1 Y N N -15.765 12.078 1.141 4.581 0.480 -0.565 C5 9L3 5 9L3 C5A C4 C 0 1 N N N -15.199 11.624 -0.183 5.897 0.470 -1.300 C5A 9L3 6 9L3 C6 C5 C 0 1 Y N N -17.097 12.415 1.283 3.523 -0.295 -0.998 C6 9L3 7 9L3 N4 N3 N 0 1 N N N -13.595 11.863 2.234 5.436 2.057 1.052 N4 9L3 8 9L3 "C1'" C6 C 0 1 N N R -19.007 13.042 2.615 1.252 -1.078 -0.782 "C1'" 9L3 9 9L3 "C2'" C7 C 0 1 N N N -19.442 14.371 2.016 1.158 -2.362 0.065 "C2'" 9L3 10 9L3 "C3'" C8 C 0 1 N N S -20.815 14.063 1.449 -0.259 -2.304 0.686 "C3'" 9L3 11 9L3 "C4'" C9 C 0 1 N N R -20.773 12.592 1.099 -0.992 -1.328 -0.270 "C4'" 9L3 12 9L3 "O4'" O1 O 0 1 N N N -19.701 12.041 1.873 0.023 -0.355 -0.606 "O4'" 9L3 13 9L3 "O3'" O2 O 0 1 N N N -21.792 14.231 2.483 -0.876 -3.593 0.670 "O3'" 9L3 14 9L3 "C5'" C10 C 0 1 N N N -20.585 12.338 -0.391 -2.168 -0.657 0.443 "C5'" 9L3 15 9L3 "O5'" O3 O 0 1 N N N -19.334 12.848 -0.843 -2.895 0.146 -0.489 "O5'" 9L3 16 9L3 PA P1 P 0 1 N N N -19.248 13.734 -2.187 -4.199 0.998 -0.082 PA 9L3 17 9L3 O1A O4 O 0 1 N N N -19.815 15.090 -1.874 -5.381 -0.004 0.354 O1A 9L3 18 9L3 O2A O5 O 0 1 N N N -19.884 12.929 -3.295 -3.869 1.893 1.050 O2A 9L3 19 9L3 O3A O6 O 0 1 N N N -17.660 13.824 -2.455 -4.679 1.879 -1.341 O3A 9L3 20 9L3 H1 H1 H 0 1 N N N -17.120 13.262 4.553 1.301 0.490 1.272 H1 9L3 21 9L3 H2 H2 H 0 1 N N N -14.856 12.499 -0.755 5.889 1.241 -2.069 H2 9L3 22 9L3 H3 H3 H 0 1 N N N -14.351 10.946 -0.006 6.707 0.665 -0.597 H3 9L3 23 9L3 H4 H4 H 0 1 N N N -15.978 11.096 -0.753 6.046 -0.505 -1.764 H4 9L3 24 9L3 H5 H5 H 0 1 N N N -17.763 12.355 0.435 3.623 -0.916 -1.876 H5 9L3 25 9L3 H6 H6 H 0 1 N N N -13.158 11.959 3.129 5.305 2.600 1.845 H6 9L3 26 9L3 H7 H7 H 0 1 N N N -13.532 10.912 1.932 6.291 2.069 0.592 H7 9L3 27 9L3 H8 H8 H 0 1 N N N -19.295 13.009 3.676 1.383 -1.336 -1.833 H8 9L3 28 9L3 H9 H9 H 0 1 N N N -18.750 14.691 1.223 1.262 -3.244 -0.567 H9 9L3 29 9L3 H10 H10 H 0 1 N N N -19.500 15.152 2.789 1.919 -2.361 0.845 H10 9L3 30 9L3 H11 H11 H 0 1 N N N -21.028 14.679 0.563 -0.224 -1.904 1.699 H11 9L3 31 9L3 H12 H12 H 0 1 N N N -21.723 12.134 1.410 -1.332 -1.850 -1.165 H12 9L3 32 9L3 H13 H13 H 0 1 N N N -21.842 15.148 2.726 -0.401 -4.262 1.182 H13 9L3 33 9L3 H14 H14 H 0 1 N N N -21.396 12.833 -0.945 -2.826 -1.421 0.856 H14 9L3 34 9L3 H15 H15 H 0 1 N N N -20.620 11.255 -0.578 -1.792 -0.027 1.250 H15 9L3 35 9L3 H16 H16 H 0 1 N N N -20.546 15.270 -2.454 -5.649 -0.622 -0.341 H16 9L3 36 9L3 H17 H17 H 0 1 N N N -17.446 13.354 -3.253 -5.462 2.420 -1.167 H17 9L3 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 9L3 O2A PA DOUB N N 1 9L3 O3A PA SING N N 2 9L3 PA O1A SING N N 3 9L3 PA "O5'" SING N N 4 9L3 "O5'" "C5'" SING N N 5 9L3 "C5'" "C4'" SING N N 6 9L3 C5A C5 SING N N 7 9L3 "C4'" "C3'" SING N N 8 9L3 "C4'" "O4'" SING N N 9 9L3 C5 C6 DOUB Y N 10 9L3 C5 C4 SING Y N 11 9L3 C6 N1 SING Y N 12 9L3 "C3'" "C2'" SING N N 13 9L3 "C3'" "O3'" SING N N 14 9L3 "O4'" "C1'" SING N N 15 9L3 "C2'" "C1'" SING N N 16 9L3 N4 C4 SING N N 17 9L3 C4 N3 DOUB Y N 18 9L3 N1 "C1'" SING N N 19 9L3 N1 C2 DOUB Y N 20 9L3 N3 C2 SING Y N 21 9L3 C2 H1 SING N N 22 9L3 C5A H2 SING N N 23 9L3 C5A H3 SING N N 24 9L3 C5A H4 SING N N 25 9L3 C6 H5 SING N N 26 9L3 N4 H6 SING N N 27 9L3 N4 H7 SING N N 28 9L3 "C1'" H8 SING N N 29 9L3 "C2'" H9 SING N N 30 9L3 "C2'" H10 SING N N 31 9L3 "C3'" H11 SING N N 32 9L3 "C4'" H12 SING N N 33 9L3 "O3'" H13 SING N N 34 9L3 "C5'" H14 SING N N 35 9L3 "C5'" H15 SING N N 36 9L3 O1A H16 SING N N 37 9L3 O3A H17 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 9L3 InChI InChI 1.03 "InChI=1S/C10H16N3O6P/c1-6-3-13(5-12-10(6)11)9-2-7(14)8(19-9)4-18-20(15,16)17/h3,5,7-9,11,14H,2,4H2,1H3,(H2,15,16,17)/p+1/t7-,8+,9+/m0/s1" 9L3 InChIKey InChI 1.03 RJJVNUWWHKQVPB-DJLDLDEBSA-O 9L3 SMILES_CANONICAL CACTVS 3.385 "Cc1c[n+](cnc1N)[C@H]2C[C@H](O)[C@@H](CO[P](O)(O)=O)O2" 9L3 SMILES CACTVS 3.385 "Cc1c[n+](cnc1N)[CH]2C[CH](O)[CH](CO[P](O)(O)=O)O2" 9L3 SMILES_CANONICAL "OpenEye OEToolkits" 2.0.6 "Cc1c[n+](cnc1N)[C@H]2C[C@@H]([C@H](O2)COP(=O)(O)O)O" 9L3 SMILES "OpenEye OEToolkits" 2.0.6 "Cc1c[n+](cnc1N)C2CC(C(O2)COP(=O)(O)O)O" # _pdbx_chem_comp_identifier.comp_id 9L3 _pdbx_chem_comp_identifier.type "SYSTEMATIC NAME" _pdbx_chem_comp_identifier.program "OpenEye OEToolkits" _pdbx_chem_comp_identifier.program_version 2.0.6 _pdbx_chem_comp_identifier.identifier "[(2~{R},3~{S},5~{R})-5-(4-azanyl-5-methyl-pyrimidin-1-ium-1-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 9L3 "Create component" 2018-05-22 PDBJ 9L3 "Initial release" 2019-04-24 RCSB 9L3 "Modify name" 2022-03-16 RCSB ##