data_Y5P # _chem_comp.id Y5P _chem_comp.name "1-(5-O-phosphono-beta-D-ribofuranosyl)-1,4-dihydropyrimidine" _chem_comp.type "RNA LINKING" _chem_comp.pdbx_type ATOMN _chem_comp.formula "C9 H15 N2 O7 P" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms "PYRIMIDINE RIBOSIDE-5'-MONOPHOSPHATE" _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2014-09-25 _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 294.198 _chem_comp.one_letter_code ? _chem_comp.three_letter_code Y5P _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 4V19 _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site EBI # # 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 Y5P OP3 OP3 O 0 1 N Y N 177.216 306.533 289.827 -3.556 1.650 1.238 OP3 Y5P 1 Y5P P P P 0 1 N N N 177.984 307.502 288.789 -3.811 0.681 -0.023 P Y5P 2 Y5P "C5'" "C5'" C 0 1 N N N 180.527 306.953 288.331 -1.655 -0.860 0.320 "C5'" Y5P 3 Y5P "O5'" "O5'" O 0 1 N N N 179.517 307.390 289.231 -2.413 0.036 -0.495 "O5'" Y5P 4 Y5P "C4'" "C4'" C 0 1 N N R 181.189 305.683 288.811 -0.389 -1.282 -0.428 "C4'" Y5P 5 Y5P "O4'" "O4'" O 0 1 N N N 180.162 304.710 289.162 0.480 -0.148 -0.595 "O4'" Y5P 6 Y5P "C3'" "C3'" C 0 1 N N S 182.059 304.973 287.777 0.382 -2.331 0.397 "C3'" Y5P 7 Y5P "O3'" "O3'" O 0 1 N N N 183.392 305.462 287.739 0.506 -3.551 -0.337 "O3'" Y5P 8 Y5P "C2'" "C2'" C 0 1 N N R 181.940 303.505 288.172 1.773 -1.690 0.622 "C2'" Y5P 9 Y5P "O2'" "O2'" O 0 1 N N N 182.790 303.190 289.268 2.812 -2.661 0.477 "O2'" Y5P 10 Y5P "C1'" "C1'" C 0 1 N N R 180.491 303.442 288.643 1.835 -0.640 -0.517 "C1'" Y5P 11 Y5P N1 N1 N 0 1 N N N 179.553 303.167 287.527 2.758 0.443 -0.170 N1 Y5P 12 Y5P C2 C2 C 0 1 N N N 179.678 302.017 286.765 2.532 1.215 0.939 C2 Y5P 13 Y5P N3 N3 N 0 1 N N N 178.739 301.902 285.769 3.108 2.355 1.086 N3 Y5P 14 Y5P C4 C4 C 0 1 N N N 177.711 302.767 285.449 4.024 2.909 0.096 C4 Y5P 15 Y5P C6 C6 C 0 1 N N N 178.547 304.065 287.251 3.875 0.694 -0.962 C6 Y5P 16 Y5P OP1 OP1 O 0 1 N N N 177.575 308.901 289.077 -4.746 -0.398 0.366 OP1 Y5P 17 Y5P OP2 OP2 O 0 1 N N N 177.794 306.975 287.410 -4.446 1.531 -1.234 OP2 Y5P 18 Y5P C5 C5 C 0 1 N N N 177.643 303.926 286.279 4.497 1.853 -0.862 C5 Y5P 19 Y5P HP3 HP3 H 0 1 N N N 176.667 307.054 290.401 -2.951 2.382 1.055 HP3 Y5P 20 Y5P HP2 HP2 H 0 1 N N N 177.411 307.650 286.862 -5.291 1.950 -1.020 HP2 Y5P 21 Y5P HA1 HA1 H 0 1 N N N 180.072 306.768 287.347 -1.380 -0.362 1.250 HA1 Y5P 22 Y5P HB2 HB2 H 0 1 N N N 181.289 307.741 288.241 -2.255 -1.742 0.544 HB2 Y5P 23 Y5P HA HA H 0 1 N N N 181.803 305.911 289.695 -0.653 -1.694 -1.402 HA Y5P 24 Y5P HB HB H 0 1 N N N 181.591 305.101 286.790 -0.117 -2.509 1.350 HB Y5P 25 Y5P HC HC H 0 1 N N N 180.393 302.664 289.414 2.128 -1.110 -1.456 HC Y5P 26 Y5P "H2'" "H2'" H 0 1 N N N 182.104 302.847 287.305 1.827 -1.209 1.598 "H2'" Y5P 27 Y5P HD HD H 0 1 N N N 182.694 302.271 289.490 2.761 -3.388 1.112 HD Y5P 28 Y5P H2 H2 H 0 1 N N N 180.445 301.277 286.938 1.857 0.859 1.704 H2 Y5P 29 Y5P H6 H6 H 0 1 N N N 178.484 304.949 287.868 4.227 -0.054 -1.657 H6 Y5P 30 Y5P H4 H4 H 0 1 N N N 177.848 303.095 284.408 3.513 3.694 -0.462 H4 Y5P 31 Y5P H5 H5 H 0 1 N N N 176.878 304.673 286.124 5.364 2.044 -1.476 H5 Y5P 32 Y5P H4A H4A H 0 1 N N N 176.760 302.221 285.539 4.885 3.338 0.607 H4A Y5P 33 Y5P "H3'" "H3'" H 0 1 N N N 183.886 304.987 287.081 0.983 -4.247 0.135 "H3'" Y5P 34 # # 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 Y5P OP3 P SING N N 1 Y5P P "O5'" SING N N 2 Y5P P OP1 DOUB N N 3 Y5P P OP2 SING N N 4 Y5P "C5'" "O5'" SING N N 5 Y5P "C5'" "C4'" SING N N 6 Y5P "C4'" "O4'" SING N N 7 Y5P "C4'" "C3'" SING N N 8 Y5P "O4'" "C1'" SING N N 9 Y5P "C3'" "O3'" SING N N 10 Y5P "C3'" "C2'" SING N N 11 Y5P "C2'" "O2'" SING N N 12 Y5P "C2'" "C1'" SING N N 13 Y5P "C1'" N1 SING N N 14 Y5P N1 C2 SING N N 15 Y5P N1 C6 SING N N 16 Y5P C5 C6 DOUB N N 17 Y5P C2 N3 DOUB N N 18 Y5P N3 C4 SING N N 19 Y5P C4 C5 SING N N 20 Y5P OP3 HP3 SING N N 21 Y5P OP2 HP2 SING N N 22 Y5P "C5'" HA1 SING N N 23 Y5P "C5'" HB2 SING N N 24 Y5P "C4'" HA SING N N 25 Y5P "C3'" HB SING N N 26 Y5P "C1'" HC SING N N 27 Y5P "C2'" "H2'" SING N N 28 Y5P "O2'" HD SING N N 29 Y5P C2 H2 SING N N 30 Y5P C6 H6 SING N N 31 Y5P C4 H4 SING N N 32 Y5P "O3'" "H3'" SING N N 33 Y5P H5 C5 SING N N 34 Y5P C4 H4A SING N N 35 # # 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 Y5P SMILES ACDLabs 12.01 "O=P(O)(O)OCC2OC(N1C=NCC=C1)C(O)C2O" Y5P InChI InChI 1.03 "InChI=1S/C9H15N2O7P/c12-7-6(4-17-19(14,15)16)18-9(8(7)13)11-3-1-2-10-5-11/h1,3,5-9,12-13H,2,4H2,(H2,14,15,16)/t6-,7-,8-,9-/m1/s1" Y5P InChIKey InChI 1.03 ZGXCQKJYIKURPN-FNCVBFRFSA-N Y5P SMILES_CANONICAL CACTVS 3.385 "O[C@H]1[C@@H](O)[C@@H](O[C@@H]1CO[P](O)(O)=O)N2C=CCN=C2" Y5P SMILES CACTVS 3.385 "O[CH]1[CH](O)[CH](O[CH]1CO[P](O)(O)=O)N2C=CCN=C2" Y5P SMILES_CANONICAL "OpenEye OEToolkits" 1.7.6 "C1C=CN(C=N1)[C@H]2[C@@H]([C@@H]([C@H](O2)COP(=O)(O)O)O)O" Y5P SMILES "OpenEye OEToolkits" 1.7.6 "C1C=CN(C=N1)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 Y5P "SYSTEMATIC NAME" ACDLabs 12.01 "1-(5-O-phosphono-beta-D-ribofuranosyl)-1,4-dihydropyrimidine" Y5P "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.7.6 "[(2R,3S,4R,5R)-3,4-bis(oxidanyl)-5-(4H-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 Y5P "Create component" 2014-09-25 EBI Y5P "Initial release" 2014-10-08 RCSB Y5P "Modify synonyms" 2020-06-05 PDBE # _pdbx_chem_comp_synonyms.ordinal 1 _pdbx_chem_comp_synonyms.comp_id Y5P _pdbx_chem_comp_synonyms.name "PYRIMIDINE RIBOSIDE-5'-MONOPHOSPHATE" _pdbx_chem_comp_synonyms.provenance ? _pdbx_chem_comp_synonyms.type ? ##