data_8RJ # _chem_comp.id 8RJ _chem_comp.name "(R)-1'-(2',3'-DIHYDROXYPROPYL)-THYMINE" _chem_comp.type "RNA linking" _chem_comp.pdbx_type ATOMN _chem_comp.formula "C8 H13 N2 O7 P" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2017-03-03 _chem_comp.pdbx_modified_date 2022-06-13 _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 280.172 _chem_comp.one_letter_code ? _chem_comp.three_letter_code 8RJ _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 5V1K _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 8RJ P P1 P 0 1 N N N 25.943 30.276 15.279 4.321 0.010 0.174 P 8RJ 1 8RJ OP2 O1 O 0 1 N N N 27.239 30.339 14.558 4.796 -1.220 -0.748 O1P 8RJ 2 8RJ O1 O2 O 0 1 N N N 24.671 30.434 14.543 4.652 1.287 -0.498 O2P 8RJ 3 8RJ "O5'" O3 O 0 1 N N N 26.031 31.249 16.551 2.730 -0.076 0.408 O3G 8RJ 4 8RJ O4 O4 O 0 1 N N N 26.044 35.009 23.858 -5.630 0.234 0.909 O4 8RJ 5 8RJ C4 C1 C 0 1 N N N 25.892 34.274 22.858 -4.509 0.219 0.433 C4 8RJ 6 8RJ N3 N1 N 0 1 N N N 27.023 34.071 22.082 -3.781 1.352 0.368 N3 8RJ 7 8RJ C2 C2 C 0 1 N N N 27.036 33.294 20.934 -2.542 1.334 -0.157 C2 8RJ 8 8RJ O2 O5 O 0 1 N N N 28.114 33.203 20.341 -1.898 2.364 -0.209 O2 8RJ 9 8RJ C5 C3 C 0 1 N N N 24.709 33.662 22.482 -3.955 -0.991 -0.051 C5 8RJ 10 8RJ C5M C4 C 0 1 N N N 23.510 33.804 23.192 -4.745 -2.273 0.015 C5M 8RJ 11 8RJ C6 C5 C 0 1 N N N 24.735 32.877 21.327 -2.710 -0.981 -0.573 C6 8RJ 12 8RJ N1 N2 N 0 1 N N N 25.894 32.697 20.558 -2.007 0.192 -0.626 N1 8RJ 13 8RJ C1G C6 C 0 1 N N N 25.806 31.848 19.368 -0.656 0.203 -1.192 C1G 8RJ 14 8RJ C2G C7 C 0 1 N N R 25.045 32.618 18.289 0.364 -0.071 -0.085 C2G 8RJ 15 8RJ O2G O6 O 0 1 N N N 25.910 33.738 17.904 0.176 -1.395 0.419 O2G 8RJ 16 8RJ C3G C8 C 0 1 N N N 24.827 31.721 17.105 1.779 0.064 -0.650 C3G 8RJ 17 8RJ OP3 O7 O 0 1 N Y N 25.907 28.950 16.178 5.076 -0.060 1.594 O1 8RJ 18 8RJ HOP2 H1 H 0 0 N Y N 27.080 30.486 13.633 4.610 -2.091 -0.370 H1 8RJ 19 8RJ H2 H2 H 0 1 N N N 27.876 34.509 22.366 -4.153 2.184 0.702 H2 8RJ 20 8RJ H3 H3 H 0 1 N N N 23.675 34.451 24.066 -5.718 -2.077 0.465 H3 8RJ 21 8RJ H4 H4 H 0 1 N N N 22.749 34.257 22.539 -4.883 -2.667 -0.992 H4 8RJ 22 8RJ H5 H5 H 0 1 N N N 23.164 32.815 23.528 -4.205 -3.001 0.620 H5 8RJ 23 8RJ H6 H6 H 0 1 N N N 23.825 32.388 21.013 -2.271 -1.894 -0.947 H6 8RJ 24 8RJ H7 H7 H 0 1 N N N 25.269 30.919 19.612 -0.576 -0.568 -1.958 H7 8RJ 25 8RJ H8 H8 H 0 1 N N N 26.817 31.604 19.009 -0.456 1.179 -1.637 H8 8RJ 26 8RJ H9 H9 H 0 1 N N N 24.084 32.977 18.685 0.225 0.648 0.723 H9 8RJ 27 8RJ H10 H10 H 0 1 N N N 26.047 34.305 18.654 0.285 -2.088 -0.247 H10 8RJ 28 8RJ H11 H11 H 0 1 N N N 24.282 32.284 16.333 1.894 1.044 -1.113 H11 8RJ 29 8RJ H12 H12 H 0 1 N N N 24.224 30.858 17.424 1.948 -0.712 -1.396 H12 8RJ 30 8RJ HOP3 H13 H 0 0 N Y N 25.070 28.514 16.067 6.040 -0.013 1.530 H13 8RJ 31 # 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 8RJ O1 P DOUB N N 1 8RJ OP2 P SING N N 2 8RJ P "O5'" SING N N 3 8RJ "O5'" C3G SING N N 4 8RJ C3G C2G SING N N 5 8RJ O2G C2G SING N N 6 8RJ C2G C1G SING N N 7 8RJ C1G N1 SING N N 8 8RJ O2 C2 DOUB N N 9 8RJ N1 C2 SING N N 10 8RJ N1 C6 SING N N 11 8RJ C2 N3 SING N N 12 8RJ C6 C5 DOUB N N 13 8RJ N3 C4 SING N N 14 8RJ C5 C4 SING N N 15 8RJ C5 C5M SING N N 16 8RJ C4 O4 DOUB N N 17 8RJ P OP3 SING N N 18 8RJ OP2 HOP2 SING N N 19 8RJ N3 H2 SING N N 20 8RJ C5M H3 SING N N 21 8RJ C5M H4 SING N N 22 8RJ C5M H5 SING N N 23 8RJ C6 H6 SING N N 24 8RJ C1G H7 SING N N 25 8RJ C1G H8 SING N N 26 8RJ C2G H9 SING N N 27 8RJ O2G H10 SING N N 28 8RJ C3G H11 SING N N 29 8RJ C3G H12 SING N N 30 8RJ OP3 HOP3 SING N N 31 # 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 8RJ SMILES ACDLabs 12.01 "P(OCC(CN1C(NC(=O)C(C)=C1)=O)O)(O)(O)=O" 8RJ InChI InChI 1.03 "InChI=1S/C8H13N2O7P/c1-5-2-10(8(13)9-7(5)12)3-6(11)4-17-18(14,15)16/h2,6,11H,3-4H2,1H3,(H,9,12,13)(H2,14,15,16)/t6-/m1/s1" 8RJ InChIKey InChI 1.03 WWYWEFRSGDVKHI-ZCFIWIBFSA-N 8RJ SMILES_CANONICAL CACTVS 3.385 "CC1=CN(C[C@@H](O)CO[P](O)(O)=O)C(=O)NC1=O" 8RJ SMILES CACTVS 3.385 "CC1=CN(C[CH](O)CO[P](O)(O)=O)C(=O)NC1=O" 8RJ SMILES_CANONICAL "OpenEye OEToolkits" 2.0.6 "CC1=CN(C(=O)NC1=O)C[C@H](COP(=O)(O)O)O" 8RJ SMILES "OpenEye OEToolkits" 2.0.6 "CC1=CN(C(=O)NC1=O)CC(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 8RJ "SYSTEMATIC NAME" ACDLabs 12.01 "(2R)-2-hydroxy-3-(5-methyl-2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)propyl dihydrogen phosphate" 8RJ "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.6 "[(2~{R})-3-[5-methyl-2,4-bis(oxidanylidene)pyrimidin-1-yl]-2-oxidanyl-propyl] 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 8RJ "Create component" 2017-03-03 RCSB 8RJ "Initial release" 2017-06-21 RCSB 8RJ "Modify parent residue" 2022-06-13 RCSB #