data_A1B9T # _chem_comp.id A1B9T _chem_comp.name "[2-[2-(2-$l^{3}-oxidanylidene-5-methyl-4-oxidanylidene-4,5-dihydro-2~{H}-pyrimidin-1-yl)ethanoylamino]-3-oxidanyl-propyl] dihydrogen phosphate" _chem_comp.type "RNA linking" _chem_comp.pdbx_type ATOMN _chem_comp.formula "C10 H16 N3 O8 P" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2025-04-11 _chem_comp.pdbx_modified_date 2026-04-17 _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 337.223 _chem_comp.one_letter_code ? _chem_comp.three_letter_code A1B9T _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 9O47 _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site RCSB _chem_comp.pdbx_pcm ? # 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.pdbx_n_terminal_atom_flag _chem_comp_atom.pdbx_backbone_atom_flag _chem_comp_atom.pdbx_c_terminal_atom_flag _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 A1B9T O2 O1 O 0 1 N N N N N N 21.680 38.735 23.478 2.930 -1.952 -1.164 O2 A1B9T 1 A1B9T N1 N1 N 0 1 N N N N N N 23.617 39.989 23.592 2.944 0.202 -0.653 N1 A1B9T 2 A1B9T N2 N2 N 0 1 N N N N N N 21.249 42.650 22.726 -0.659 0.102 0.138 N2 A1B9T 3 A1B9T C2 C1 C 0 1 N N N N N N 22.766 38.856 23.933 3.560 -0.988 -0.773 C2 A1B9T 4 A1B9T C4 C2 C 0 1 N N N N N N 24.541 37.993 25.393 5.575 -0.068 -0.032 C4 A1B9T 5 A1B9T C5 C3 C 0 1 N N N N N N 25.427 39.177 25.030 4.940 1.191 0.099 C5 A1B9T 6 A1B9T C6 C4 C 0 1 N N N N N N 24.976 40.111 24.176 3.631 1.301 -0.215 C6 A1B9T 7 A1B9T C7 C5 C 0 1 N N N N N N 26.820 39.291 25.641 5.713 2.390 0.583 C7 A1B9T 8 A1B9T "C1'" C6 C 0 1 N N N N N N 23.169 41.000 22.667 1.526 0.324 -1.000 "C1'" A1B9T 9 A1B9T "C2'" C7 C 0 1 N N N N N N 22.423 42.119 23.374 0.685 0.047 0.220 "C2'" A1B9T 10 A1B9T "C3'" C8 C 0 1 N N N N N N 19.111 43.260 23.752 -1.693 -1.675 1.462 "C3'" A1B9T 11 A1B9T "C4'" C9 C 0 1 N N S N N N 20.499 43.713 23.352 -1.477 -0.167 1.323 "C4'" A1B9T 12 A1B9T "C5'" C10 C 0 1 N N N N N N 20.409 44.807 22.293 -2.830 0.531 1.178 "C5'" A1B9T 13 A1B9T N3 N3 N 0 1 N N N N N N 23.245 37.871 24.835 4.863 -1.127 -0.467 N3 A1B9T 14 A1B9T "O2'" O2 O 0 1 N N N N N N 22.786 42.545 24.418 1.218 -0.225 1.275 "O2'" A1B9T 15 A1B9T "O3'" O3 O 0 1 N N N N N N 18.520 44.155 24.255 -2.464 -2.150 0.356 "O3'" A1B9T 16 A1B9T O4 O4 O 0 1 N N N N N N 24.934 37.172 26.143 6.755 -0.192 0.245 O4 A1B9T 17 A1B9T "O5'" O5 O 0 1 N N N N N N 21.685 44.981 21.741 -3.549 -0.044 0.085 "O5'" A1B9T 18 A1B9T OP1 O6 O 0 1 N N N N N N 21.018 47.537 21.251 -5.930 0.380 0.807 OP1 A1B9T 19 A1B9T OP2 O7 O 0 1 N N N N N N 23.405 47.120 21.618 -4.936 1.967 -0.887 OP2 A1B9T 20 A1B9T P P1 P 0 1 N N N N N N 22.064 46.558 21.512 -5.017 0.449 -0.356 P A1B9T 21 A1B9T H2 H1 H 0 1 N N N N N N 20.955 42.282 21.844 -1.085 0.320 -0.706 H2 A1B9T 22 A1B9T H52 H11 H 0 1 N N N N N N 20.071 45.746 22.755 -3.404 0.405 2.097 H52 A1B9T 23 A1B9T H51 H12 H 0 1 N N N N N N 19.700 44.508 21.507 -2.673 1.593 0.991 H51 A1B9T 24 A1B9T H3 H13 H 0 1 N N N N N N 22.668 37.091 25.077 5.291 -1.992 -0.559 H3 A1B9T 25 A1B9T H1 H14 H 0 1 N N N N N N 17.651 43.862 24.503 -2.640 -3.100 0.378 H1 A1B9T 26 A1B9T H5 H15 H 0 1 N N N N N N 23.365 48.061 21.494 -4.354 2.086 -1.649 H5 A1B9T 27 A1B9T OP3 OP3 O 0 1 N Y N N N N 22.447 46.165 20.050 -5.571 -0.502 -1.531 OP3 A1B9T 28 A1B9T HP3 HP3 H 0 1 N Y N N N N 21.911 46.656 19.439 -6.453 -0.263 -1.847 HP3 A1B9T 29 A1B9T H4 H4 H 0 1 N N N N N N 25.603 40.951 23.914 3.130 2.253 -0.122 H4 A1B9T 30 A1B9T H6 H6 H 0 1 N N N N N N 27.000 38.435 26.308 6.745 2.100 0.784 H6 A1B9T 31 A1B9T H7 H7 H 0 1 N N N N N N 27.573 39.295 24.839 5.696 3.166 -0.182 H7 A1B9T 32 A1B9T H8 H8 H 0 1 N N N N N N 26.892 40.226 26.216 5.258 2.770 1.498 H8 A1B9T 33 A1B9T H9 H9 H 0 1 N N N N N N 22.499 40.536 21.929 1.325 1.334 -1.359 H9 A1B9T 34 A1B9T H10 H10 H 0 1 N N N N N N 24.043 41.424 22.152 1.280 -0.395 -1.782 H10 A1B9T 35 A1B9T H11 H14 H 0 1 N N N N N N 18.567 42.922 22.858 -0.728 -2.181 1.476 H11 A1B9T 36 A1B9T H12 H15 H 0 1 N N N N N N 19.192 42.429 24.468 -2.225 -1.882 2.390 H12 A1B9T 37 A1B9T H13 H16 H 0 1 N N N N N N 21.032 44.098 24.234 -0.966 0.210 2.210 H13 A1B9T 38 # 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 A1B9T OP1 P DOUB N N 1 A1B9T P OP2 SING N N 2 A1B9T P "O5'" SING N N 3 A1B9T "O5'" "C5'" SING N N 4 A1B9T "C5'" "C4'" SING N N 5 A1B9T "C1'" "C2'" SING N N 6 A1B9T "C1'" N1 SING N N 7 A1B9T N2 "C4'" SING N N 8 A1B9T N2 "C2'" SING N N 9 A1B9T "C4'" "C3'" SING N N 10 A1B9T "C2'" "O2'" DOUB N N 11 A1B9T O2 C2 DOUB N N 12 A1B9T N1 C2 SING N N 13 A1B9T N1 C6 SING N N 14 A1B9T "C3'" "O3'" SING N N 15 A1B9T C2 N3 SING N N 16 A1B9T C6 C5 DOUB N N 17 A1B9T N3 C4 SING N N 18 A1B9T C5 C4 SING N N 19 A1B9T C5 C7 SING N N 20 A1B9T C4 O4 DOUB N N 21 A1B9T N2 H2 SING N N 22 A1B9T "C5'" H52 SING N N 23 A1B9T "C5'" H51 SING N N 24 A1B9T N3 H3 SING N N 25 A1B9T "O3'" H1 SING N N 26 A1B9T OP2 H5 SING N N 27 A1B9T P OP3 SING N N 28 A1B9T OP3 HP3 SING N N 29 A1B9T C6 H4 SING N N 30 A1B9T C7 H6 SING N N 31 A1B9T C7 H7 SING N N 32 A1B9T C7 H8 SING N N 33 A1B9T "C1'" H9 SING N N 34 A1B9T "C1'" H10 SING N N 35 A1B9T "C3'" H11 SING N N 36 A1B9T "C3'" H12 SING N N 37 A1B9T "C4'" H13 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 A1B9T SMILES ACDLabs 14.52 "O=C(CN1C=C(C)C(=O)NC1=O)NC(CO)COP(=O)(O)O" A1B9T InChI InChI 1.06 "InChI=1S/C10H16N3O8P/c1-6-2-13(10(17)12-9(6)16)3-8(15)11-7(4-14)5-21-22(18,19)20/h2,7,14H,3-5H2,1H3,(H,11,15)(H,12,16,17)(H2,18,19,20)" A1B9T InChIKey InChI 1.06 GBTVWYHTXPOXOI-UHFFFAOYSA-N A1B9T SMILES_CANONICAL CACTVS 3.385 "CC1=CN(CC(=O)N[C@@H](CO)CO[P](O)(O)=O)C(=O)NC1=O" A1B9T SMILES CACTVS 3.385 "CC1=CN(CC(=O)N[CH](CO)CO[P](O)(O)=O)C(=O)NC1=O" A1B9T SMILES_CANONICAL "OpenEye OEToolkits" 3.1.0.0 "CC1=CN(C(=O)NC1=O)CC(=O)NC(CO)COP(=O)(O)O" A1B9T SMILES "OpenEye OEToolkits" 3.1.0.0 "CC1=CN(C(=O)NC1=O)CC(=O)NC(CO)COP(=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 A1B9T "SYSTEMATIC NAME" ACDLabs 14.52 "(2S)-3-hydroxy-2-[2-(5-methyl-2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)acetamido]propyl dihydrogen phosphate" A1B9T "SYSTEMATIC NAME" "OpenEye OEToolkits" 3.1.0.0 "[2-[2-[5-methyl-2,4-bis(oxidanylidene)pyrimidin-1-yl]ethanoylamino]-3-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 A1B9T "Create component" 2025-04-11 RCSB A1B9T "Initial release" 2026-04-22 RCSB #