data_RCA # _chem_comp.id RCA _chem_comp.name "6-{[4-(HYDROXYMETHYL)-5-METHYL-2,6-DIOXOHEXAHYDROPYRIMIDIN-5-YL]METHYL}-5-METHYLPYRIMIDINE-2,4(1H,3H)-DIONE" _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C12 H16 N4 O5" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms "HYDROXYMETHYL-HYDROTHYMYL-THYMINE; 5-[THYMIN-6-YL]METHYL-6-HYDRO-6-HYDROXYMETHYL-THYMINE" _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2000-05-24 _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 296.279 _chem_comp.one_letter_code ? _chem_comp.three_letter_code RCA _chem_comp.pdbx_model_coordinates_details ? _chem_comp.pdbx_model_coordinates_missing_flag N _chem_comp.pdbx_ideal_coordinates_details ? _chem_comp.pdbx_ideal_coordinates_missing_flag N _chem_comp.pdbx_model_coordinates_db_code 1E2N _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 RCA O2 O2 O 0 1 N N N 42.934 35.023 1.953 1.374 -1.124 4.306 O2 RCA 1 RCA C3 C3 C 0 1 Y N N 45.278 35.549 1.500 1.160 -0.147 2.250 C3 RCA 2 RCA C4 C4 C 0 1 N N N 45.340 36.685 2.457 2.541 -0.566 1.818 C4 RCA 3 RCA C5 C5 C 0 1 Y N N 46.369 35.185 0.761 0.365 0.555 1.415 C5 RCA 4 RCA C1 C1 C 0 1 Y N N 45.099 33.361 -0.309 -1.332 0.599 3.050 C1 RCA 5 RCA N1 N1 N 0 1 Y N N 46.296 34.107 -0.138 -0.886 0.927 1.823 N1 RCA 6 RCA C2 C2 C 0 1 Y N N 44.004 34.827 1.377 0.675 -0.490 3.536 C2 RCA 7 RCA N2 N2 N 0 1 Y N N 43.964 33.731 0.449 -0.561 -0.100 3.902 N2 RCA 8 RCA O1 O1 O 0 1 N N N 45.079 32.427 -1.103 -2.448 0.940 3.392 O1 RCA 9 RCA C11 C11 C 0 1 N N R 50.094 35.838 1.750 1.065 0.142 -2.323 C11 RCA 10 RCA O4 O4 O 0 1 N N N 52.317 32.959 1.719 -1.410 -1.563 -4.205 O4 RCA 11 RCA O3 O3 O 0 1 N N N 48.724 33.612 -0.821 -1.761 0.253 -0.190 O3 RCA 12 RCA N4 N4 N 0 1 N N N 51.155 34.887 2.222 0.423 -0.684 -3.347 N4 RCA 13 RCA C10 C10 C 0 1 N N N 51.457 33.772 1.401 -0.888 -0.963 -3.286 C10 RCA 14 RCA C12 C12 C 0 1 N N N 50.710 36.752 0.648 0.874 1.620 -2.668 C12 RCA 15 RCA O5 O5 O 0 1 N N N 50.660 38.072 1.132 1.464 1.893 -3.940 O5 RCA 16 RCA C7 C7 C 0 1 N N R 48.896 34.979 1.220 0.433 -0.150 -0.960 C7 RCA 17 RCA N3 N3 N 0 1 N N N 50.696 33.557 0.205 -1.637 -0.595 -2.234 N3 RCA 18 RCA C9 C9 C 0 1 N N N 49.424 34.159 0.024 -1.068 -0.149 -1.099 C9 RCA 19 RCA C6 C6 C 0 1 N N N 47.709 35.884 0.852 0.855 0.928 0.039 C6 RCA 20 RCA C8 C8 C 0 1 N N N 48.508 33.995 2.321 0.900 -1.519 -0.463 C8 RCA 21 RCA H43 3H4 H 0 1 N N N 44.450 36.981 3.059 3.058 -1.033 2.656 H43 RCA 22 RCA H42 2H4 H 0 1 N N N 46.185 36.498 3.159 2.465 -1.278 0.996 H42 RCA 23 RCA H41 1H4 H 0 1 N N N 45.696 37.584 1.902 3.100 0.309 1.489 H41 RCA 24 RCA H1 H1 H 0 1 N N N 47.042 33.452 0.096 -1.457 1.432 1.223 H1 RCA 25 RCA H2 H2 H 0 1 N N N 43.102 33.198 0.324 -0.899 -0.328 4.783 H2 RCA 26 RCA H11 H11 H 0 1 N N N 49.718 36.501 2.563 2.130 -0.087 -2.286 H11 RCA 27 RCA H4 H4 H 0 1 N N N 50.919 34.559 3.158 0.953 -1.034 -4.080 H4 RCA 28 RCA H122 2H12 H 0 0 N N N 51.734 36.437 0.340 -0.190 1.850 -2.704 H122 RCA 29 RCA H121 1H12 H 0 0 N N N 50.219 36.631 -0.345 1.352 2.235 -1.906 H121 RCA 30 RCA H5 H5 H 0 1 N N N 51.035 38.629 0.460 1.322 2.833 -4.119 H5 RCA 31 RCA H3 H3 H 0 1 N N N 51.068 32.961 -0.534 -2.604 -0.652 -2.293 H3 RCA 32 RCA H62 2H6 H 0 1 N N N 47.922 36.429 -0.096 0.422 1.884 -0.253 H62 RCA 33 RCA H61 1H6 H 0 1 N N N 47.646 36.742 1.561 1.942 1.009 0.050 H61 RCA 34 RCA H83 3H8 H 0 1 N N N 47.655 33.383 1.943 0.574 -1.662 0.566 H83 RCA 35 RCA H82 2H8 H 0 1 N N N 49.366 33.373 2.669 0.472 -2.299 -1.092 H82 RCA 36 RCA H81 1H8 H 0 1 N N N 48.285 34.496 3.291 1.988 -1.571 -0.510 H81 RCA 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 RCA O2 C2 DOUB N N 1 RCA C3 C4 SING N N 2 RCA C3 C5 DOUB Y N 3 RCA C3 C2 SING Y N 4 RCA C4 H43 SING N N 5 RCA C4 H42 SING N N 6 RCA C4 H41 SING N N 7 RCA C5 N1 SING Y N 8 RCA C5 C6 SING N N 9 RCA C1 N1 SING Y N 10 RCA C1 N2 SING Y N 11 RCA C1 O1 DOUB N N 12 RCA N1 H1 SING N N 13 RCA C2 N2 SING Y N 14 RCA N2 H2 SING N N 15 RCA C11 N4 SING N N 16 RCA C11 C12 SING N N 17 RCA C11 C7 SING N N 18 RCA C11 H11 SING N N 19 RCA O4 C10 DOUB N N 20 RCA O3 C9 DOUB N N 21 RCA N4 C10 SING N N 22 RCA N4 H4 SING N N 23 RCA C10 N3 SING N N 24 RCA C12 O5 SING N N 25 RCA C12 H122 SING N N 26 RCA C12 H121 SING N N 27 RCA O5 H5 SING N N 28 RCA C7 C9 SING N N 29 RCA C7 C6 SING N N 30 RCA C7 C8 SING N N 31 RCA N3 C9 SING N N 32 RCA N3 H3 SING N N 33 RCA C6 H62 SING N N 34 RCA C6 H61 SING N N 35 RCA C8 H83 SING N N 36 RCA C8 H82 SING N N 37 RCA C8 H81 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 RCA SMILES ACDLabs 10.04 "O=C1NC(CO)C(C(=O)N1)(C)CC2=C(C(=O)NC(=O)N2)C" RCA SMILES_CANONICAL CACTVS 3.341 "CC1=C(C[C@]2(C)[C@H](CO)NC(=O)NC2=O)NC(=O)NC1=O" RCA SMILES CACTVS 3.341 "CC1=C(C[C]2(C)[CH](CO)NC(=O)NC2=O)NC(=O)NC1=O" RCA SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "CC1=C(NC(=O)NC1=O)C[C@@]2([C@@H](NC(=O)NC2=O)CO)C" RCA SMILES "OpenEye OEToolkits" 1.5.0 "CC1=C(NC(=O)NC1=O)CC2(C(NC(=O)NC2=O)CO)C" RCA InChI InChI 1.03 "InChI=1S/C12H16N4O5/c1-5-6(13-10(20)15-8(5)18)3-12(2)7(4-17)14-11(21)16-9(12)19/h7,17H,3-4H2,1-2H3,(H2,13,15,18,20)(H2,14,16,19,21)/t7-,12+/m0/s1" RCA InChIKey InChI 1.03 KBBKHMIEEMSXSM-JVXZTZIISA-N # # 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 RCA "SYSTEMATIC NAME" ACDLabs 10.04 "6-{[(4R,5R)-4-(hydroxymethyl)-5-methyl-2,6-dioxohexahydropyrimidin-5-yl]methyl}-5-methylpyrimidine-2,4(1H,3H)-dione" RCA "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "6-[[(4R,5R)-4-(hydroxymethyl)-5-methyl-2,6-dioxo-1,3-diazinan-5-yl]methyl]-5-methyl-1H-pyrimidine-2,4-dione" # # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site RCA "Create component" 2000-05-24 EBI RCA "Modify descriptor" 2011-06-04 RCSB RCA "Modify synonyms" 2020-06-05 PDBE # # loop_ _pdbx_chem_comp_synonyms.ordinal _pdbx_chem_comp_synonyms.comp_id _pdbx_chem_comp_synonyms.name _pdbx_chem_comp_synonyms.provenance _pdbx_chem_comp_synonyms.type 1 RCA HYDROXYMETHYL-HYDROTHYMYL-THYMINE ? ? 2 RCA 5-[THYMIN-6-YL]METHYL-6-HYDRO-6-HYDROXYMETHYL-THYMINE ? ? ##