data_2L4 # _chem_comp.id 2L4 _chem_comp.name "1-deoxy-1-({2,6-dioxo-5-[(E)-(2-oxoethylidene)amino]-1,2,3,6-tetrahydropyrimidin-4-yl}amino)-D-ribitol" _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C11 H16 N4 O7" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms "5-(2-oxoethylideneamino)-6-D-ribitylaminouracil" _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2013-11-25 _chem_comp.pdbx_modified_date 2021-03-01 _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 316.267 _chem_comp.one_letter_code ? _chem_comp.three_letter_code 2L4 _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 4NQE _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 2L4 C4 C4 C 0 1 N N N -92.587 65.644 93.157 3.904 0.742 -0.246 C4 2L4 1 2L4 C6 C6 C 0 1 N N N -91.503 68.351 92.689 3.507 -2.100 0.323 C6 2L4 2 2L4 C7 C7 C 0 1 N N N -90.995 69.734 92.411 3.464 -3.507 0.245 C7 2L4 3 2L4 N1 N1 N 0 1 N N N -90.870 64.087 94.673 1.469 2.005 0.028 N1 2L4 4 2L4 N3 N3 N 0 1 N N N -92.926 64.395 93.553 3.818 2.080 -0.097 N3 2L4 5 2L4 N5 N5 N 0 1 N N N -90.777 67.473 93.233 2.689 -1.379 -0.404 N5 2L4 6 2L4 C4A C4A C 0 1 N N N -91.249 66.184 93.522 2.662 -0.045 -0.259 C4A 2L4 7 2L4 O4 O4 O 0 1 N N N -93.399 66.347 92.512 4.986 0.199 -0.371 O4 2L4 8 2L4 C2 C2 C 0 1 N N N -92.108 63.661 94.317 2.626 2.685 0.035 C2 2L4 9 2L4 O2 O2 O 0 1 N N N -92.438 62.503 94.622 2.595 3.893 0.166 O2 2L4 10 2L4 C8A C8A C 0 1 N N N -90.407 65.302 94.333 1.444 0.647 -0.116 C8A 2L4 11 2L4 N8 N8 N 0 1 N N N -89.213 65.769 94.737 0.261 -0.027 -0.120 N8 2L4 12 2L4 "C1'" "C1'" C 0 1 N N N -88.543 65.322 95.932 -0.999 0.705 0.030 "C1'" 2L4 13 2L4 "C2'" "C2'" C 0 1 N N S -87.408 64.367 95.580 -2.169 -0.281 -0.008 "C2'" 2L4 14 2L4 "O2'" "O2'" O 0 1 N N N -86.458 65.002 94.702 -2.167 -0.974 -1.258 "O2'" 2L4 15 2L4 "C3'" "C3'" C 0 1 N N S -87.870 62.994 95.052 -3.485 0.484 0.149 "C3'" 2L4 16 2L4 "O3'" "O3'" O 0 1 N N N -88.915 62.422 95.852 -3.487 1.177 1.398 "O3'" 2L4 17 2L4 "C4'" "C4'" C 0 1 N N R -86.726 62.003 94.984 -4.655 -0.502 0.110 "C4'" 2L4 18 2L4 "O4'" "O4'" O 0 1 N N N -87.203 60.831 94.330 -4.653 -1.195 -1.139 "O4'" 2L4 19 2L4 "C5'" "C5'" C 0 1 N N N -86.109 61.683 96.348 -5.971 0.262 0.267 "C5'" 2L4 20 2L4 "O5'" "O5'" O 0 1 N N N -85.086 60.687 96.214 -7.054 -0.666 0.348 "O5'" 2L4 21 2L4 H1 H1 H 0 1 N N N -92.517 68.099 92.417 4.213 -1.617 0.981 H1 2L4 22 2L4 O1 O1 O 0 1 N Y N -91.263 71.073 92.835 4.222 -4.176 0.919 O1 2L4 23 2L4 H5 H5 H 0 1 N N N -93.805 64.013 93.269 4.629 2.613 -0.086 H5 2L4 24 2L4 H7 H7 H 0 1 N N N -88.580 65.586 93.985 0.253 -0.991 -0.223 H7 2L4 25 2L4 H8 H8 H 0 1 N N N -88.132 66.193 96.464 -1.001 1.234 0.983 H8 2L4 26 2L4 H9 H9 H 0 1 N N N -89.265 64.803 96.580 -1.102 1.423 -0.784 H9 2L4 27 2L4 H10 H10 H 0 1 N N N -86.882 64.162 96.524 -2.066 -0.998 0.805 H10 2L4 28 2L4 H11 H11 H 0 1 N N N -85.760 64.392 94.495 -2.255 -0.396 -2.028 H11 2L4 29 2L4 H12 H12 H 0 1 N N N -88.247 63.143 94.029 -3.588 1.201 -0.665 H12 2L4 30 2L4 H13 H13 H 0 1 N N N -89.167 61.580 95.490 -3.399 0.599 2.169 H13 2L4 31 2L4 H14 H14 H 0 1 N N N -85.936 62.453 94.365 -4.552 -1.220 0.924 H14 2L4 32 2L4 H15 H15 H 0 1 N N N -86.503 60.192 94.274 -4.741 -0.617 -1.910 H15 2L4 33 2L4 H16 H16 H 0 1 N N N -85.670 62.599 96.771 -5.937 0.861 1.177 H16 2L4 34 2L4 H17 H17 H 0 1 N N N -86.894 61.308 97.021 -6.116 0.916 -0.593 H17 2L4 35 2L4 H18 H18 H 0 1 N N N -84.713 60.499 97.067 -7.921 -0.251 0.449 H18 2L4 36 2L4 H2 H2 H 0 1 N N N -90.199 69.713 91.682 2.757 -3.991 -0.413 H2 2L4 37 2L4 H161 H161 H 0 0 N N N -90.283 63.477 95.206 0.634 2.488 0.128 H161 2L4 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 2L4 C4 C4A SING N N 1 2L4 C4 N3 SING N N 2 2L4 C6 N5 DOUB N N 3 2L4 C6 H1 SING N N 4 2L4 C7 C6 SING N N 5 2L4 C7 O1 DOUB N N 6 2L4 N3 C2 SING N N 7 2L4 N3 H5 SING N N 8 2L4 N5 C4A SING N N 9 2L4 C4A C8A DOUB N N 10 2L4 O4 C4 DOUB N N 11 2L4 C2 O2 DOUB N N 12 2L4 C2 N1 SING N N 13 2L4 C8A N1 SING N N 14 2L4 C8A N8 SING N N 15 2L4 N8 "C1'" SING N N 16 2L4 N8 H7 SING N N 17 2L4 "C1'" H8 SING N N 18 2L4 "C1'" H9 SING N N 19 2L4 "C2'" "C1'" SING N N 20 2L4 "C2'" H10 SING N N 21 2L4 "O2'" "C2'" SING N N 22 2L4 "O2'" H11 SING N N 23 2L4 "C3'" "C2'" SING N N 24 2L4 "C3'" "O3'" SING N N 25 2L4 "C3'" H12 SING N N 26 2L4 "O3'" H13 SING N N 27 2L4 "C4'" "C3'" SING N N 28 2L4 "C4'" "C5'" SING N N 29 2L4 "C4'" H14 SING N N 30 2L4 "O4'" "C4'" SING N N 31 2L4 "O4'" H15 SING N N 32 2L4 "C5'" H16 SING N N 33 2L4 "C5'" H17 SING N N 34 2L4 "O5'" "C5'" SING N N 35 2L4 "O5'" H18 SING N N 36 2L4 C7 H2 SING N N 37 2L4 N1 H161 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 2L4 SMILES ACDLabs 12.01 "O=C1NC(NCC(O)C(O)C(O)CO)=C(\N=C\C=O)C(=O)N1" 2L4 InChI InChI 1.03 "InChI=1S/C11H16N4O7/c16-2-1-12-7-9(14-11(22)15-10(7)21)13-3-5(18)8(20)6(19)4-17/h1-2,5-6,8,17-20H,3-4H2,(H3,13,14,15,21,22)/b12-1+/t5-,6+,8-/m0/s1" 2L4 InChIKey InChI 1.03 PUEQUELBQOQOOV-GJQDMXJLSA-N 2L4 SMILES_CANONICAL CACTVS 3.370 "OC[C@@H](O)[C@@H](O)[C@@H](O)CNC1=C(N=CC=O)C(=O)NC(=O)N1" 2L4 SMILES CACTVS 3.370 "OC[CH](O)[CH](O)[CH](O)CNC1=C(N=CC=O)C(=O)NC(=O)N1" 2L4 SMILES_CANONICAL "OpenEye OEToolkits" 1.7.6 "C(C(C(C(CO)O)O)O)NC1=C(C(=O)NC(=O)N1)/N=C/C=O" 2L4 SMILES "OpenEye OEToolkits" 1.7.6 "C(C(C(C(CO)O)O)O)NC1=C(C(=O)NC(=O)N1)N=CC=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 2L4 "SYSTEMATIC NAME" ACDLabs 12.01 "1-deoxy-1-({2,6-dioxo-5-[(E)-(2-oxoethylidene)amino]-1,2,3,6-tetrahydropyrimidin-4-yl}amino)-D-ribitol" 2L4 "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.7.6 "(2E)-2-[[2,4-bis(oxidanylidene)-6-[2,3,4,5-tetrakis(oxidanyl)pentylamino]-1H-pyrimidin-5-yl]imino]ethanal" # # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site 2L4 "Create component" 2013-11-25 RCSB 2L4 "Initial release" 2014-04-16 RCSB 2L4 "Modify synonyms" 2021-03-01 PDBE # _pdbx_chem_comp_synonyms.ordinal 1 _pdbx_chem_comp_synonyms.comp_id 2L4 _pdbx_chem_comp_synonyms.name "5-(2-oxoethylideneamino)-6-D-ribitylaminouracil" _pdbx_chem_comp_synonyms.provenance ? _pdbx_chem_comp_synonyms.type ? ##