data_L2B # _chem_comp.id L2B _chem_comp.name "3'-DEOXYURIDINE-5'-MONOPHOSPHATE" _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C9 H13 N2 O8 P" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms "[(2~{S},4~{R},5~{R})-5-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-4-oxidanyl-oxolan-2-yl]methyl dihydrogen phosphate" _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2019-07-16 _chem_comp.pdbx_modified_date 2020-11-13 _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 308.182 _chem_comp.one_letter_code ? _chem_comp.three_letter_code L2B _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 6SA1 _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site PDBE # # 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 L2B "C1'" C1 C 0 1 N N R -32.450 -19.402 27.822 1.270 0.991 0.388 "C1'" L2B 1 L2B C2 C2 C 0 1 N N N -33.297 -21.124 26.207 3.364 -0.084 0.996 C2 L2B 2 L2B "C2'" C3 C 0 1 N N R -31.308 -18.754 27.046 1.221 2.103 -0.683 "C2'" L2B 3 L2B "C3'" C4 C 0 1 N N N -31.102 -17.382 27.666 -0.288 2.359 -0.890 "C3'" L2B 4 L2B C4 C5 C 0 1 N N N -35.453 -21.011 25.330 4.415 -1.658 -0.373 C4 L2B 5 L2B "C4'" C6 C 0 1 N N S -32.004 -17.373 28.891 -0.973 1.371 0.080 "C4'" L2B 6 L2B C5 C7 C 0 1 N N N -35.692 -19.848 26.055 3.366 -1.525 -1.313 C5 L2B 7 L2B "C5'" C8 C 0 1 N N N -32.672 -16.015 29.078 -2.250 0.808 -0.547 "C5'" L2B 8 L2B C6 C9 C 0 1 N N N -34.696 -19.324 26.873 2.358 -0.664 -1.055 C6 L2B 9 L2B N1 N1 N 0 1 N N N -33.511 -19.941 26.953 2.364 0.057 0.108 N1 L2B 10 L2B N3 N2 N 0 1 N N N -34.266 -21.621 25.424 4.384 -0.930 0.762 N3 L2B 11 L2B O2 O1 O 0 1 N N N -32.196 -21.716 26.276 3.349 0.567 2.024 O2 L2B 12 L2B "O2'" O2 O 0 1 N N N -30.112 -19.524 27.197 1.869 3.284 -0.208 "O2'" L2B 13 L2B O4 O3 O 0 1 N N N -36.343 -21.491 24.594 5.337 -2.425 -0.585 O4 L2B 14 L2B "O4'" O4 O 0 1 N N N -32.987 -18.387 28.673 -0.004 0.319 0.281 "O4'" L2B 15 L2B "O5'" O5 O 0 1 N N N -33.337 -15.982 30.340 -2.928 -0.011 0.408 "O5'" L2B 16 L2B OP1 O6 O 0 1 N N N -35.293 -15.680 31.914 -5.471 0.320 -0.170 OP1 L2B 17 L2B OP2 O7 O 0 1 N N N -35.156 -14.279 29.889 -4.148 -1.609 -1.118 OP2 L2B 18 L2B P P1 P 0 1 N N N -34.913 -15.660 30.452 -4.312 -0.768 0.088 P L2B 19 L2B O1 O8 O 0 1 N Y N -35.302 -17.151 30.681 -4.718 -1.697 1.339 O1 L2B 20 L2B H1 H1 H 0 1 N N N -32.036 -20.218 28.433 1.388 1.425 1.381 H1 L2B 21 L2B H2 H2 H 0 1 N N N -31.586 -18.650 25.987 1.684 1.761 -1.610 H2 L2B 22 L2B H3 H3 H 0 1 N N N -30.051 -17.242 27.957 -0.540 3.387 -0.630 H3 L2B 23 L2B H4 H4 H 0 1 N N N -31.396 -16.590 26.962 -0.575 2.144 -1.919 H4 L2B 24 L2B H5 H5 H 0 1 N N N -31.404 -17.605 29.783 -1.201 1.865 1.025 H5 L2B 25 L2B H6 H6 H 0 1 N N N -36.649 -19.353 25.983 3.374 -2.100 -2.227 H6 L2B 26 L2B H7 H7 H 0 1 N N N -31.909 -15.223 29.045 -2.900 1.629 -0.848 H7 L2B 27 L2B H8 H8 H 0 1 N N N -33.404 -15.853 28.273 -1.992 0.209 -1.420 H8 L2B 28 L2B H9 H9 H 0 1 N N N -34.878 -18.424 27.441 1.549 -0.549 -1.761 H9 L2B 29 L2B H10 H10 H 0 1 N N N -34.099 -22.458 24.904 5.099 -1.016 1.411 H10 L2B 30 L2B H11 H11 H 0 1 N N N -30.237 -20.383 26.810 1.816 4.034 -0.817 H11 L2B 31 L2B H12 H12 H 0 1 N N N -35.605 -14.821 32.172 -5.634 0.907 0.581 H12 L2B 32 L2B H13 H13 H 0 1 N N N -36.131 -17.332 30.254 -5.544 -2.184 1.216 H13 L2B 33 # # 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 L2B O4 C4 DOUB N N 1 L2B C4 N3 SING N N 2 L2B C4 C5 SING N N 3 L2B N3 C2 SING N N 4 L2B C5 C6 DOUB N N 5 L2B C2 O2 DOUB N N 6 L2B C2 N1 SING N N 7 L2B C6 N1 SING N N 8 L2B N1 "C1'" SING N N 9 L2B "C2'" "O2'" SING N N 10 L2B "C2'" "C3'" SING N N 11 L2B "C2'" "C1'" SING N N 12 L2B "C3'" "C4'" SING N N 13 L2B "C1'" "O4'" SING N N 14 L2B "O4'" "C4'" SING N N 15 L2B "C4'" "C5'" SING N N 16 L2B "C5'" "O5'" SING N N 17 L2B OP2 P DOUB N N 18 L2B "O5'" P SING N N 19 L2B P OP1 SING N N 20 L2B P O1 SING N N 21 L2B "C1'" H1 SING N N 22 L2B "C2'" H2 SING N N 23 L2B "C3'" H3 SING N N 24 L2B "C3'" H4 SING N N 25 L2B "C4'" H5 SING N N 26 L2B C5 H6 SING N N 27 L2B "C5'" H7 SING N N 28 L2B "C5'" H8 SING N N 29 L2B C6 H9 SING N N 30 L2B N3 H10 SING N N 31 L2B "O2'" H11 SING N N 32 L2B OP1 H12 SING N N 33 L2B O1 H13 SING N N 34 # # 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 L2B InChI InChI 1.03 "InChI=1S/C9H13N2O8P/c12-6-3-5(4-18-20(15,16)17)19-8(6)11-2-1-7(13)10-9(11)14/h1-2,5-6,8,12H,3-4H2,(H,10,13,14)(H2,15,16,17)/t5-,6+,8+/m0/s1" L2B InChIKey InChI 1.03 SEOHEWZQAGEAGZ-SHYZEUOFSA-N L2B SMILES_CANONICAL CACTVS 3.385 "O[C@@H]1C[C@@H](CO[P](O)(O)=O)O[C@H]1N2C=CC(=O)NC2=O" L2B SMILES CACTVS 3.385 "O[CH]1C[CH](CO[P](O)(O)=O)O[CH]1N2C=CC(=O)NC2=O" L2B SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "C1[C@H](O[C@H]([C@@H]1O)N2C=CC(=O)NC2=O)COP(=O)(O)O" L2B SMILES "OpenEye OEToolkits" 2.0.7 "C1C(OC(C1O)N2C=CC(=O)NC2=O)COP(=O)(O)O" # _pdbx_chem_comp_identifier.comp_id L2B _pdbx_chem_comp_identifier.type "SYSTEMATIC NAME" _pdbx_chem_comp_identifier.program "OpenEye OEToolkits" _pdbx_chem_comp_identifier.program_version 2.0.7 _pdbx_chem_comp_identifier.identifier "[(2~{S},4~{R},5~{R})-5-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-4-oxidanyl-oxolan-2-yl]methyl dihydrogen phosphate" # _pdbx_chem_comp_synonyms.ordinal 1 _pdbx_chem_comp_synonyms.comp_id L2B _pdbx_chem_comp_synonyms.name "[(2~{S},4~{R},5~{R})-5-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-4-oxidanyl-oxolan-2-yl]methyl dihydrogen phosphate" _pdbx_chem_comp_synonyms.provenance ? _pdbx_chem_comp_synonyms.type ? # # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site L2B "Create component" 2019-07-16 PDBE L2B "Modify synonyms" 2020-06-05 PDBE L2B "Initial release" 2020-11-18 RCSB ##