data_AWC # _chem_comp.id AWC _chem_comp.name "2'-deoxy-5'-O-[(R)-hydroxy(oxo)-lambda~5~-phosphanyl]-5-selenophen-2-yluridine" _chem_comp.type "DNA linking" _chem_comp.pdbx_type ATOMN _chem_comp.formula "C13 H15 N2 O7 P Se" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2018-11-28 _chem_comp.pdbx_modified_date 2019-05-10 _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 421.201 _chem_comp.one_letter_code ? _chem_comp.three_letter_code AWC _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 6IP7 _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 AWC P P1 P 0 1 N N N 4.285 10.966 -5.664 5.996 1.490 -0.720 P AWC 1 AWC "C5'" C1 C 0 1 N N N 2.064 12.347 -5.980 4.404 -0.434 0.229 "C5'" AWC 2 AWC "O5'" O1 O 0 1 N N N 2.740 11.285 -5.321 4.735 0.952 0.123 "O5'" AWC 3 AWC "C4'" C2 C 0 1 N N R 0.705 12.246 -5.291 3.155 -0.596 1.099 "C4'" AWC 4 AWC "O4'" O2 O 0 1 N N N 0.869 12.567 -3.905 2.003 -0.021 0.445 "O4'" AWC 5 AWC "C3'" C3 C 0 1 N N S -0.296 13.221 -5.850 2.780 -2.092 1.242 "C3'" AWC 6 AWC "O3'" O3 O 0 1 N N N -1.504 12.459 -5.978 3.491 -2.695 2.325 "O3'" AWC 7 AWC "C2'" C4 C 0 1 N N N -0.439 14.305 -4.810 1.265 -2.019 1.550 "C2'" AWC 8 AWC "C1'" C5 C 0 1 N N R -0.205 13.478 -3.552 0.841 -0.631 1.031 "C1'" AWC 9 AWC N1 N1 N 0 1 N N N 0.195 14.235 -2.336 -0.208 -0.776 0.019 N1 AWC 10 AWC C2 C6 C 0 1 N N N -0.210 13.764 -1.132 0.074 -1.404 -1.134 C2 AWC 11 AWC O2 O4 O 0 1 N N N -0.908 12.744 -1.040 1.196 -1.838 -1.311 O2 AWC 12 AWC N3 N2 N 0 1 N N N 0.149 14.440 0.047 -0.847 -1.567 -2.099 N3 AWC 13 AWC C4 C7 C 0 1 N N N 0.939 15.604 -0.001 -2.101 -1.097 -1.932 C4 AWC 14 AWC O4 O5 O 0 1 N N N 1.207 16.118 1.087 -2.940 -1.241 -2.802 O4 AWC 15 AWC C5 C8 C 0 1 N N N 1.378 16.100 -1.247 -2.433 -0.405 -0.676 C5 AWC 16 AWC C6 C9 C 0 1 N N N 1.006 15.410 -2.413 -1.452 -0.276 0.270 C6 AWC 17 AWC OP1 O6 O 0 1 N N N 4.803 9.809 -4.887 5.849 3.077 -0.952 OP1 AWC 18 AWC OP2 O7 O 0 1 N N N 4.421 10.830 -7.124 7.244 1.214 0.027 OP2 AWC 19 AWC C7 C10 C 0 1 Y N N 2.138 17.205 -1.342 -3.783 0.128 -0.441 C7 AWC 20 AWC C8 C11 C 0 1 Y N N 2.703 17.713 -2.454 -4.871 0.085 -1.248 C8 AWC 21 AWC C9 C12 C 0 1 Y N N 3.442 18.866 -2.333 -6.122 0.663 -0.854 C9 AWC 22 AWC C10 C13 C 0 1 Y N N 3.569 19.418 -1.108 -6.286 1.274 0.326 C10 AWC 23 AWC SE SE1 SE 0 0 Y N N 2.593 18.324 0.126 -4.490 1.089 1.141 SE AWC 24 AWC H5S H1 H 0 1 N N N 2.547 13.318 -5.795 4.210 -0.838 -0.764 H5S AWC 25 AWC "H5'" H2 H 0 1 N N N 1.988 12.175 -7.064 5.236 -0.973 0.684 "H5'" AWC 26 AWC "H4'" H3 H 0 1 N N N 0.320 11.222 -5.404 3.309 -0.140 2.077 "H4'" AWC 27 AWC "H3'" H4 H 0 1 N N N 0.043 13.634 -6.812 2.962 -2.630 0.312 "H3'" AWC 28 AWC H1 H5 H 0 1 N N N -2.192 13.012 -6.329 3.290 -3.632 2.455 H1 AWC 29 AWC H5T H6 H 0 1 N N N 0.320 15.092 -4.931 0.729 -2.805 1.018 H5T AWC 30 AWC "H2'" H7 H 0 1 N N N -1.442 14.757 -4.823 1.089 -2.095 2.623 "H2'" AWC 31 AWC "H1'" H8 H 0 1 N N N -1.118 12.904 -3.334 0.479 -0.021 1.858 "H1'" AWC 32 AWC H3 H9 H 0 1 N N N -0.161 14.090 0.931 -0.610 -2.026 -2.921 H3 AWC 33 AWC H6 H10 H 0 1 N N N 1.336 15.770 -3.376 -1.660 0.221 1.206 H6 AWC 34 AWC H2 H11 H 0 1 N N N 5.146 9.154 -5.484 6.576 3.470 -1.454 H2 AWC 35 AWC H4 H12 H 0 1 N N N 5.022 12.113 -5.266 6.042 0.831 -1.977 H4 AWC 36 AWC H8 H13 H 0 1 N N N 2.579 17.229 -3.412 -4.793 -0.396 -2.212 H8 AWC 37 AWC H9 H14 H 0 1 N N N 3.909 19.318 -3.196 -6.960 0.605 -1.533 H9 AWC 38 AWC H10 H15 H 0 1 N N N 4.121 20.314 -0.867 -7.171 1.743 0.730 H10 AWC 39 # # 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 AWC OP2 P DOUB N N 1 AWC "C5'" "O5'" SING N N 2 AWC "C5'" "C4'" SING N N 3 AWC "O3'" "C3'" SING N N 4 AWC "C3'" "C4'" SING N N 5 AWC "C3'" "C2'" SING N N 6 AWC P "O5'" SING N N 7 AWC P OP1 SING N N 8 AWC "C4'" "O4'" SING N N 9 AWC "C2'" "C1'" SING N N 10 AWC "O4'" "C1'" SING N N 11 AWC "C1'" N1 SING N N 12 AWC C8 C9 SING Y N 13 AWC C8 C7 DOUB Y N 14 AWC C6 N1 SING N N 15 AWC C6 C5 DOUB N N 16 AWC N1 C2 SING N N 17 AWC C9 C10 DOUB Y N 18 AWC C7 C5 SING N N 19 AWC C7 SE SING Y N 20 AWC C5 C4 SING N N 21 AWC C2 O2 DOUB N N 22 AWC C2 N3 SING N N 23 AWC C10 SE SING Y N 24 AWC C4 N3 SING N N 25 AWC C4 O4 DOUB N N 26 AWC "C5'" H5S SING N N 27 AWC "C5'" "H5'" SING N N 28 AWC "C4'" "H4'" SING N N 29 AWC "C3'" "H3'" SING N N 30 AWC "O3'" H1 SING N N 31 AWC "C2'" H5T SING N N 32 AWC "C2'" "H2'" SING N N 33 AWC "C1'" "H1'" SING N N 34 AWC N3 H3 SING N N 35 AWC C6 H6 SING N N 36 AWC OP1 H2 SING N N 37 AWC C8 H8 SING N N 38 AWC C9 H9 SING N N 39 AWC C10 H10 SING N N 40 AWC P H4 SING N N 41 # # 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 AWC SMILES ACDLabs 12.01 "P(OCC1OC(CC1O)N2C(=O)NC(=O)C(=C2)c3[se]ccc3)(O)=O" AWC InChI InChI 1.03 "InChI=1S/C13H15N2O7PSe/c16-8-4-11(22-9(8)6-21-23(19)20)15-5-7(10-2-1-3-24-10)12(17)14-13(15)18/h1-3,5,8-9,11,16,23H,4,6H2,(H,19,20)(H,14,17,18)/t8-,9+,11+/m0/s1" AWC InChIKey InChI 1.03 WYJQDKVLIYFCFU-IQJOONFLSA-N AWC SMILES_CANONICAL CACTVS 3.385 "O[C@H]1C[C@@H](O[C@@H]1CO[PH](O)=O)N2C=C(C(=O)NC2=O)c3[se]ccc3" AWC SMILES CACTVS 3.385 "O[CH]1C[CH](O[CH]1CO[PH](O)=O)N2C=C(C(=O)NC2=O)c3[se]ccc3" AWC SMILES_CANONICAL "OpenEye OEToolkits" 2.0.6 "c1cc([se]c1)C2=CN(C(=O)NC2=O)[C@H]3C[C@@H]([C@H](O3)COP(=O)O)O" AWC SMILES "OpenEye OEToolkits" 2.0.6 "c1cc([se]c1)C2=CN(C(=O)NC2=O)C3CC(C(O3)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 AWC "SYSTEMATIC NAME" ACDLabs 12.01 "2'-deoxy-5'-O-[(R)-hydroxy(oxo)-lambda~5~-phosphanyl]-5-selenophen-2-yluridine" AWC "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.6 "[(2~{R},3~{S},5~{R})-5-[2,4-bis(oxidanylidene)-5-selenophen-2-yl-pyrimidin-1-yl]-3-oxidanyl-oxolan-2-yl]methoxyphosphinic acid" # # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site AWC "Create component" 2018-11-28 RCSB AWC "Initial release" 2019-05-15 RCSB ##