data_XC # _chem_comp.id XC _chem_comp.name "[(2~{R},3~{R},5~{R})-5-(6-azanyl-2-oxidanylidene-4,5-dihydropyrimidin-3-yl)-3-oxidanyl-oxolan-2-yl]methyl dihydrogen phosphate" _chem_comp.type non-polymer _chem_comp.pdbx_type HETAIN _chem_comp.formula "C9 H16 N3 O7 P" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2021-01-12 _chem_comp.pdbx_modified_date 2021-01-22 _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 309.213 _chem_comp.one_letter_code ? _chem_comp.three_letter_code XC _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 7BFS _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 XC P P1 P 0 1 N N N 38.977 33.367 16.850 4.012 -0.931 -0.007 P XC 1 XC O1P O1 O 0 1 N N N 40.117 33.925 16.239 5.077 0.062 0.257 O1P XC 2 XC O2P O2 O 0 1 N N N 37.641 33.976 16.702 3.637 -1.692 1.362 O2P XC 3 XC "O5'" O3 O 0 1 N N N 38.931 31.857 16.376 2.707 -0.181 -0.579 "O5'" XC 4 XC "C5'" C1 C 0 1 N N N 37.874 30.958 16.727 2.070 0.900 0.104 "C5'" XC 5 XC "C4'" C2 C 0 1 N N R 38.126 29.580 16.081 0.866 1.379 -0.710 "C4'" XC 6 XC "O4'" O4 O 0 1 N N N 39.111 28.899 16.886 -0.181 0.384 -0.693 "O4'" XC 7 XC "C1'" C3 C 0 1 N N R 38.942 27.477 16.705 -1.389 1.098 -1.032 "C1'" XC 8 XC N1 N1 N 0 1 N N N 39.467 26.821 17.956 -2.566 0.350 -0.584 N1 XC 9 XC C6 C4 C 0 1 N N N 38.607 26.492 19.030 -3.632 0.029 -1.537 C6 XC 10 XC C5 C5 C 0 1 N N N 39.064 25.772 20.071 -4.208 -1.350 -1.202 C5 XC 11 XC C4 C6 C 0 1 N N N 40.402 25.372 20.069 -4.455 -1.439 0.282 C4 XC 12 XC N4 N2 N 0 1 N N N 40.920 24.675 21.052 -5.489 -2.174 0.747 N4 XC 13 XC N3 N3 N 0 1 N N N 41.212 25.605 19.067 -3.678 -0.809 1.122 N3 XC 14 XC C2 C7 C 0 1 N N N 40.762 26.330 18.045 -2.660 -0.044 0.698 C2 XC 15 XC O2 O5 O 0 1 N N N 41.688 26.737 17.282 -1.806 0.305 1.492 O2 XC 16 XC "C3'" C8 C 0 1 N N R 36.869 28.678 16.154 0.235 2.628 -0.055 "C3'" XC 17 XC "C2'" C9 C 0 1 N N N 37.430 27.252 16.317 -1.283 2.438 -0.271 "C2'" XC 18 XC "O3'" O6 O 0 1 N N N 36.094 28.955 17.335 0.541 2.669 1.340 "O3'" XC 19 XC O1 O7 O 0 1 N Y N 39.305 33.203 18.409 4.534 -2.001 -1.090 O1 XC 20 XC H1 H1 H 0 1 N N N 37.705 34.752 16.158 2.944 -2.359 1.263 H1 XC 21 XC "H5'2" H2 H 0 0 N N N 36.916 31.361 16.366 1.733 0.563 1.085 "H5'2" XC 22 XC "H5'1" H3 H 0 0 N N N 37.836 30.847 17.821 2.776 1.721 0.225 "H5'1" XC 23 XC "H4'" H4 H 0 1 N N N 38.455 29.697 15.038 1.166 1.599 -1.735 "H4'" XC 24 XC "H1'" H5 H 0 1 N N N 39.556 27.144 15.855 -1.438 1.273 -2.107 "H1'" XC 25 XC H6 H6 H 0 1 N N N 38.238 27.443 19.442 -4.420 0.779 -1.468 H6 XC 26 XC H2 H7 H 0 1 N N N 37.767 25.927 18.600 -3.226 0.018 -2.548 H2 XC 27 XC H3 H8 H 0 1 N N N 38.907 26.376 20.977 -5.147 -1.492 -1.737 H3 XC 28 XC H5 H9 H 0 1 N N N 38.452 24.859 20.128 -3.499 -2.122 -1.501 H5 XC 29 XC H41 H10 H 0 1 N N N 41.869 24.364 20.999 -6.069 -2.642 0.126 H41 XC 30 XC H42 H11 H 0 1 N N N 40.366 24.454 21.855 -5.651 -2.233 1.701 H42 XC 31 XC "H3'" H12 H 0 1 N N N 36.274 28.762 15.232 0.582 3.535 -0.550 "H3'" XC 32 XC "H2'2" H13 H 0 0 N N N 36.898 26.712 17.114 -1.687 3.252 -0.873 "H2'2" XC 33 XC "H2'1" H14 H 0 0 N N N 37.348 26.690 15.375 -1.800 2.376 0.686 "H2'1" XC 34 XC H4 H15 H 0 1 N N N 35.331 28.389 17.354 0.169 3.433 1.802 H4 XC 35 XC H7 H16 H 0 1 N N N 40.186 33.514 18.582 5.319 -2.492 -0.812 H7 XC 36 # # 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 XC "C4'" "C3'" SING N N 1 XC "C4'" "C5'" SING N N 2 XC "C4'" "O4'" SING N N 3 XC "C3'" "C2'" SING N N 4 XC "C3'" "O3'" SING N N 5 XC O1P P DOUB N N 6 XC "C2'" "C1'" SING N N 7 XC "O5'" "C5'" SING N N 8 XC "O5'" P SING N N 9 XC O2P P SING N N 10 XC "C1'" "O4'" SING N N 11 XC "C1'" N1 SING N N 12 XC O2 C2 DOUB N N 13 XC N1 C2 SING N N 14 XC N1 C6 SING N N 15 XC C2 N3 SING N N 16 XC C6 C5 SING N N 17 XC N3 C4 DOUB N N 18 XC C4 C5 SING N N 19 XC C4 N4 SING N N 20 XC P O1 SING N N 21 XC O2P H1 SING N N 22 XC "C5'" "H5'2" SING N N 23 XC "C5'" "H5'1" SING N N 24 XC "C4'" "H4'" SING N N 25 XC "C1'" "H1'" SING N N 26 XC C6 H6 SING N N 27 XC C6 H2 SING N N 28 XC C5 H3 SING N N 29 XC C5 H5 SING N N 30 XC N4 H41 SING N N 31 XC N4 H42 SING N N 32 XC "C3'" "H3'" SING N N 33 XC "C2'" "H2'2" SING N N 34 XC "C2'" "H2'1" SING N N 35 XC "O3'" H4 SING N N 36 XC O1 H7 SING N N 37 # # 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 XC InChI InChI 1.03 "InChI=1S/C9H16N3O7P/c10-7-1-2-12(9(14)11-7)8-3-5(13)6(19-8)4-18-20(15,16)17/h5-6,8,13H,1-4H2,(H2,10,11,14)(H2,15,16,17)/t5-,6-,8-/m1/s1" XC InChIKey InChI 1.03 RARHVLRQJXIMCB-ATRFCDNQSA-N XC SMILES_CANONICAL CACTVS 3.385 "NC1=NC(=O)N(CC1)[C@H]2C[C@@H](O)[C@@H](CO[P](O)(O)=O)O2" XC SMILES CACTVS 3.385 "NC1=NC(=O)N(CC1)[CH]2C[CH](O)[CH](CO[P](O)(O)=O)O2" XC SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "C1CN(C(=O)N=C1N)[C@H]2C[C@H]([C@H](O2)COP(=O)(O)O)O" XC SMILES "OpenEye OEToolkits" 2.0.7 "C1CN(C(=O)N=C1N)C2CC(C(O2)COP(=O)(O)O)O" # _pdbx_chem_comp_identifier.comp_id XC _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~{R},3~{R},5~{R})-5-(6-azanyl-2-oxidanylidene-4,5-dihydropyrimidin-3-yl)-3-oxidanyl-oxolan-2-yl]methyl 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 XC "Create component" 2021-01-12 PDBE XC "Initial release" 2021-01-27 RCSB ##