data_U3J # _chem_comp.id U3J _chem_comp.name "xanthosine diphosphate" _chem_comp.type non-polymer _chem_comp.pdbx_type HETAIN _chem_comp.formula "C10 H14 N4 O12 P2" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2020-04-13 _chem_comp.pdbx_modified_date 2020-08-28 _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 444.185 _chem_comp.one_letter_code ? _chem_comp.three_letter_code U3J _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 6WJ3 _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 U3J N1 N1 N 0 1 N N N 165.977 181.588 131.942 6.770 1.399 -0.380 N1 U3J 1 U3J C8 C1 C 0 1 Y N N 162.220 183.879 132.642 2.650 0.679 1.347 C8 U3J 2 U3J N3 N2 N 0 1 N N N 164.271 182.069 130.471 4.979 0.180 -1.303 N3 U3J 3 U3J C6 C2 C 0 1 N N N 165.372 182.231 132.937 6.051 1.719 0.717 C6 U3J 4 U3J O2 O1 O 0 1 N N N 166.132 180.810 129.721 6.920 0.383 -2.330 O2 U3J 5 U3J N7 N3 N 0 1 Y N N 163.248 183.551 133.423 3.700 1.334 1.752 N7 U3J 6 U3J C2 C3 C 0 1 N N N 165.439 181.511 130.744 6.239 0.648 -1.359 C2 U3J 7 U3J C4 C4 C 0 1 Y N N 163.604 182.732 131.421 4.177 0.447 -0.217 C4 U3J 8 U3J C5 C5 C 0 1 Y N N 164.141 182.834 132.697 4.677 1.224 0.821 C5 U3J 9 U3J N9 N4 N 0 1 Y N N 162.416 183.379 131.413 2.901 0.126 0.125 N9 U3J 10 U3J O6 O2 O 0 1 N N N 165.964 182.296 134.194 6.534 2.403 1.601 O6 U3J 11 U3J "C1'" C6 C 0 1 N N R 161.543 183.509 130.254 1.966 -0.672 -0.672 "C1'" U3J 12 U3J "C2'" C7 C 0 1 N N S 160.129 182.789 130.444 2.186 -2.178 -0.409 "C2'" U3J 13 U3J "C3'" C8 C 0 1 N N R 159.078 183.853 130.065 0.761 -2.776 -0.437 "C3'" U3J 14 U3J "C4'" C9 C 0 1 N N R 159.686 185.032 130.221 -0.150 -1.560 -0.715 "C4'" U3J 15 U3J "C5'" C10 C 0 1 N N N 159.440 185.583 131.565 -1.457 -1.684 0.072 "C5'" U3J 16 U3J O1A O3 O 0 1 N N N 156.613 186.244 132.286 -3.667 -0.120 1.924 O1A U3J 17 U3J O1B O4 O 0 1 N N N 155.088 189.731 130.028 -6.975 0.124 -0.548 O1B U3J 18 U3J "O2'" O5 O 0 1 N N N 159.941 182.382 131.697 2.788 -2.380 0.872 "O2'" U3J 19 U3J O2A O6 O 0 1 N N N 156.884 186.748 129.890 -4.581 -1.669 0.153 O2A U3J 20 U3J O2B O7 O 0 1 N N N 154.414 188.300 131.897 -6.430 2.115 0.905 O2B U3J 21 U3J "O3'" O8 O 0 1 N N N 157.875 183.744 130.965 0.440 -3.365 0.825 "O3'" U3J 22 U3J O3A O9 O 0 1 N N N 156.943 188.741 131.572 -4.549 0.799 -0.375 O3A U3J 23 U3J O3B O10 O 0 1 N N N 155.237 190.578 132.349 -6.282 2.251 -1.716 O3B U3J 24 U3J "O4'" O11 O 0 1 N N N 161.303 184.768 130.013 0.607 -0.419 -0.256 "O4'" U3J 25 U3J "O5'" O12 O 0 1 N N N 158.950 186.915 131.423 -2.332 -0.612 -0.286 "O5'" U3J 26 U3J PA P1 P 0 1 N N N 157.327 187.128 131.277 -3.799 -0.428 0.350 PA U3J 27 U3J PB P2 P 0 1 N N N 155.376 189.349 131.459 -6.078 1.296 -0.436 PB U3J 28 U3J H1 H1 H 0 1 N N N 166.862 181.153 132.109 7.682 1.719 -0.464 H1 U3J 29 U3J H2 H2 H 0 1 N N N 161.362 184.458 132.951 1.720 0.595 1.890 H2 U3J 30 U3J H3 H3 H 0 1 N N N 163.886 181.995 129.551 4.635 -0.358 -2.032 H3 U3J 31 U3J H4 H4 H 0 1 N N N 162.031 183.031 129.392 2.088 -0.451 -1.733 H4 U3J 32 U3J H5 H5 H 0 1 N N N 160.068 181.957 129.727 2.802 -2.618 -1.193 H5 U3J 33 U3J H6 H6 H 0 1 N N N 158.767 183.688 129.023 0.671 -3.511 -1.237 H6 U3J 34 U3J H7 H7 H 0 1 N N N 159.369 185.759 129.459 -0.357 -1.477 -1.781 H7 U3J 35 U3J H8 H8 H 0 1 N N N 158.694 184.967 132.088 -1.933 -2.635 -0.162 H8 U3J 36 U3J H9 H9 H 0 1 N N N 160.378 185.591 132.140 -1.244 -1.637 1.140 H9 U3J 37 U3J H10 H10 H 0 1 N N N 156.040 185.640 131.829 -3.165 0.681 2.128 H10 U3J 38 U3J H11 H11 H 0 1 N N N 160.593 181.728 131.919 2.948 -3.309 1.089 H11 U3J 39 U3J H12 H12 H 0 1 N N N 153.823 188.094 131.183 -5.881 2.898 1.043 H12 U3J 40 U3J H13 H13 H 0 1 N N N 157.459 182.899 130.838 0.983 -4.133 1.049 H13 U3J 41 U3J H14 H14 H 0 1 N N N 154.998 191.329 131.818 -7.183 2.589 -1.816 H14 U3J 42 # # 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 U3J O2 C2 DOUB N N 1 U3J O2A PA DOUB N N 2 U3J "O4'" "C4'" SING N N 3 U3J "O4'" "C1'" SING N N 4 U3J O1B PB DOUB N N 5 U3J "C3'" "C4'" SING N N 6 U3J "C3'" "C2'" SING N N 7 U3J "C3'" "O3'" SING N N 8 U3J "C4'" "C5'" SING N N 9 U3J "C1'" "C2'" SING N N 10 U3J "C1'" N9 SING N N 11 U3J "C2'" "O2'" SING N N 12 U3J N3 C2 SING N N 13 U3J N3 C4 SING N N 14 U3J C2 N1 SING N N 15 U3J PA "O5'" SING N N 16 U3J PA O3A SING N N 17 U3J PA O1A SING N N 18 U3J N9 C4 SING Y N 19 U3J N9 C8 SING Y N 20 U3J C4 C5 DOUB Y N 21 U3J "O5'" "C5'" SING N N 22 U3J PB O3A SING N N 23 U3J PB O2B SING N N 24 U3J PB O3B SING N N 25 U3J N1 C6 SING N N 26 U3J C8 N7 DOUB Y N 27 U3J C5 C6 SING N N 28 U3J C5 N7 SING Y N 29 U3J C6 O6 DOUB N N 30 U3J N1 H1 SING N N 31 U3J C8 H2 SING N N 32 U3J N3 H3 SING N N 33 U3J "C1'" H4 SING N N 34 U3J "C2'" H5 SING N N 35 U3J "C3'" H6 SING N N 36 U3J "C4'" H7 SING N N 37 U3J "C5'" H8 SING N N 38 U3J "C5'" H9 SING N N 39 U3J O1A H10 SING N N 40 U3J "O2'" H11 SING N N 41 U3J O2B H12 SING N N 42 U3J "O3'" H13 SING N N 43 U3J O3B H14 SING N N 44 # # 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 U3J SMILES ACDLabs 12.01 "N1C(=O)c2ncn(c2NC1=O)C3C(O)C(C(COP(O)(=O)OP(=O)(O)O)O3)O" U3J InChI InChI 1.03 "InChI=1S/C10H14N4O12P2/c15-5-3(1-24-28(22,23)26-27(19,20)21)25-9(6(5)16)14-2-11-4-7(14)12-10(18)13-8(4)17/h2-3,5-6,9,15-16H,1H2,(H,22,23)(H2,19,20,21)(H2,12,13,17,18)/t3-,5+,6+,9-/m1/s1" U3J InChIKey InChI 1.03 YMOPVQQBWLGDOD-GFRUICAKSA-N U3J SMILES_CANONICAL CACTVS 3.385 "O[C@@H]1[C@H](O)[C@@H](O[C@@H]1CO[P](O)(=O)O[P](O)(O)=O)n2cnc3C(=O)NC(=O)Nc23" U3J SMILES CACTVS 3.385 "O[CH]1[CH](O)[CH](O[CH]1CO[P](O)(=O)O[P](O)(O)=O)n2cnc3C(=O)NC(=O)Nc23" U3J SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "c1nc2c(n1[C@H]3[C@H]([C@H]([C@H](O3)COP(=O)(O)OP(=O)(O)O)O)O)NC(=O)NC2=O" U3J SMILES "OpenEye OEToolkits" 2.0.7 "c1nc2c(n1C3C(C(C(O3)COP(=O)(O)OP(=O)(O)O)O)O)NC(=O)NC2=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 U3J "SYSTEMATIC NAME" ACDLabs 12.01 "9-{5-O-[(R)-hydroxy(phosphonooxy)phosphoryl]-beta-D-lyxofuranosyl}-3,9-dihydro-1H-purine-2,6-dione" U3J "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 "[(2~{R},3~{R},4~{S},5~{R})-5-[2,6-bis(oxidanylidene)-3~{H}-purin-9-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methyl phosphono hydrogen 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 U3J "Create component" 2020-04-13 RCSB U3J "Initial release" 2020-09-02 RCSB ##