data_HHX # _chem_comp.id HHX _chem_comp.name "[(2R,3S,4R,5R)-5-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-4-[methanoyl(methyl)amino]-3-oxidanyl-oxolan-2-yl]methyl dihydrogen phosphate" _chem_comp.type "RNA linking" _chem_comp.pdbx_type ATOMN _chem_comp.formula "C11 H16 N3 O9 P" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2021-01-13 _chem_comp.pdbx_modified_date 2025-01-17 _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 365.233 _chem_comp.one_letter_code ? _chem_comp.three_letter_code HHX _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 7DS9 _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site PDBJ _chem_comp.pdbx_pcm ? # 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.pdbx_backbone_atom_flag _chem_comp_atom.pdbx_n_terminal_atom_flag _chem_comp_atom.pdbx_c_terminal_atom_flag _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 HHX "C1'" C1 C 0 1 N N R N N N -10.879 11.055 -18.954 1.087 -0.225 -0.339 "C1'" HHX 1 HHX C2 C2 C 0 1 N N N N N N -8.873 11.983 -17.989 3.038 1.069 -0.993 C2 HHX 2 HHX "C2'" C3 C 0 1 N N R N N N -10.772 11.217 -20.585 1.168 -1.281 0.786 "C2'" HHX 3 HHX "C3'" C4 C 0 1 N N S N N N -11.077 10.065 -21.018 -0.300 -1.711 1.003 "C3'" HHX 4 HHX C4 C5 C 0 1 N N N N N N -7.356 10.651 -16.867 3.874 2.828 0.299 C4 HHX 5 HHX "C4'" C6 C 0 1 N N R N N N -12.092 9.381 -19.994 -1.094 -0.864 -0.015 "C4'" HHX 6 HHX C5 C7 C 0 1 N N N N N N -8.129 9.527 -17.140 2.845 2.606 1.245 C5 HHX 7 HHX "C5'" C8 C 0 1 N N N N N N -12.057 7.972 -19.958 -2.435 -0.432 0.581 "C5'" HHX 8 HHX C6 C9 C 0 1 N N N N N N -9.294 9.703 -17.865 1.952 1.617 1.026 C6 HHX 9 HHX "C6'" C10 C 0 1 N N N N N N -13.160 12.340 -20.793 3.191 -2.779 1.109 "C6'" HHX 10 HHX "C7'" C11 C 0 1 N N N N N N -11.148 13.636 -21.431 1.620 -3.145 -0.718 "C7'" HHX 11 HHX N1 N1 N 0 1 N N N N N N -9.631 10.920 -18.269 2.056 0.848 -0.101 N1 HHX 12 HHX "N2'" N2 N 0 1 N N N N N N -11.716 12.394 -20.944 1.982 -2.422 0.361 "N2'" HHX 13 HHX N3 N3 N 0 1 N N N N N N -7.747 11.837 -17.310 3.941 2.048 -0.800 N3 HHX 14 HHX O2 O1 O 0 1 N N N N N N -9.171 13.078 -18.364 3.114 0.371 -1.986 O2 HHX 15 HHX "O3'" O2 O 0 1 N N N N N N -11.741 10.068 -22.350 -0.460 -3.104 0.729 "O3'" HHX 16 HHX O4 O3 O 0 1 N N N N N N -6.176 10.527 -16.141 4.690 3.714 0.474 O4 HHX 17 HHX "O4'" O4 O 0 1 N N N N N N -11.661 10.012 -18.709 -0.261 0.289 -0.266 "O4'" HHX 18 HHX "O5'" O5 O 0 1 N N N N N N -10.838 7.479 -19.484 -3.202 0.250 -0.414 "O5'" HHX 19 HHX "O6'" O6 O 0 1 N N N N N N -11.869 14.542 -21.700 2.294 -4.089 -1.069 "O6'" HHX 20 HHX OP1 O7 O 0 1 N N N N N N -11.205 4.914 -19.797 -4.620 1.758 1.031 OP1 HHX 21 HHX OP2 O8 O 0 1 N N N N N N -9.303 5.775 -18.363 -5.178 1.655 -1.429 OP2 HHX 22 HHX P P1 P 0 1 N N N N N N -10.716 5.973 -18.837 -4.671 0.845 -0.133 P HHX 23 HHX H1 H1 H 0 1 N N N N N N -11.367 11.973 -18.596 1.266 -0.688 -1.309 H1 HHX 24 HHX H2 H2 H 0 1 N N N N N N -9.738 11.508 -20.824 1.576 -0.840 1.696 H2 HHX 25 HHX H3 H3 H 0 1 N N N N N N -10.194 9.411 -21.077 -0.618 -1.482 2.020 H3 HHX 26 HHX H4 H4 H 0 1 N N N N N N -13.105 9.730 -20.242 -1.253 -1.427 -0.935 H4 HHX 27 HHX H5 H5 H 0 1 N N N N N N -7.829 8.548 -16.797 2.774 3.220 2.131 H5 HHX 28 HHX H6 H6 H 0 1 N N N N N N -12.862 7.616 -19.298 -2.981 -1.311 0.922 H6 HHX 29 HHX H7 H7 H 0 1 N N N N N N -12.221 7.589 -20.976 -2.259 0.236 1.425 H7 HHX 30 HHX H8 H8 H 0 1 N N N N N N -9.923 8.857 -18.100 1.160 1.433 1.737 H8 HHX 31 HHX H9 H9 H 0 1 N N N N N N -13.453 11.348 -20.419 4.046 -2.246 0.692 H9 HHX 32 HHX H10 H10 H 0 1 N N N N N N -13.483 13.112 -20.079 3.066 -2.502 2.155 H10 HHX 33 HHX H11 H11 H 0 1 N N N N N N -13.637 12.520 -21.768 3.361 -3.853 1.035 H11 HHX 34 HHX H12 H12 H 0 1 N N N N N N -10.079 13.737 -21.548 0.729 -2.882 -1.269 H12 HHX 35 HHX H13 H13 H 0 1 N N N N N N -7.179 12.639 -17.127 4.643 2.194 -1.453 H13 HHX 36 HHX "HO3'" H14 H 0 1 N Y N N N N -11.939 9.175 -22.608 -1.363 -3.428 0.849 H14 HHX 37 HHX HOP2 H16 H 0 1 N N N N N N -8.942 4.991 -18.760 -6.059 2.042 -1.331 H16 HHX 38 HHX OP3 O9 O 0 1 N Y N N N N -11.764 5.972 -17.622 -5.689 -0.363 0.177 O1 HHX 39 HHX HOP3 H15 H 0 1 N N N N N N -12.436 5.320 -17.783 -5.773 -1.002 -0.544 H15 HHX 40 # 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 HHX "O3'" "C3'" SING N N 1 HHX "O6'" "C7'" DOUB N N 2 HHX "C7'" "N2'" SING N N 3 HHX "C3'" "C2'" SING N N 4 HHX "C3'" "C4'" SING N N 5 HHX "N2'" "C6'" SING N N 6 HHX "N2'" "C2'" SING N N 7 HHX "C2'" "C1'" SING N N 8 HHX "C4'" "C5'" SING N N 9 HHX "C4'" "O4'" SING N N 10 HHX "C5'" "O5'" SING N N 11 HHX OP1 P DOUB N N 12 HHX "O5'" P SING N N 13 HHX "C1'" "O4'" SING N N 14 HHX "C1'" N1 SING N N 15 HHX P OP2 SING N N 16 HHX O2 C2 DOUB N N 17 HHX N1 C2 SING N N 18 HHX N1 C6 SING N N 19 HHX C2 N3 SING N N 20 HHX C6 C5 DOUB N N 21 HHX N3 C4 SING N N 22 HHX C5 C4 SING N N 23 HHX C4 O4 DOUB N N 24 HHX "C1'" H1 SING N N 25 HHX "C2'" H2 SING N N 26 HHX "C3'" H3 SING N N 27 HHX "C4'" H4 SING N N 28 HHX C5 H5 SING N N 29 HHX "C5'" H6 SING N N 30 HHX "C5'" H7 SING N N 31 HHX C6 H8 SING N N 32 HHX "C6'" H9 SING N N 33 HHX "C6'" H10 SING N N 34 HHX "C6'" H11 SING N N 35 HHX "C7'" H12 SING N N 36 HHX N3 H13 SING N N 37 HHX "O3'" "HO3'" SING N N 38 HHX OP2 HOP2 SING N N 39 HHX P OP3 SING N N 40 HHX OP3 HOP3 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 HHX InChI InChI 1.03 "InChI=1S/C11H16N3O9P/c1-13(5-15)8-9(17)6(4-22-24(19,20)21)23-10(8)14-3-2-7(16)12-11(14)18/h2-3,5-6,8-10,17H,4H2,1H3,(H,12,16,18)(H2,19,20,21)/t6-,8-,9-,10-/m1/s1" HHX InChIKey InChI 1.03 CCDZTXGHNXOAPJ-PEBGCTIMSA-N HHX SMILES_CANONICAL CACTVS 3.385 "CN(C=O)[C@@H]1[C@H](O)[C@@H](CO[P](O)(O)=O)O[C@H]1N2C=CC(=O)NC2=O" HHX SMILES CACTVS 3.385 "CN(C=O)[CH]1[CH](O)[CH](CO[P](O)(O)=O)O[CH]1N2C=CC(=O)NC2=O" HHX SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "CN(C=O)[C@@H]1[C@@H]([C@H](O[C@H]1N2C=CC(=O)NC2=O)COP(=O)(O)O)O" HHX SMILES "OpenEye OEToolkits" 2.0.7 "CN(C=O)C1C(C(OC1N2C=CC(=O)NC2=O)COP(=O)(O)O)O" # _pdbx_chem_comp_identifier.comp_id HHX _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~{S},4~{R},5~{R})-5-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-4-[methanoyl(methyl)amino]-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 HHX "Create component" 2021-01-13 PDBJ HHX "Initial release" 2025-01-22 RCSB #