data_HHU # _chem_comp.id HHU _chem_comp.name "[(2R,3S,4R,5R)-5-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-4-formamido-3-oxidanyl-oxolan-2-yl]methyl dihydrogen phosphate" _chem_comp.type "RNA linking" _chem_comp.pdbx_type ATOMN _chem_comp.formula "C10 H14 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 2024-11-15 _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 351.207 _chem_comp.one_letter_code ? _chem_comp.three_letter_code HHU _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 7DS5 _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 HHU "C1'" C1 C 0 1 N N R N N N 0.386 17.835 0.541 -1.129 0.297 -0.657 "C1'" HHU 1 HHU C2 C2 C 0 1 N N N N N N 0.821 15.475 0.570 -3.095 -1.069 -1.082 C2 HHU 2 HHU "C2'" C3 C 0 1 N N R N N N 0.437 18.280 -1.044 -1.218 1.584 0.192 "C2'" HHU 3 HHU "C3'" C4 C 0 1 N N S N N N -0.707 18.757 -1.236 0.254 2.019 0.369 "C3'" HHU 4 HHU C4 C5 C 0 1 N N N N N N -0.805 13.930 1.080 -4.033 -2.465 0.539 C4 HHU 5 HHU "C4'" C6 C 0 1 N N R N N N -1.031 19.584 0.090 1.058 0.944 -0.394 "C4'" HHU 6 HHU C5 C7 C 0 1 N N N N N N -1.732 14.952 1.232 -3.033 -2.055 1.454 C5 HHU 7 HHU "C5'" C8 C 0 1 N N N N N N -2.398 19.846 0.295 2.361 0.630 0.343 "C5'" HHU 8 HHU C6 C9 C 0 1 N N N N N N -1.306 16.258 1.029 -2.102 -1.163 1.054 C6 HHU 9 HHU "C7'" C10 C 0 1 N N N N N N 2.961 18.868 -0.991 -2.605 3.588 0.177 "C7'" HHU 10 HHU N1 N1 N 0 1 N N N N N N -0.044 16.481 0.701 -2.139 -0.671 -0.223 N1 HHU 11 HHU "N2'" N2 N 0 1 N N N N N N 1.591 19.290 -1.216 -1.979 2.616 -0.517 "N2'" HHU 12 HHU N3 N3 N 0 1 N N N N N N 0.437 14.221 0.756 -4.035 -1.957 -0.710 N3 HHU 13 HHU O2 O1 O 0 1 N N N N N N 1.950 15.685 0.262 -3.112 -0.615 -2.211 O2 HHU 14 HHU "O3'" O2 O 0 1 N N N N N N -0.746 19.680 -2.411 0.468 3.309 -0.209 "O3'" HHU 15 HHU O4 O3 O 0 1 N N N N N N -1.176 12.601 1.274 -4.884 -3.268 0.877 O4 HHU 16 HHU "O4'" O4 O 0 1 N N N N N N -0.447 18.673 1.132 0.198 -0.217 -0.411 "O4'" HHU 17 HHU "O5'" O5 O 0 1 N N N N N N -3.131 18.659 0.339 3.142 -0.279 -0.437 "O5'" HHU 18 HHU "O6'" O6 O 0 1 N N N N N N 3.847 19.648 -1.135 -2.537 3.608 1.387 "O6'" HHU 19 HHU OP1 O7 O 0 1 N N N N N N -5.514 19.690 0.111 5.471 0.318 0.332 OP1 HHU 20 HHU OP2 O8 O 0 1 N N N N N N -5.239 17.245 0.580 4.404 -1.727 1.359 OP2 HHU 21 HHU P P1 P 0 1 N N N N N N -4.701 18.626 0.814 4.581 -0.827 0.035 P HHU 22 HHU H1 H1 H 0 1 N N N N N N 1.407 17.945 0.936 -1.257 0.529 -1.715 H1 HHU 23 HHU H2 H2 H 0 1 N N N N N N 0.651 17.382 -1.642 -1.673 1.373 1.160 H2 HHU 24 HHU H3 H3 H 0 1 N N N N N N -1.483 17.986 -1.354 0.527 2.023 1.424 H3 HHU 25 HHU H4 H4 H 0 1 N N N N N N -0.455 20.521 0.060 1.268 1.277 -1.411 H4 HHU 26 HHU H5 H5 H 0 1 N N N N N N -2.756 14.737 1.501 -3.015 -2.451 2.459 H5 HHU 27 HHU H6 H6 H 0 1 N N N N N N -2.523 20.382 1.247 2.923 1.551 0.497 H6 HHU 28 HHU H7 H7 H 0 1 N N N N N N -2.773 20.470 -0.529 2.133 0.177 1.308 H7 HHU 29 HHU H8 H8 H 0 1 N N N N N N -1.996 17.081 1.138 -1.332 -0.839 1.738 H8 HHU 30 HHU H9 H9 H 0 1 N N N N N N 3.175 17.852 -0.695 -3.166 4.348 -0.346 H9 HHU 31 HHU H10 H10 H 0 1 N N N N N N 1.395 20.234 -1.482 -2.033 2.599 -1.485 H10 HHU 32 HHU H11 H11 H 0 1 N N N N N N 1.102 13.482 0.648 -4.717 -2.232 -1.342 H11 HHU 33 HHU "HO3'" H12 H 0 0 N Y N N N N -1.627 20.017 -2.520 1.376 3.631 -0.127 "HO3'" HHU 34 HHU HOP2 H14 H 0 0 N N N N N N -6.007 17.294 0.022 3.832 -2.496 1.237 HOP2 HHU 35 HHU OP3 OP3 O 0 1 N Y N N N N -4.686 18.965 2.383 5.227 -1.719 -1.139 OP3 HHU 36 HHU HOP3 H13 H 0 0 N N N N N N -5.187 19.757 2.541 6.096 -2.083 -0.923 HOP3 HHU 37 # 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 HHU "O3'" "C3'" SING N N 1 HHU "C3'" "C2'" SING N N 2 HHU "C3'" "C4'" SING N N 3 HHU "N2'" "C2'" SING N N 4 HHU "N2'" "C7'" SING N N 5 HHU "O6'" "C7'" DOUB N N 6 HHU "C2'" "C1'" SING N N 7 HHU "C4'" "C5'" SING N N 8 HHU "C4'" "O4'" SING N N 9 HHU OP1 P DOUB N N 10 HHU O2 C2 DOUB N N 11 HHU "C5'" "O5'" SING N N 12 HHU "O5'" P SING N N 13 HHU "C1'" N1 SING N N 14 HHU "C1'" "O4'" SING N N 15 HHU C2 N1 SING N N 16 HHU C2 N3 SING N N 17 HHU OP2 P SING N N 18 HHU N1 C6 SING N N 19 HHU N3 C4 SING N N 20 HHU C6 C5 DOUB N N 21 HHU C4 C5 SING N N 22 HHU C4 O4 DOUB N N 23 HHU "C1'" H1 SING N N 24 HHU "C2'" H2 SING N N 25 HHU "C3'" H3 SING N N 26 HHU "C4'" H4 SING N N 27 HHU C5 H5 SING N N 28 HHU "C5'" H6 SING N N 29 HHU "C5'" H7 SING N N 30 HHU C6 H8 SING N N 31 HHU "C7'" H9 SING N N 32 HHU "N2'" H10 SING N N 33 HHU N3 H11 SING N N 34 HHU "O3'" "HO3'" SING N N 35 HHU OP2 HOP2 SING N N 36 HHU P OP3 SING N N 37 HHU OP3 HOP3 SING N N 38 # 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 HHU InChI InChI 1.03 "InChI=1S/C10H14N3O9P/c14-4-11-7-8(16)5(3-21-23(18,19)20)22-9(7)13-2-1-6(15)12-10(13)17/h1-2,4-5,7-9,16H,3H2,(H,11,14)(H,12,15,17)(H2,18,19,20)/t5-,7-,8-,9-/m1/s1" HHU InChIKey InChI 1.03 BVKBFAYJTMOFKA-ZOQUXTDFSA-N HHU SMILES_CANONICAL CACTVS 3.385 "O[C@@H]1[C@@H](CO[P](O)(O)=O)O[C@H]([C@@H]1NC=O)N2C=CC(=O)NC2=O" HHU SMILES CACTVS 3.385 "O[CH]1[CH](CO[P](O)(O)=O)O[CH]([CH]1NC=O)N2C=CC(=O)NC2=O" HHU SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "C1=CN(C(=O)NC1=O)[C@H]2[C@@H]([C@@H]([C@H](O2)COP(=O)(O)O)O)NC=O" HHU SMILES "OpenEye OEToolkits" 2.0.7 "C1=CN(C(=O)NC1=O)C2C(C(C(O2)COP(=O)(O)O)O)NC=O" # _pdbx_chem_comp_identifier.comp_id HHU _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-formamido-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 HHU "Create component" 2021-01-13 PDBJ HHU "Modify leaving atom flag" 2021-01-13 PDBJ HHU "Initial release" 2024-11-20 RCSB #