data_YA4 # _chem_comp.id YA4 _chem_comp.name "[(2~{R},3~{S},4~{S})-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-sulfanyl-phosphinic acid" _chem_comp.type "RNA linking" _chem_comp.pdbx_type ATOMN _chem_comp.formula "C5 H11 O6 P S" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2021-02-12 _chem_comp.pdbx_modified_date 2024-09-27 _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 230.176 _chem_comp.one_letter_code ? _chem_comp.three_letter_code YA4 _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 7LPJ _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site RCSB _chem_comp.pdbx_pcm Y # 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 YA4 "C1'" C1 C 0 1 N N N N N N -149.244 -52.772 -68.581 3.204 1.489 -0.247 "C1'" YA4 1 YA4 "C2'" C2 C 0 1 N N S N N N -149.870 -54.239 -68.635 3.719 0.218 0.465 "C2'" YA4 2 YA4 "C3'" C3 C 0 1 N N S N N N -149.796 -54.681 -67.469 2.501 -0.734 0.462 "C3'" YA4 3 YA4 "C4'" C4 C 0 1 N N R N N N -149.814 -53.348 -66.463 1.395 0.075 -0.252 "C4'" YA4 4 YA4 "C5'" C5 C 0 1 N N N N N N -148.736 -53.596 -65.491 0.035 -0.198 0.395 "C5'" YA4 5 YA4 "O2'" O1 O 0 1 N N N N N N -151.307 -54.177 -68.963 4.806 -0.357 -0.262 "O2'" YA4 6 YA4 "O3'" O2 O 0 1 N N N N N N -150.995 -55.476 -67.231 2.800 -1.926 -0.267 "O3'" YA4 7 YA4 "O4'" O3 O 0 1 N N N N N N -149.574 -52.287 -67.156 1.771 1.457 -0.068 "O4'" YA4 8 YA4 "O5'" O4 O 0 1 N N N N N N -148.447 -52.418 -64.828 -0.988 0.465 -0.350 "O5'" YA4 9 YA4 OP1 O5 O 0 1 N N N N N N -147.902 -50.923 -62.634 -2.719 0.836 1.449 OP1 YA4 10 YA4 P P1 P 0 1 N N N N N N -147.850 -52.411 -63.410 -2.547 0.395 0.047 P YA4 11 YA4 SP3 S1 S 0 1 N N N N N N -145.888 -53.215 -63.680 -3.239 -1.598 -0.157 SP3 YA4 12 YA4 "H1'" H1 H 0 1 N N N N N N -148.156 -52.803 -68.743 3.624 2.381 0.217 H1 YA4 13 YA4 "H1''" H2 H 0 0 N N N N N N -149.708 -52.119 -69.335 3.454 1.459 -1.307 H2 YA4 14 YA4 "H2'" H3 H 0 1 N N N N N N -149.327 -54.833 -69.385 4.021 0.449 1.487 H3 YA4 15 YA4 "H3'" H4 H 0 1 N N N N N N -148.888 -55.263 -67.254 2.203 -0.976 1.482 H4 YA4 16 YA4 "H4'" H5 H 0 1 N N N N N N -150.789 -53.324 -65.954 1.367 -0.175 -1.312 H5 YA4 17 YA4 "H5'" H6 H 0 1 N N N N N N -149.061 -54.357 -64.766 -0.156 -1.271 0.399 H6 YA4 18 YA4 "H5''" H7 H 0 0 N N N N N N -147.839 -53.952 -66.018 0.039 0.174 1.419 H7 YA4 19 YA4 "HO2'" H8 H 0 0 N N N N N N -151.664 -55.057 -68.991 5.576 0.223 -0.343 H8 YA4 20 YA4 "HO3'" H9 H 0 0 N Y N N N N -150.972 -55.829 -66.349 3.529 -2.441 0.104 H9 YA4 21 YA4 HSP3 H11 H 0 0 N N N N N N -145.418 -53.193 -62.468 -4.532 -1.507 0.201 H11 YA4 22 YA4 OP3 OP3 O 0 1 N Y N N N N -148.847 -53.399 -62.731 -3.392 1.359 -0.927 OP3 YA4 23 YA4 HOP3 H10 H 0 0 N Y N N N N -149.287 -52.961 -62.011 -3.326 1.128 -1.863 "HO3'" YA4 24 # 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 YA4 "O2'" "C2'" SING N N 1 YA4 "C2'" "C1'" SING N N 2 YA4 "C2'" "C3'" SING N N 3 YA4 "C1'" "O4'" SING N N 4 YA4 "C3'" "O3'" SING N N 5 YA4 "C3'" "C4'" SING N N 6 YA4 "O4'" "C4'" SING N N 7 YA4 "C4'" "C5'" SING N N 8 YA4 "C5'" "O5'" SING N N 9 YA4 "O5'" P SING N N 10 YA4 SP3 P SING N N 11 YA4 P OP1 DOUB N N 12 YA4 "C1'" "H1'" SING N N 13 YA4 "C1'" "H1''" SING N N 14 YA4 "C2'" "H2'" SING N N 15 YA4 "C3'" "H3'" SING N N 16 YA4 "C4'" "H4'" SING N N 17 YA4 "C5'" "H5'" SING N N 18 YA4 "C5'" "H5''" SING N N 19 YA4 "O2'" "HO2'" SING N N 20 YA4 "O3'" "HO3'" SING N N 21 YA4 SP3 HSP3 SING N N 22 YA4 P OP3 SING N N 23 YA4 OP3 HOP3 SING N N 24 # 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 YA4 InChI InChI 1.03 "InChI=1S/C5H11O6PS/c6-3-1-10-4(5(3)7)2-11-12(8,9)13/h3-7H,1-2H2,(H2,8,9,13)/t3-,4+,5-/m0/s1" YA4 InChIKey InChI 1.03 HBCHIJUQXWEATM-LMVFSUKVSA-N YA4 SMILES_CANONICAL CACTVS 3.385 "O[C@H]1CO[C@H](CO[P](O)(S)=O)[C@H]1O" YA4 SMILES CACTVS 3.385 "O[CH]1CO[CH](CO[P](O)(S)=O)[CH]1O" YA4 SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "C1[C@@H]([C@@H]([C@H](O1)COP(=O)(O)S)O)O" YA4 SMILES "OpenEye OEToolkits" 2.0.7 "C1C(C(C(O1)COP(=O)(O)S)O)O" # _pdbx_chem_comp_identifier.comp_id YA4 _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~{S})-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-sulfanyl-phosphinic 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 YA4 "Create component" 2021-02-12 RCSB YA4 "Initial release" 2021-08-04 RCSB YA4 "Modify PCM" 2024-09-27 PDBE # _pdbx_chem_comp_pcm.pcm_id 1 _pdbx_chem_comp_pcm.comp_id YA4 _pdbx_chem_comp_pcm.modified_residue_id ASN _pdbx_chem_comp_pcm.type None _pdbx_chem_comp_pcm.category "Covalent chemical modification" _pdbx_chem_comp_pcm.position "Amino-acid side chain" _pdbx_chem_comp_pcm.polypeptide_position "Any position" _pdbx_chem_comp_pcm.comp_id_linking_atom "O2'" _pdbx_chem_comp_pcm.modified_residue_id_linking_atom ND2 _pdbx_chem_comp_pcm.uniprot_specific_ptm_accession ? _pdbx_chem_comp_pcm.uniprot_generic_ptm_accession ? #