data_QPJ # _chem_comp.id QPJ _chem_comp.name 2-deoxy-3,5-di-O-phosphono-D-erythro-pentitol _chem_comp.type non-polymer _chem_comp.pdbx_type HETAIN _chem_comp.formula "C5 H14 O10 P2" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2019-12-05 _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 296.106 _chem_comp.one_letter_code ? _chem_comp.three_letter_code QPJ _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 6V5Y _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 QPJ P P1 P 0 1 N N N N N N 9.608 10.872 44.023 -3.694 -0.012 -0.063 P QPJ 1 QPJ "O5'" O1 O 0 1 N N N N N N 10.708 9.789 43.562 -2.347 0.836 -0.307 "O5'" QPJ 2 QPJ "C2'" C1 C 0 1 N N N N N N 11.043 6.227 40.956 2.443 1.928 -0.324 "C2'" QPJ 3 QPJ "C5'" C2 C 0 1 N N N N N N 10.409 8.644 42.775 -1.057 0.385 0.111 "C5'" QPJ 4 QPJ "C4'" C3 C 0 1 N N R N N N 11.459 8.613 41.685 -0.003 1.425 -0.274 "C4'" QPJ 5 QPJ "O4'" O2 O 0 1 N N N N N N 12.717 8.256 42.277 -0.236 2.632 0.456 "O4'" QPJ 6 QPJ "C1'" C4 C 0 1 N N S N N N 11.053 7.683 40.549 1.390 0.888 0.061 "C1'" QPJ 7 QPJ "C3'" C5 C 0 1 N N N N N N 10.344 5.406 39.897 3.824 1.445 0.123 "C3'" QPJ 8 QPJ OP3 O3 O 0 1 N N N N N N 9.352 11.769 42.837 -3.535 -1.366 -0.639 OP3 QPJ 9 QPJ OP1 O4 O 0 1 N N N N N N 10.392 11.526 45.147 -3.975 -0.130 1.517 OP1 QPJ 10 QPJ OP2 O5 O 0 1 N N N N N N 8.420 9.997 44.405 -4.932 0.732 -0.775 OP2 QPJ 11 QPJ O32 O6 O 0 1 N N N N N N 12.861 10.571 38.634 3.330 -1.642 0.829 O32 QPJ 12 QPJ P2 P2 P 0 1 N N N N N N 11.598 9.336 38.674 1.928 -1.729 0.044 P2 QPJ 13 QPJ O22 O7 O 0 1 N N N N N N 9.906 9.703 38.326 0.844 -2.042 1.003 O22 QPJ 14 QPJ OPP O8 O 0 1 N N N N N N 11.905 7.833 39.406 1.623 -0.319 -0.669 OPP QPJ 15 QPJ H1 H1 H 0 1 N N N N N N 10.511 6.119 41.913 2.440 2.066 -1.406 H1 QPJ 16 QPJ H2 H2 H 0 1 N N N N N N 12.078 5.872 41.070 2.214 2.875 0.164 H2 QPJ 17 QPJ H3 H3 H 0 1 N N N N N N 9.404 8.731 42.337 -1.053 0.247 1.192 H3 QPJ 18 QPJ H4 H4 H 0 1 N N N N N N 10.465 7.732 43.388 -0.828 -0.562 -0.377 H4 QPJ 19 QPJ H5 H5 H 0 1 N N N N N N 11.540 9.629 41.270 -0.067 1.629 -1.343 H5 QPJ 20 QPJ H6 H6 H 0 1 N N N N N N 12.922 8.865 42.977 -0.195 2.525 1.416 H6 QPJ 21 QPJ H7 H7 H 0 1 N N N N N N 10.027 7.951 40.256 1.454 0.684 1.130 H7 QPJ 22 QPJ H8 H8 H 0 1 N N N N N N 9.464 5.949 39.523 3.828 1.307 1.204 H8 QPJ 23 QPJ H9 H9 H 0 1 N N N N N N 11.033 5.206 39.063 4.054 0.498 -0.365 H9 QPJ 24 QPJ H11 H11 H 0 1 N N N N N N 10.599 12.422 44.910 -4.090 0.722 1.961 H11 QPJ 25 QPJ H12 H12 H 0 1 N N N N N N 7.696 10.169 43.814 -5.778 0.276 -0.669 H12 QPJ 26 QPJ H13 H13 H 0 1 N N N N N N 13.698 10.176 38.849 4.087 -1.440 0.262 H13 QPJ 27 QPJ O2 O9 O 0 1 N Y N N N N 9.931 4.159 40.505 4.809 2.417 -0.236 O2 QPJ 28 QPJ O1 O10 O 0 1 N Y N N N N 12.008 8.810 37.313 2.008 -2.888 -1.071 O1 QPJ 29 QPJ H10 H10 H 0 1 N N N N N N 9.488 3.623 39.858 5.710 2.176 0.017 H10 QPJ 30 QPJ H14 H14 H 0 1 N N N N N N 11.263 8.840 36.724 2.189 -3.767 -0.712 H14 QPJ 31 # 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 QPJ O22 P2 DOUB N N 1 QPJ O32 P2 SING N N 2 QPJ P2 OPP SING N N 3 QPJ OPP "C1'" SING N N 4 QPJ "C3'" "C2'" SING N N 5 QPJ "C1'" "C2'" SING N N 6 QPJ "C1'" "C4'" SING N N 7 QPJ "C4'" "O4'" SING N N 8 QPJ "C4'" "C5'" SING N N 9 QPJ "C5'" "O5'" SING N N 10 QPJ OP3 P DOUB N N 11 QPJ "O5'" P SING N N 12 QPJ P OP2 SING N N 13 QPJ P OP1 SING N N 14 QPJ "C2'" H1 SING N N 15 QPJ "C2'" H2 SING N N 16 QPJ "C5'" H3 SING N N 17 QPJ "C5'" H4 SING N N 18 QPJ "C4'" H5 SING N N 19 QPJ "O4'" H6 SING N N 20 QPJ "C1'" H7 SING N N 21 QPJ "C3'" H8 SING N N 22 QPJ "C3'" H9 SING N N 23 QPJ OP1 H11 SING N N 24 QPJ OP2 H12 SING N N 25 QPJ O32 H13 SING N N 26 QPJ "C3'" O2 SING N N 27 QPJ P2 O1 SING N N 28 QPJ O2 H10 SING N N 29 QPJ O1 H14 SING N N 30 # 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 QPJ SMILES ACDLabs 12.01 "P(O)(O)(OCC(O)C(CCO)OP(O)(O)=O)=O" QPJ InChI InChI 1.03 "InChI=1S/C5H14O10P2/c6-2-1-5(15-17(11,12)13)4(7)3-14-16(8,9)10/h4-7H,1-3H2,(H2,8,9,10)(H2,11,12,13)/t4-,5+/m1/s1" QPJ InChIKey InChI 1.03 BUWHXMOYXFBKFR-UHNVWZDZSA-N QPJ SMILES_CANONICAL CACTVS 3.385 "OCC[C@H](O[P](O)(O)=O)[C@H](O)CO[P](O)(O)=O" QPJ SMILES CACTVS 3.385 "OCC[CH](O[P](O)(O)=O)[CH](O)CO[P](O)(O)=O" QPJ SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "C(CO)[C@@H]([C@@H](COP(=O)(O)O)O)OP(=O)(O)O" QPJ SMILES "OpenEye OEToolkits" 2.0.7 "C(CO)C(C(COP(=O)(O)O)O)OP(=O)(O)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 QPJ "SYSTEMATIC NAME" ACDLabs 12.01 2-deoxy-3,5-di-O-phosphono-D-erythro-pentitol QPJ "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 "[(2~{R},3~{S})-2,5-bis(oxidanyl)-1-phosphonooxy-pentan-3-yl] 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 QPJ "Create component" 2019-12-05 RCSB QPJ "Initial release" 2022-03-09 RCSB QPJ "Modify PCM" 2024-09-27 PDBE # _pdbx_chem_comp_pcm.pcm_id 1 _pdbx_chem_comp_pcm.comp_id QPJ _pdbx_chem_comp_pcm.modified_residue_id LYS _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 "C3'" _pdbx_chem_comp_pcm.modified_residue_id_linking_atom NZ _pdbx_chem_comp_pcm.uniprot_specific_ptm_accession ? _pdbx_chem_comp_pcm.uniprot_generic_ptm_accession ? #