data_XRE # _chem_comp.id XRE _chem_comp.name 5-hydroxyproline _chem_comp.type "L-peptide linking" _chem_comp.pdbx_type ATOMP _chem_comp.formula "C5 H9 N O3" _chem_comp.mon_nstd_parent_comp_id PRO _chem_comp.pdbx_synonyms "(2~{S},5~{S})-5-oxidanylpyrrolidine-2-carboxylic acid" _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2023-11-08 _chem_comp.pdbx_modified_date 2024-09-20 _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 131.130 _chem_comp.one_letter_code P _chem_comp.three_letter_code XRE _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 8R38 _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site PDBE # 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 _chem_comp_atom.pdbx_n_terminal_atom_flag _chem_comp_atom.pdbx_backbone_atom_flag _chem_comp_atom.pdbx_c_terminal_atom_flag XRE CB C1 C 0 1 N N N 3.079 -21.382 -0.835 0.021 1.514 -0.153 CB XRE 1 N N N XRE CG C2 C 0 1 N N N 2.176 -21.484 0.380 1.448 1.153 -0.626 CG XRE 2 N N N XRE CD C3 C 0 1 N N S 3.109 -21.148 1.470 1.867 0.034 0.361 CD XRE 3 N N N XRE N N1 N 0 1 N N N 4.010 -20.161 0.920 0.609 -0.731 0.561 N XRE 4 Y Y N XRE CA C4 C 0 1 N N S 3.774 -20.066 -0.540 -0.471 0.278 0.623 CA XRE 5 N Y N XRE C C5 C 0 1 N N N 2.954 -18.792 -0.746 -1.720 -0.268 -0.019 C XRE 6 N Y Y XRE O O1 O 0 1 N N N 2.613 -17.986 0.170 -1.654 -1.225 -0.753 O XRE 7 N Y Y XRE OD O2 O 0 1 N N N 2.312 -20.651 2.520 2.875 -0.797 -0.218 OD XRE 8 N N N XRE OXT O3 O 0 1 N Y N 2.662 -18.596 -2.064 -2.907 0.309 0.226 O1 XRE 9 N Y Y XRE HB2 H1 H 0 1 N N N 2.501 -21.337 -1.770 0.048 2.385 0.501 H1 XRE 10 N N N XRE HB3 H2 H 0 1 N N N 3.792 -22.218 -0.884 -0.625 1.704 -1.011 H2 XRE 11 N N N XRE HG2 H3 H 0 1 N N N 1.346 -20.764 0.325 1.432 0.779 -1.650 H3 XRE 12 N N N XRE HG3 H4 H 0 1 N N N 1.772 -22.501 0.496 2.112 2.013 -0.539 H4 XRE 13 N N N XRE HD2 H5 H 0 1 N N N 3.663 -22.045 1.784 2.214 0.461 1.301 H5 XRE 14 N N N XRE H H6 H 0 1 N Y N 4.956 -20.436 1.091 0.647 -1.272 1.412 H6 XRE 15 N Y N XRE HA H8 H 0 1 N N N 4.725 -20.001 -1.089 -0.669 0.546 1.660 H8 XRE 16 N Y N XRE H9 H9 H 0 1 N N N 2.866 -20.417 3.255 3.173 -1.513 0.359 H9 XRE 17 N N N XRE HXT H10 H 0 1 N Y N 2.180 -17.784 -2.165 -3.681 -0.076 -0.209 H10 XRE 18 N Y Y # 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 XRE CB CA SING N N 1 XRE CB CG SING N N 2 XRE C CA SING N N 3 XRE C O DOUB N N 4 XRE CA N SING N N 5 XRE CG CD SING N N 6 XRE N CD SING N N 7 XRE CD OD SING N N 8 XRE C OXT SING N N 9 XRE CB HB2 SING N N 10 XRE CB HB3 SING N N 11 XRE CG HG2 SING N N 12 XRE CG HG3 SING N N 13 XRE CD HD2 SING N N 14 XRE N H SING N N 15 XRE CA HA SING N N 16 XRE OD H9 SING N N 17 XRE OXT HXT SING N N 18 # 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 XRE InChI InChI 1.06 "InChI=1S/C5H9NO3/c7-4-2-1-3(6-4)5(8)9/h3-4,6-7H,1-2H2,(H,8,9)/t3-,4-/m0/s1" XRE InChIKey InChI 1.06 KYBXNPIASYUWLN-IMJSIDKUSA-N XRE SMILES_CANONICAL CACTVS 3.385 "O[C@H]1CC[C@H](N1)C(O)=O" XRE SMILES CACTVS 3.385 "O[CH]1CC[CH](N1)C(O)=O" XRE SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "C1C[C@@H](N[C@@H]1C(=O)O)O" XRE SMILES "OpenEye OEToolkits" 2.0.7 "C1CC(NC1C(=O)O)O" # _pdbx_chem_comp_identifier.comp_id XRE _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~{S},5~{S})-5-oxidanylpyrrolidine-2-carboxylic 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 XRE "Create component" 2023-11-08 PDBE XRE "Modify name" 2023-11-09 PDBE XRE "Modify internal type" 2023-11-09 PDBE XRE "Initial release" 2024-09-25 RCSB # _pdbx_chem_comp_synonyms.ordinal 1 _pdbx_chem_comp_synonyms.comp_id XRE _pdbx_chem_comp_synonyms.name "(2~{S},5~{S})-5-oxidanylpyrrolidine-2-carboxylic acid" _pdbx_chem_comp_synonyms.provenance PDB _pdbx_chem_comp_synonyms.type ? #