data_VY9 # _chem_comp.id VY9 _chem_comp.name "(3R)-3-(2-hydroxy-2-oxoethylamino)decanoic acid" _chem_comp.type non-polymer _chem_comp.pdbx_type HETAIN _chem_comp.formula "C12 H23 N O4" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2023-09-03 _chem_comp.pdbx_modified_date 2024-04-12 _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 245.315 _chem_comp.one_letter_code ? _chem_comp.three_letter_code VY9 _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 8KIF _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site PDBJ # 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 VY9 C10 C1 C 0 1 N N N N N N 3.049 -1.502 38.016 -0.051 0.990 0.466 C10 VY9 1 VY9 C13 C2 C 0 1 N N N N N N 0.898 -0.396 35.302 3.468 -0.377 -0.294 C13 VY9 2 VY9 C15 C3 C 0 1 N N N N N N -0.716 -0.228 33.384 5.917 -0.854 -0.416 C15 VY9 3 VY9 C11 C4 C 0 1 N N N N N N 2.407 -1.846 36.669 1.018 0.101 -0.172 C11 VY9 4 VY9 C12 C5 C 0 1 N N N N N N 2.371 -0.644 35.708 2.399 0.512 0.344 C12 VY9 5 VY9 C14 C6 C 0 1 N N N N N N 0.641 -0.777 33.834 4.848 0.035 0.222 C14 VY9 6 VY9 C16 C7 C 0 1 N N N N N N -1.843 -1.049 34.000 7.297 -0.443 0.100 C16 VY9 7 VY9 C02 C8 C 0 1 N N N N N N 3.160 -1.258 41.070 -2.262 2.915 -0.098 C02 VY9 8 VY9 C03 C9 C 0 1 N N N N N N 3.549 -2.485 40.259 -2.486 1.546 0.491 C03 VY9 9 VY9 C04 C10 C 0 1 N N S N N N 2.683 -2.607 39.011 -1.431 0.579 -0.050 C04 VY9 10 VY9 C06 C11 C 0 1 N N N N N N 2.111 -4.943 39.039 -2.746 -1.412 -0.460 C06 VY9 11 VY9 C07 C12 C 0 1 N N N N N N 1.998 -6.108 38.052 -2.935 -2.849 -0.049 C07 VY9 12 VY9 N05 N1 N 0 1 N N N N N N 2.916 -3.914 38.384 -1.737 -0.784 0.404 N05 VY9 13 VY9 O01 O1 O 0 1 N N N N N N 4.058 -0.537 41.588 -1.426 3.074 -0.955 O01 VY9 14 VY9 O08 O2 O 0 1 N N N N N N 1.730 -5.850 36.845 -2.294 -3.304 0.869 O08 VY9 15 VY9 O09 O3 O 0 1 N N N N N N 2.190 -7.297 38.448 -3.815 -3.625 -0.702 O09 VY9 16 VY9 O17 O4 O 0 1 N N N N N N 1.940 -0.988 41.201 -2.991 3.957 0.331 O17 VY9 17 VY9 H1 H1 H 0 1 N N N N N N 2.667 -0.535 38.375 -0.019 0.875 1.550 H1 VY9 18 VY9 H2 H2 H 0 1 N N N N N N 4.142 -1.447 37.905 0.140 2.031 0.206 H2 VY9 19 VY9 H3 H3 H 0 1 N N N N N N 0.244 -1.001 35.947 3.278 -1.418 -0.034 H3 VY9 20 VY9 H4 H4 H 0 1 N N N N N N 0.665 0.670 35.440 3.436 -0.262 -1.378 H4 VY9 21 VY9 H5 H5 H 0 1 N N N N N N -0.810 0.819 33.707 5.727 -1.895 -0.156 H5 VY9 22 VY9 H6 H6 H 0 1 N N N N N N -0.785 -0.281 32.287 5.885 -0.739 -1.500 H6 VY9 23 VY9 H7 H7 H 0 1 N N N N N N 2.985 -2.656 36.199 0.828 -0.940 0.089 H7 VY9 24 VY9 H8 H8 H 0 1 N N N N N N 1.376 -2.187 36.846 0.987 0.216 -1.256 H8 VY9 25 VY9 H9 H9 H 0 1 N N N N N N 2.774 0.247 36.211 2.430 0.398 1.428 H9 VY9 26 VY9 H10 H10 H 0 1 N N N N N N 2.972 -0.864 34.813 2.589 1.554 0.084 H10 VY9 27 VY9 H11 H11 H 0 1 N N N N N N 1.435 -0.351 33.202 5.038 1.076 -0.038 H11 VY9 28 VY9 H12 H12 H 0 1 N N N N N N 0.642 -1.873 33.736 4.880 -0.080 1.306 H12 VY9 29 VY9 H13 H13 H 0 1 N N N N N N -2.813 -0.647 33.671 8.059 -1.076 -0.355 H13 VY9 30 VY9 H14 H14 H 0 1 N N N N N N -1.752 -2.097 33.677 7.488 0.598 -0.161 H14 VY9 31 VY9 H15 H15 H 0 1 N N N N N N -1.778 -0.996 35.097 7.329 -0.558 1.183 H15 VY9 32 VY9 H16 H16 H 0 1 N N N N N N 3.416 -3.384 40.879 -2.408 1.600 1.576 H16 VY9 33 VY9 H17 H17 H 0 1 N N N N N N 4.604 -2.399 39.959 -3.479 1.190 0.215 H17 VY9 34 VY9 H18 H18 H 0 1 N N N N N N 1.624 -2.506 39.291 -1.435 0.609 -1.140 H18 VY9 35 VY9 H19 H19 H 0 1 N N N N N N 2.603 -5.277 39.965 -2.413 -1.371 -1.497 H19 VY9 36 VY9 H20 H20 H 0 1 N N N N N N 1.112 -4.549 39.276 -3.692 -0.879 -0.360 H20 VY9 37 VY9 H21 H21 H 0 1 N N N N N N 3.884 -4.151 38.466 -2.034 -0.786 1.368 H21 VY9 38 VY9 H23 H23 H 0 1 N N N N N N 2.098 -7.894 37.715 -3.901 -4.540 -0.403 H23 VY9 39 VY9 H24 H24 H 0 1 N N N N N N 1.844 -0.200 41.723 -2.811 4.816 -0.077 H24 VY9 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 VY9 C02 O01 DOUB N N 1 VY9 C04 C03 SING N N 2 VY9 C06 N05 SING N N 3 VY9 C07 C06 SING N N 4 VY9 O08 C07 DOUB N N 5 VY9 O09 C07 SING N N 6 VY9 N05 C04 SING N N 7 VY9 C10 C04 SING N N 8 VY9 C11 C10 SING N N 9 VY9 C12 C11 SING N N 10 VY9 C13 C12 SING N N 11 VY9 C14 C13 SING N N 12 VY9 C15 C14 SING N N 13 VY9 C16 C15 SING N N 14 VY9 C03 C02 SING N N 15 VY9 O17 C02 SING N N 16 VY9 C10 H1 SING N N 17 VY9 C10 H2 SING N N 18 VY9 C13 H3 SING N N 19 VY9 C13 H4 SING N N 20 VY9 C15 H5 SING N N 21 VY9 C15 H6 SING N N 22 VY9 C11 H7 SING N N 23 VY9 C11 H8 SING N N 24 VY9 C12 H9 SING N N 25 VY9 C12 H10 SING N N 26 VY9 C14 H11 SING N N 27 VY9 C14 H12 SING N N 28 VY9 C16 H13 SING N N 29 VY9 C16 H14 SING N N 30 VY9 C16 H15 SING N N 31 VY9 C03 H16 SING N N 32 VY9 C03 H17 SING N N 33 VY9 C04 H18 SING N N 34 VY9 C06 H19 SING N N 35 VY9 C06 H20 SING N N 36 VY9 N05 H21 SING N N 37 VY9 O09 H23 SING N N 38 VY9 O17 H24 SING N N 39 # 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 VY9 InChI InChI 1.06 "InChI=1S/C12H23NO4/c1-2-3-4-5-6-7-10(8-11(14)15)13-9-12(16)17/h10,13H,2-9H2,1H3,(H,14,15)(H,16,17)" VY9 InChIKey InChI 1.06 DKLSSPDDVJYWNG-UHFFFAOYSA-N VY9 SMILES_CANONICAL CACTVS 3.385 "CCCCCCC[C@@H](CC(O)=O)NCC(O)=O" VY9 SMILES CACTVS 3.385 "CCCCCCC[CH](CC(O)=O)NCC(O)=O" VY9 SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "CCCCCCC[C@H](CC(=O)O)NCC(=O)O" VY9 SMILES "OpenEye OEToolkits" 2.0.7 "CCCCCCCC(CC(=O)O)NCC(=O)O" # _pdbx_chem_comp_identifier.comp_id VY9 _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 "(3~{R})-3-(2-hydroxy-2-oxoethylamino)decanoic 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 VY9 "Create component" 2023-09-03 PDBJ VY9 "Initial release" 2024-04-17 RCSB #