data_VBP # _chem_comp.id VBP _chem_comp.name "4-({3-[(2R)-2-amino-2-carboxyethyl]-2,6-dioxo-3,6-dihydropyrimidin-1(2H)-yl}methyl)benzoic acid" _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C15 H15 N3 O6" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms "(S)-1-(2-amino-2-carboxyethyl)-3-(4-carboxybenzyl)pyrimidine-2,4-dione" _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2009-04-09 _chem_comp.pdbx_modified_date 2020-06-17 _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 333.296 _chem_comp.one_letter_code ? _chem_comp.three_letter_code VBP _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 3H06 _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site RCSB # # 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 VBP C10 C10 C 0 1 N N N 4.362 16.551 12.352 -0.848 1.151 -1.642 C1 VBP 1 VBP C11 C11 C 0 1 Y N N 4.223 15.144 11.802 -2.075 0.516 -1.041 C2 VBP 2 VBP C12 C12 C 0 1 Y N N 5.294 14.097 12.151 -3.058 1.311 -0.480 C3 VBP 3 VBP C13 C13 C 0 1 Y N N 5.189 12.667 11.600 -4.184 0.736 0.071 C4 VBP 4 VBP C14 C14 C 0 1 Y N N 4.006 12.282 10.690 -4.331 -0.652 0.062 C5 VBP 5 VBP C15 C15 C 0 1 Y N N 2.922 13.339 10.333 -3.335 -1.449 -0.506 C6 VBP 6 VBP C16 C16 C 0 1 Y N N 3.024 14.783 10.890 -2.216 -0.861 -1.059 C7 VBP 7 VBP C17 C17 C 0 1 N N N 3.913 10.857 10.153 -5.534 -1.275 0.651 C8 VBP 8 VBP C20 C20 C 0 1 N N N 5.323 17.669 10.163 1.071 0.285 -0.421 C9 VBP 9 VBP C22 C22 C 0 1 N N N 7.290 18.798 5.752 5.224 -1.567 0.079 C10 VBP 10 VBP N01 N01 N 0 1 N N N 7.814 16.969 7.291 4.774 0.821 0.067 N1 VBP 11 VBP C02 C02 C 0 1 N N R 7.596 18.410 7.207 4.195 -0.502 -0.200 C11 VBP 12 VBP C03 C03 C 0 1 N N N 6.404 18.792 8.104 2.979 -0.719 0.703 C12 VBP 13 VBP N04 N04 N 0 1 N N N 6.446 18.443 9.504 2.031 0.383 0.517 N2 VBP 14 VBP C05 C05 C 0 1 N N N 7.626 18.862 10.306 2.129 1.501 1.300 C13 VBP 15 VBP C06 C06 C 0 1 N N N 7.704 18.510 11.767 1.255 2.516 1.128 C14 VBP 16 VBP C07 C07 C 0 1 N N N 6.574 17.719 12.432 0.250 2.400 0.138 C15 VBP 17 VBP O08 O08 O 0 1 N N N 6.636 17.374 13.789 -0.549 3.303 -0.036 O1 VBP 18 VBP N09 N09 N 0 1 N N N 5.398 17.305 11.640 0.187 1.282 -0.613 N3 VBP 19 VBP O18 O18 O 0 1 N N N 4.281 10.748 9.026 -5.672 -2.615 0.640 O2 VBP 20 VBP O19 O19 O 0 1 N N N 2.740 10.039 10.153 -6.398 -0.579 1.144 O3 VBP 21 VBP O21 O21 O 0 1 N N N 4.209 17.276 9.423 1.006 -0.715 -1.109 O4 VBP 22 VBP O23 O23 O 0 1 N N N 6.392 18.255 5.216 5.086 -2.790 -0.456 O5 VBP 23 VBP O24 O24 O 0 1 N N N 7.545 20.205 5.752 6.173 -1.320 0.785 O6 VBP 24 VBP H10 H10 H 0 1 N N N 3.401 17.073 12.237 -0.476 0.527 -2.454 H1 VBP 25 VBP H10A H10A H 0 0 N N N 4.650 16.482 13.411 -1.102 2.138 -2.029 H2 VBP 26 VBP H12 H12 H 0 1 N N N 6.124 14.368 12.787 -2.943 2.385 -0.474 H3 VBP 27 VBP H13 H13 H 0 1 N N N 5.942 11.934 11.849 -4.951 1.359 0.509 H4 VBP 28 VBP H15 H15 H 0 1 N N N 2.095 13.066 9.695 -3.442 -2.524 -0.516 H5 VBP 29 VBP H16 H16 H 0 1 N N N 2.274 15.522 10.647 -1.445 -1.476 -1.498 H6 VBP 30 VBP HN01 HN01 H 0 0 N N N 7.864 16.585 6.369 5.068 0.899 1.030 H7 VBP 31 VBP HN0A HN0A H 0 0 N N N 8.671 16.789 7.774 5.540 1.014 -0.561 H8 VBP 32 VBP H02 H02 H 0 1 N N N 8.498 18.943 7.543 3.887 -0.560 -1.244 H9 VBP 33 VBP H03 H03 H 0 1 N N N 6.318 19.888 8.058 2.496 -1.661 0.443 H10 VBP 34 VBP H03A H03A H 0 0 N N N 5.564 18.206 7.703 3.300 -0.750 1.744 H11 VBP 35 VBP H05 H05 H 0 1 N N N 8.426 19.418 9.840 2.902 1.571 2.051 H12 VBP 36 VBP H06 H06 H 0 1 N N N 8.561 18.817 12.349 1.321 3.404 1.740 H13 VBP 37 VBP HO18 HO18 H 0 0 N N N 3.686 10.179 8.552 -6.476 -2.977 1.037 H14 VBP 38 VBP HO23 HO23 H 0 0 N N N 5.850 18.899 4.775 5.772 -3.440 -0.248 H15 VBP 39 # # 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 VBP C11 C10 SING N N 1 VBP C11 C12 SING Y N 2 VBP C13 C12 DOUB Y N 3 VBP C14 C13 SING Y N 4 VBP C15 C14 DOUB Y N 5 VBP C15 C16 SING Y N 6 VBP C16 C11 DOUB Y N 7 VBP C17 C14 SING N N 8 VBP C17 O19 DOUB N N 9 VBP C20 N09 SING N N 10 VBP C22 C02 SING N N 11 VBP C02 N01 SING N N 12 VBP C02 C03 SING N N 13 VBP C03 N04 SING N N 14 VBP N04 C20 SING N N 15 VBP N04 C05 SING N N 16 VBP C05 C06 DOUB N N 17 VBP C06 C07 SING N N 18 VBP C07 O08 DOUB N N 19 VBP N09 C10 SING N N 20 VBP N09 C07 SING N N 21 VBP O18 C17 SING N N 22 VBP O21 C20 DOUB N N 23 VBP O23 C22 SING N N 24 VBP O24 C22 DOUB N N 25 VBP C10 H10 SING N N 26 VBP C10 H10A SING N N 27 VBP C12 H12 SING N N 28 VBP C13 H13 SING N N 29 VBP C15 H15 SING N N 30 VBP C16 H16 SING N N 31 VBP N01 HN01 SING N N 32 VBP N01 HN0A SING N N 33 VBP C02 H02 SING N N 34 VBP C03 H03 SING N N 35 VBP C03 H03A SING N N 36 VBP C05 H05 SING N N 37 VBP C06 H06 SING N N 38 VBP O18 HO18 SING N N 39 VBP O23 HO23 SING N N 40 # # 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 VBP SMILES ACDLabs 10.04 "O=C(O)c1ccc(cc1)CN2C(=O)C=CN(C2=O)CC(N)C(=O)O" VBP SMILES_CANONICAL CACTVS 3.341 "N[C@H](CN1C=CC(=O)N(Cc2ccc(cc2)C(O)=O)C1=O)C(O)=O" VBP SMILES CACTVS 3.341 "N[CH](CN1C=CC(=O)N(Cc2ccc(cc2)C(O)=O)C1=O)C(O)=O" VBP SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "c1cc(ccc1CN2C(=O)C=CN(C2=O)C[C@H](C(=O)O)N)C(=O)O" VBP SMILES "OpenEye OEToolkits" 1.5.0 "c1cc(ccc1CN2C(=O)C=CN(C2=O)CC(C(=O)O)N)C(=O)O" VBP InChI InChI 1.03 "InChI=1S/C15H15N3O6/c16-11(14(22)23)8-17-6-5-12(19)18(15(17)24)7-9-1-3-10(4-2-9)13(20)21/h1-6,11H,7-8,16H2,(H,20,21)(H,22,23)/t11-/m1/s1" VBP InChIKey InChI 1.03 XLRLZPOBHPIDFX-LLVKDONJSA-N # # 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 VBP "SYSTEMATIC NAME" ACDLabs 10.04 "4-({3-[(2R)-2-amino-2-carboxyethyl]-2,6-dioxo-3,6-dihydropyrimidin-1(2H)-yl}methyl)benzoic acid" VBP "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "4-[[3-[(2R)-2-amino-3-hydroxy-3-oxo-propyl]-2,6-dioxo-pyrimidin-1-yl]methyl]benzoic 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 VBP "Create component" 2009-04-09 RCSB VBP "Modify aromatic_flag" 2011-06-04 RCSB VBP "Modify descriptor" 2011-06-04 RCSB VBP "Modify synonyms" 2020-06-05 PDBE # _pdbx_chem_comp_synonyms.ordinal 1 _pdbx_chem_comp_synonyms.comp_id VBP _pdbx_chem_comp_synonyms.name "(S)-1-(2-amino-2-carboxyethyl)-3-(4-carboxybenzyl)pyrimidine-2,4-dione" _pdbx_chem_comp_synonyms.provenance ? _pdbx_chem_comp_synonyms.type ? ##