data_XDY # _chem_comp.id XDY _chem_comp.name "N-[(1S,2S)-2-aminocyclopentyl]-N-[(5-methyl-2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)acetyl]glycine" _chem_comp.type peptide-like _chem_comp.pdbx_type HETAIN _chem_comp.formula "C14 H20 N4 O5" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2020-12-11 _chem_comp.pdbx_modified_date 2023-11-03 _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 324.332 _chem_comp.one_letter_code ? _chem_comp.three_letter_code XDY _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 7KZL _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.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 XDY C C02 C 0 1 N N N Y N Y -38.208 6.784 -17.091 -2.190 2.222 -0.568 C02 XDY 1 XDY C03 C03 C 0 1 N N N Y N N -39.263 7.612 -17.055 -2.133 0.817 -1.111 C03 XDY 2 XDY C05 C05 C 0 1 N N S Y N N -39.451 10.164 -16.961 -2.512 -0.837 0.775 C05 XDY 3 XDY CA C06 C 0 1 N N S Y N N -40.881 10.402 -17.452 -3.378 -1.781 -0.076 C06 XDY 4 XDY C08 C08 C 0 1 N N N N N N -40.792 11.306 -18.692 -4.845 -1.359 0.151 C08 XDY 5 XDY C09 C09 C 0 1 N N N N N N -39.280 11.293 -19.113 -4.748 0.121 0.600 C09 XDY 6 XDY C10 C10 C 0 1 N N N N N N -38.556 10.239 -18.202 -3.481 0.126 1.492 C10 XDY 7 XDY C11 C11 C 0 1 N N N N N N -39.046 8.827 -14.887 -0.265 -0.213 0.067 C11 XDY 8 XDY C12 C12 C 0 1 N N N N N N -39.040 10.101 -14.106 0.674 0.476 -0.889 C12 XDY 9 XDY C14 C14 C 0 1 N N N N N N -37.364 9.902 -12.337 2.674 -0.898 -1.035 C14 XDY 10 XDY C16 C16 C 0 1 N N N N N N -38.083 9.592 -9.994 4.625 -0.412 0.156 C16 XDY 11 XDY C17 C17 C 0 1 N N N N N N -39.495 9.549 -10.439 3.989 0.724 0.712 C17 XDY 12 XDY C18 C18 C 0 1 N N N N N N -39.776 9.683 -11.747 2.713 0.998 0.366 C18 XDY 13 XDY C19 C19 C 0 1 N N N N N N -40.579 9.369 -9.411 4.727 1.616 1.678 C19 XDY 14 XDY N04 N04 N 0 1 N N N Y N N -39.253 8.873 -16.285 -1.598 -0.082 -0.085 N04 XDY 15 XDY N N07 N 0 1 N N N Y Y N -41.737 11.010 -16.409 -3.182 -3.171 0.356 N07 XDY 16 XDY N13 N13 N 0 1 N N N N N N -38.721 9.909 -12.708 2.058 0.179 -0.513 N13 XDY 17 XDY N15 N15 N 0 1 N N N N N N -37.106 9.762 -10.975 3.945 -1.194 -0.707 N15 XDY 18 XDY O O01 O 0 1 N N N Y N Y -38.368 5.652 -17.483 -1.722 2.469 0.518 O01 XDY 19 XDY O20 O20 O 0 1 N N N N N N -37.761 9.486 -8.837 5.775 -0.679 0.453 O20 XDY 20 XDY O21 O21 O 0 1 N N N N N N -36.475 10.039 -13.115 2.072 -1.615 -1.810 O21 XDY 21 XDY O22 O22 O 0 1 N N N N N N -38.889 7.801 -14.313 0.178 -0.887 0.973 O22 XDY 22 XDY H032 H032 H 0 0 N N N Y N N -39.468 7.892 -18.099 -3.136 0.494 -1.390 H032 XDY 23 XDY H031 H031 H 0 0 N N N Y N N -40.103 7.020 -16.663 -1.486 0.793 -1.988 H031 XDY 24 XDY H051 H051 H 0 0 N N N Y N N -39.174 10.981 -16.278 -1.945 -1.411 1.509 H051 XDY 25 XDY HA H061 H 0 0 N N N Y N N -41.312 9.436 -17.755 -3.119 -1.678 -1.130 H061 XDY 26 XDY H081 H081 H 0 0 N N N N N N -41.114 12.329 -18.446 -5.413 -1.440 -0.775 H081 XDY 27 XDY H082 H082 H 0 0 N N N N N N -41.420 10.909 -19.503 -5.300 -1.967 0.932 H082 XDY 28 XDY H092 H092 H 0 0 N N N N N N -39.185 11.006 -20.171 -4.619 0.778 -0.260 H092 XDY 29 XDY H091 H091 H 0 0 N N N N N N -38.838 12.289 -18.962 -5.628 0.407 1.177 H091 XDY 30 XDY H101 H101 H 0 0 N N N N N N -38.496 9.262 -18.703 -3.716 -0.241 2.491 H101 XDY 31 XDY H102 H102 H 0 0 N N N N N N -37.544 10.578 -17.937 -3.055 1.128 1.543 H102 XDY 32 XDY H121 H121 H 0 0 N N N N N N -38.292 10.778 -14.546 0.488 0.120 -1.902 H121 XDY 33 XDY H122 H122 H 0 0 N N N N N N -40.037 10.560 -14.178 0.509 1.553 -0.846 H122 XDY 34 XDY H181 H181 H 0 0 N N N N N N -40.801 9.621 -12.083 2.212 1.861 0.780 H181 XDY 35 XDY H191 H191 H 0 0 N N N N N N -40.127 9.280 -8.412 5.735 1.232 1.829 H191 XDY 36 XDY H192 H192 H 0 0 N N N N N N -41.253 10.238 -9.432 4.780 2.626 1.271 H192 XDY 37 XDY H193 H193 H 0 0 N N N N N N -41.151 8.457 -9.637 4.198 1.635 2.631 H193 XDY 38 XDY H H071 H 0 0 N N N Y Y N -41.778 10.403 -15.615 -3.745 -3.803 -0.194 H071 XDY 39 XDY H2 H2 H 0 1 N Y N Y Y N -41.353 11.892 -16.135 -2.207 -3.428 0.317 H2 XDY 40 XDY H151 H151 H 0 0 N N N N N N -36.151 9.785 -10.679 4.374 -1.974 -1.092 H151 XDY 41 XDY OXT O1 O 0 1 N Y N Y N Y -36.937 7.443 -17.055 -2.756 3.199 -1.293 O1 XDY 42 XDY HXT H1 H 0 1 N Y N Y N Y -36.266 6.855 -17.382 -2.769 4.084 -0.903 H1 XDY 43 # 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 XDY C09 C08 SING N N 1 XDY C09 C10 SING N N 2 XDY C08 CA SING N N 3 XDY C10 C05 SING N N 4 XDY O C DOUB N N 5 XDY CA C05 SING N N 6 XDY CA N SING N N 7 XDY C C03 SING N N 8 XDY C03 N04 SING N N 9 XDY C05 N04 SING N N 10 XDY N04 C11 SING N N 11 XDY C11 O22 DOUB N N 12 XDY C11 C12 SING N N 13 XDY C12 N13 SING N N 14 XDY O21 C14 DOUB N N 15 XDY N13 C14 SING N N 16 XDY N13 C18 SING N N 17 XDY C14 N15 SING N N 18 XDY C18 C17 DOUB N N 19 XDY N15 C16 SING N N 20 XDY C17 C16 SING N N 21 XDY C17 C19 SING N N 22 XDY C16 O20 DOUB N N 23 XDY C03 H032 SING N N 24 XDY C03 H031 SING N N 25 XDY C05 H051 SING N N 26 XDY CA HA SING N N 27 XDY C08 H081 SING N N 28 XDY C08 H082 SING N N 29 XDY C09 H092 SING N N 30 XDY C09 H091 SING N N 31 XDY C10 H101 SING N N 32 XDY C10 H102 SING N N 33 XDY C12 H121 SING N N 34 XDY C12 H122 SING N N 35 XDY C18 H181 SING N N 36 XDY C19 H191 SING N N 37 XDY C19 H192 SING N N 38 XDY C19 H193 SING N N 39 XDY N H SING N N 40 XDY N H2 SING N N 41 XDY N15 H151 SING N N 42 XDY C OXT SING N N 43 XDY OXT HXT SING N N 44 # 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 XDY SMILES ACDLabs 12.01 "C(CN(C1C(N)CCC1)C(=O)CN2C(NC(=O)C(C)=C2)=O)(O)=O" XDY InChI InChI 1.03 "InChI=1S/C14H20N4O5/c1-8-5-17(14(23)16-13(8)22)6-11(19)18(7-12(20)21)10-4-2-3-9(10)15/h5,9-10H,2-4,6-7,15H2,1H3,(H,20,21)(H,16,22,23)/t9-,10-/m0/s1" XDY InChIKey InChI 1.03 LPWTXUYWYQYXJR-UWVGGRQHSA-N XDY SMILES_CANONICAL CACTVS 3.385 "CC1=CN(CC(=O)N(CC(O)=O)[C@H]2CCC[C@@H]2N)C(=O)NC1=O" XDY SMILES CACTVS 3.385 "CC1=CN(CC(=O)N(CC(O)=O)[CH]2CCC[CH]2N)C(=O)NC1=O" XDY SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "CC1=CN(C(=O)NC1=O)CC(=O)N(CC(=O)O)[C@H]2CCC[C@@H]2N" XDY SMILES "OpenEye OEToolkits" 2.0.7 "CC1=CN(C(=O)NC1=O)CC(=O)N(CC(=O)O)C2CCCC2N" # 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 XDY "SYSTEMATIC NAME" ACDLabs 12.01 "N-[(1S,2S)-2-aminocyclopentyl]-N-[(5-methyl-2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)acetyl]glycine" XDY "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 "2-[[(1~{S},2~{S})-2-azanylcyclopentyl]-[2-[5-methyl-2,4-bis(oxidanylidene)pyrimidin-1-yl]ethanoyl]amino]ethanoic 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 XDY "Create component" 2020-12-11 RCSB XDY "Initial release" 2020-12-23 RCSB XDY "Modify backbone" 2023-11-03 PDBE #