data_NRL # _chem_comp.id NRL _chem_comp.name "N-[(3R,4R)-4-aminooxolan-3-yl]-N-[(4-amino-2-oxopyrimidin-1(2H)-yl)acetyl]glycine" _chem_comp.type peptide-like _chem_comp.pdbx_type HETAIN _chem_comp.formula "C12 H17 N5 O5" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2022-04-07 _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 311.294 _chem_comp.one_letter_code ? _chem_comp.three_letter_code ? _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 7UID _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 NRL C10 C10 C 0 1 N N N N N N 30.521 13.088 15.710 2.161 2.030 -1.416 C10 NRL 1 NRL C14 C14 C 0 1 N N N N N N 27.253 15.891 20.113 -2.806 -0.211 -0.992 C14 NRL 2 NRL C17 C17 C 0 1 N N N N N N 28.249 18.088 21.511 -3.615 -0.384 1.584 C17 NRL 3 NRL C18 C18 C 0 1 N N N N N N 29.053 17.472 20.599 -2.380 -0.820 1.237 C18 NRL 4 NRL O21 O21 O 0 1 N N N N N N 26.907 14.888 19.497 -2.431 -0.132 -2.150 O21 NRL 5 NRL C C02 C 0 1 N N N Y N Y 28.559 16.293 14.425 2.504 -2.398 0.103 C02 NRL 6 NRL C03 C03 C 0 1 N N N Y N N 29.876 16.062 15.123 2.086 -1.576 -1.089 C03 NRL 7 NRL C05 C05 C 0 1 N N R Y N N 30.803 14.297 16.638 2.590 0.845 -0.523 C05 NRL 8 NRL CA C06 C 0 1 N N R Y N N 32.326 14.507 16.367 2.576 1.429 0.908 C06 NRL 9 NRL C08 C08 C 0 1 N N N N N N 32.807 13.088 16.048 2.141 2.898 0.709 C08 NRL 10 NRL C11 C11 C 0 1 N N N N N N 29.317 16.138 17.569 0.336 -0.060 -0.331 C11 NRL 11 NRL C12 C12 C 0 1 N N N N N N 29.453 15.623 18.989 -0.648 -1.195 -0.451 C12 NRL 12 NRL C16 C16 C 0 1 N N N N N N 26.945 17.529 21.782 -4.457 0.147 0.585 C16 NRL 13 NRL N04 N04 N 0 1 N N N Y N N 29.926 15.492 16.450 1.633 -0.258 -0.639 N04 NRL 14 NRL N N07 N 0 1 N N N Y Y N 32.997 15.068 17.544 3.918 1.366 1.502 N07 NRL 15 NRL N13 N13 N 0 1 N N N N N N 28.620 16.330 19.927 -1.982 -0.728 -0.063 N13 NRL 16 NRL N15 N15 N 0 1 N N N N N N 26.469 16.481 21.125 -4.024 0.221 -0.667 N15 NRL 17 NRL N19 N19 N 0 1 N N N N N N 26.148 18.183 22.712 -5.716 0.597 0.909 N19 NRL 18 NRL O O01 O 0 1 N N N Y N Y 28.566 17.144 13.568 2.431 -1.930 1.215 O01 NRL 19 NRL O09 O09 O 0 1 N N N N N N 31.749 12.410 15.499 1.415 2.902 -0.539 O09 NRL 20 NRL O22 O22 O 0 1 N N N N N N 28.609 17.121 17.421 -0.039 1.031 0.041 O22 NRL 21 NRL H101 H101 H 0 0 N N N N N N 30.117 13.440 14.749 3.037 2.546 -1.809 H101 NRL 22 NRL H102 H102 H 0 0 N N N N N N 29.796 12.411 16.186 1.530 1.680 -2.233 H102 NRL 23 NRL H171 H171 H 0 0 N N N N N N 28.581 18.979 22.023 -3.949 -0.444 2.609 H171 NRL 24 NRL H181 H181 H 0 0 N N N N N N 30.035 17.873 20.395 -1.717 -1.231 1.984 H181 NRL 25 NRL HXT H1 H 0 1 N Y N Y N Y 27.068 15.245 14.057 3.214 -4.137 0.725 H1 NRL 26 NRL H032 H032 H 0 0 N N N Y N N 30.461 15.394 14.474 2.934 -1.458 -1.764 H032 NRL 27 NRL H031 H031 H 0 0 N N N Y N N 30.373 17.041 15.185 1.273 -2.081 -1.611 H031 NRL 28 NRL H051 H051 H 0 0 N N N Y N N 30.697 13.951 17.677 3.592 0.510 -0.789 H051 NRL 29 NRL HA H061 H 0 0 N N N Y N N 32.460 15.157 15.490 1.858 0.897 1.531 H061 NRL 30 NRL H082 H082 H 0 0 N N N N N N 33.137 12.587 16.970 1.493 3.215 1.526 H082 NRL 31 NRL H081 H081 H 0 0 N N N N N N 33.641 13.126 15.332 3.014 3.547 0.645 H081 NRL 32 NRL H122 H122 H 0 0 N N N N N N 29.173 14.559 19.004 -0.673 -1.548 -1.482 H122 NRL 33 NRL H121 H121 H 0 0 N N N N N N 30.502 15.731 19.302 -0.344 -2.010 0.205 H121 NRL 34 NRL H H071 H 0 0 N N N Y Y N 32.654 15.992 17.715 3.918 1.746 2.437 H071 NRL 35 NRL H2 H2 H 0 1 N Y N Y Y N 32.812 14.491 18.340 4.273 0.421 1.496 H2 NRL 36 NRL H192 H192 H 0 0 N N N N N N 25.216 17.863 22.885 -6.027 0.548 1.827 H192 NRL 37 NRL H191 H191 H 0 0 N N N N N N 26.505 18.974 23.209 -6.293 0.962 0.220 H191 NRL 38 NRL OXT O02 O 0 1 N Y N Y N Y 27.770 15.280 14.696 2.958 -3.649 -0.070 O02 NRL 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 NRL O C DOUB N N 1 NRL C C03 SING N N 2 NRL C03 N04 SING N N 3 NRL O09 C10 SING N N 4 NRL O09 C08 SING N N 5 NRL C10 C05 SING N N 6 NRL C08 CA SING N N 7 NRL CA C05 SING N N 8 NRL CA N SING N N 9 NRL N04 C05 SING N N 10 NRL N04 C11 SING N N 11 NRL O22 C11 DOUB N N 12 NRL C11 C12 SING N N 13 NRL C12 N13 SING N N 14 NRL O21 C14 DOUB N N 15 NRL N13 C14 SING N N 16 NRL N13 C18 SING N N 17 NRL C14 N15 SING N N 18 NRL C18 C17 DOUB N N 19 NRL N15 C16 DOUB N N 20 NRL C17 C16 SING N N 21 NRL C16 N19 SING N N 22 NRL C10 H101 SING N N 23 NRL C10 H102 SING N N 24 NRL C17 H171 SING N N 25 NRL C18 H181 SING N N 26 NRL C03 H032 SING N N 27 NRL C03 H031 SING N N 28 NRL C05 H051 SING N N 29 NRL CA HA SING N N 30 NRL C08 H082 SING N N 31 NRL C08 H081 SING N N 32 NRL C12 H122 SING N N 33 NRL C12 H121 SING N N 34 NRL N H SING N N 35 NRL N H2 SING N N 36 NRL N19 H192 SING N N 37 NRL N19 H191 SING N N 38 NRL C OXT SING N N 39 NRL OXT HXT 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 NRL SMILES ACDLabs 12.01 "OC(=O)CN(C1COCC1N)C(=O)CN1C=CC(N)=NC1=O" NRL InChI InChI 1.03 "InChI=1S/C12H17N5O5/c13-7-5-22-6-8(7)17(4-11(19)20)10(18)3-16-2-1-9(14)15-12(16)21/h1-2,7-8H,3-6,13H2,(H,19,20)(H2,14,15,21)/t7-,8-/m0/s1" NRL InChIKey InChI 1.03 SSCQFEZTHMEZLU-YUMQZZPRSA-N NRL SMILES_CANONICAL CACTVS 3.385 "N[C@H]1COC[C@@H]1N(CC(O)=O)C(=O)CN2C=CC(=NC2=O)N" NRL SMILES CACTVS 3.385 "N[CH]1COC[CH]1N(CC(O)=O)C(=O)CN2C=CC(=NC2=O)N" NRL SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "C1[C@@H]([C@H](CO1)N(CC(=O)O)C(=O)CN2C=CC(=NC2=O)N)N" NRL SMILES "OpenEye OEToolkits" 2.0.7 "C1C(C(CO1)N(CC(=O)O)C(=O)CN2C=CC(=NC2=O)N)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 NRL "SYSTEMATIC NAME" ACDLabs 12.01 "N-[(3R,4R)-4-aminooxolan-3-yl]-N-[(4-amino-2-oxopyrimidin-1(2H)-yl)acetyl]glycine" NRL "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 "2-[2-(4-azanyl-2-oxidanylidene-pyrimidin-1-yl)ethanoyl-[(3~{R},4~{R})-4-azanyloxolan-3-yl]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 NRL "Create component" 2022-04-07 RCSB NRL "Modify internal type" 2022-08-15 RCSB NRL "Initial release" 2023-04-05 RCSB NRL "Modify backbone" 2023-11-03 PDBE NRL "Modify PCM" 2024-09-27 PDBE # _pdbx_chem_comp_pcm.pcm_id 1 _pdbx_chem_comp_pcm.comp_id NRL _pdbx_chem_comp_pcm.modified_residue_id ? _pdbx_chem_comp_pcm.type None _pdbx_chem_comp_pcm.category "Non-standard residue" _pdbx_chem_comp_pcm.position "Amino-acid side chain and backbone" _pdbx_chem_comp_pcm.polypeptide_position "Any position" _pdbx_chem_comp_pcm.comp_id_linking_atom ? _pdbx_chem_comp_pcm.modified_residue_id_linking_atom ? _pdbx_chem_comp_pcm.uniprot_specific_ptm_accession ? _pdbx_chem_comp_pcm.uniprot_generic_ptm_accession ? #