data_XDD # _chem_comp.id XDD _chem_comp.name "N-[(1S,2S)-2-aminocyclopentyl]-N-[(6-amino-9H-purin-9-yl)acetyl]glycine" _chem_comp.type peptide-like _chem_comp.pdbx_type HETAIN _chem_comp.formula "C14 H19 N7 O3" _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 333.346 _chem_comp.one_letter_code ? _chem_comp.three_letter_code XDD _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 XDD C12 C12 C 0 1 N N N N N N -41.985 13.497 -12.851 -0.281 1.107 0.289 C12 XDD 1 XDD C14 C14 C 0 1 Y N N N N N -41.368 12.923 -10.476 -2.300 1.843 -1.035 C14 XDD 2 XDD C16 C16 C 0 1 Y N N N N N -39.733 13.228 -11.904 -2.646 0.211 0.408 C16 XDD 3 XDD C10 C10 C 0 1 N N N N N N -43.663 13.909 -16.723 3.372 -0.018 1.545 C10 XDD 4 XDD C11 C11 C 0 1 N N N N N N -42.487 12.231 -13.514 0.493 0.081 -0.498 C11 XDD 5 XDD C C02 C 0 1 N N N Y N Y -42.964 10.344 -16.118 2.601 -2.278 -0.608 C02 XDD 6 XDD C03 C03 C 0 1 N N N Y N N -43.877 11.182 -15.235 2.598 -0.905 -1.229 C03 XDD 7 XDD C05 C05 C 0 1 N N S Y N N -43.822 13.728 -15.075 2.527 0.857 0.596 C05 XDD 8 XDD CA C06 C 0 1 N N S Y N N -45.154 13.934 -14.883 3.508 1.799 -0.123 C06 XDD 9 XDD C08 C08 C 0 1 N N N N N N -45.477 15.204 -15.875 4.915 1.463 0.414 C08 XDD 10 XDD C09 C09 C 0 1 N N N N N N -44.521 14.969 -17.066 4.790 0.006 0.922 C09 XDD 11 XDD C17 C17 C 0 1 Y N N N N N -39.221 12.959 -10.643 -3.839 0.523 -0.266 C17 XDD 12 XDD C18 C18 C 0 1 Y N N N N N -37.824 12.957 -10.549 -4.996 -0.204 0.064 C18 XDD 13 XDD C21 C21 C 0 1 Y N N N N N -37.628 13.465 -12.783 -3.763 -1.405 1.601 C21 XDD 14 XDD N04 N04 N 0 1 N N N Y N N -43.358 12.382 -14.636 1.834 0.013 -0.380 N04 XDD 15 XDD N N07 N 0 1 N N N Y Y N -45.471 14.260 -13.469 3.175 3.197 0.178 N07 XDD 16 XDD N13 N13 N 0 1 Y N N N N N -41.056 13.212 -11.755 -1.693 1.057 -0.100 N13 XDD 17 XDD N15 N15 N 0 1 Y N N N N N -40.236 12.759 -9.795 -3.559 1.530 -1.128 N15 XDD 18 XDD N19 N19 N 0 1 N N N N N N -37.174 12.696 -9.307 -6.200 0.058 -0.567 N19 XDD 19 XDD N20 N20 N 0 1 Y N N N N N -37.068 13.196 -11.606 -4.907 -1.148 0.995 N20 XDD 20 XDD N22 N22 N 0 1 Y N N N N N -38.946 13.481 -12.982 -2.653 -0.753 1.322 N22 XDD 21 XDD O O01 O 0 1 N N N Y N Y -43.380 9.307 -16.547 1.944 -2.495 0.382 O01 XDD 22 XDD O23 O23 O 0 1 N N N N N N -42.148 11.142 -13.143 -0.090 -0.683 -1.237 O23 XDD 23 XDD H121 H121 H 0 0 N N N N N N -41.469 14.111 -13.603 -0.191 0.892 1.354 H121 XDD 24 XDD H122 H122 H 0 0 N N N N N N -42.845 14.054 -12.451 0.118 2.100 0.083 H122 XDD 25 XDD H141 H141 H 0 0 N N N N N N -42.366 12.839 -10.072 -1.809 2.614 -1.610 H141 XDD 26 XDD H101 H101 H 0 0 N N N N N N -43.963 12.987 -17.242 3.388 0.411 2.547 H101 XDD 27 XDD H102 H102 H 0 0 N N N N N N -42.623 14.155 -16.985 2.983 -1.036 1.573 H102 XDD 28 XDD H032 H032 H 0 0 N N N Y N N -44.740 11.476 -15.851 3.623 -0.545 -1.321 H032 XDD 29 XDD H031 H031 H 0 0 N N N Y N N -44.216 10.533 -14.414 2.140 -0.953 -2.217 H031 XDD 30 XDD H051 H051 H 0 0 N N N Y N N -43.214 14.508 -14.593 1.804 1.437 1.169 H051 XDD 31 XDD HA H061 H 0 0 N N N Y N N -45.757 13.077 -15.218 3.468 1.629 -1.199 H061 XDD 32 XDD H082 H082 H 0 0 N N N N N N -45.259 16.160 -15.376 5.653 1.526 -0.386 H082 XDD 33 XDD H081 H081 H 0 0 N N N N N N -46.527 15.192 -16.203 5.181 2.133 1.231 H081 XDD 34 XDD H092 H092 H 0 0 N N N N N N -43.934 15.879 -17.260 5.547 -0.206 1.677 H092 XDD 35 XDD H091 H091 H 0 0 N N N N N N -45.099 14.707 -17.964 4.860 -0.700 0.094 H091 XDD 36 XDD H211 H211 H 0 0 N N N N N N -36.981 13.682 -13.620 -3.735 -2.181 2.352 H211 XDD 37 XDD H2 H2 H 0 1 N Y N Y Y N -45.265 13.471 -12.890 3.810 3.829 -0.287 H2 XDD 38 XDD H H3 H 0 1 N N N Y Y N -44.920 15.041 -13.176 2.218 3.402 -0.067 H3 XDD 39 XDD H192 H192 H 0 0 N N N N N N -36.183 12.736 -9.434 -6.252 0.750 -1.245 H192 XDD 40 XDD H191 H191 H 0 0 N N N N N N -37.452 13.382 -8.635 -6.992 -0.450 -0.331 H191 XDD 41 XDD OXT O1 O 0 1 N Y N Y N Y -41.737 11.010 -16.409 3.334 -3.260 -1.156 O1 XDD 42 XDD HXT H1 H 0 1 N Y N Y N Y -41.239 10.498 -17.036 3.304 -4.124 -0.722 H1 XDD 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 XDD C09 C10 SING N N 1 XDD C09 C08 SING N N 2 XDD C10 C05 SING N N 3 XDD O C DOUB N N 4 XDD C C03 SING N N 5 XDD C08 CA SING N N 6 XDD C03 N04 SING N N 7 XDD C05 CA SING N N 8 XDD C05 N04 SING N N 9 XDD CA N SING N N 10 XDD N04 C11 SING N N 11 XDD C11 O23 DOUB N N 12 XDD C11 C12 SING N N 13 XDD N22 C21 DOUB Y N 14 XDD N22 C16 SING Y N 15 XDD C12 N13 SING N N 16 XDD C21 N20 SING Y N 17 XDD C16 N13 SING Y N 18 XDD C16 C17 DOUB Y N 19 XDD N13 C14 SING Y N 20 XDD N20 C18 DOUB Y N 21 XDD C17 C18 SING Y N 22 XDD C17 N15 SING Y N 23 XDD C18 N19 SING N N 24 XDD C14 N15 DOUB Y N 25 XDD C12 H121 SING N N 26 XDD C12 H122 SING N N 27 XDD C14 H141 SING N N 28 XDD C10 H101 SING N N 29 XDD C10 H102 SING N N 30 XDD C03 H032 SING N N 31 XDD C03 H031 SING N N 32 XDD C05 H051 SING N N 33 XDD CA HA SING N N 34 XDD C08 H082 SING N N 35 XDD C08 H081 SING N N 36 XDD C09 H092 SING N N 37 XDD C09 H091 SING N N 38 XDD C21 H211 SING N N 39 XDD N H2 SING N N 40 XDD N H SING N N 41 XDD N19 H192 SING N N 42 XDD N19 H191 SING N N 43 XDD C OXT SING N N 44 XDD OXT HXT SING N N 45 # 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 XDD SMILES ACDLabs 12.01 "C(n1cnc2c1ncnc2N)C(=O)N(CC(O)=O)C3CCCC3N" XDD InChI InChI 1.03 "InChI=1S/C14H19N7O3/c15-8-2-1-3-9(8)21(5-11(23)24)10(22)4-20-7-19-12-13(16)17-6-18-14(12)20/h6-9H,1-5,15H2,(H,23,24)(H2,16,17,18)/t8-,9-/m0/s1" XDD InChIKey InChI 1.03 ZTNYOEGLXUSDRB-IUCAKERBSA-N XDD SMILES_CANONICAL CACTVS 3.385 "N[C@H]1CCC[C@@H]1N(CC(O)=O)C(=O)Cn2cnc3c(N)ncnc23" XDD SMILES CACTVS 3.385 "N[CH]1CCC[CH]1N(CC(O)=O)C(=O)Cn2cnc3c(N)ncnc23" XDD SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "c1nc(c2c(n1)n(cn2)CC(=O)N(CC(=O)O)[C@H]3CCC[C@@H]3N)N" XDD SMILES "OpenEye OEToolkits" 2.0.7 "c1nc(c2c(n1)n(cn2)CC(=O)N(CC(=O)O)C3CCCC3N)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 XDD "SYSTEMATIC NAME" ACDLabs 12.01 "N-[(1S,2S)-2-aminocyclopentyl]-N-[(6-amino-9H-purin-9-yl)acetyl]glycine" XDD "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 "2-[2-(6-aminopurin-9-yl)ethanoyl-[(1~{S},2~{S})-2-azanylcyclopentyl]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 XDD "Create component" 2020-12-11 RCSB XDD "Initial release" 2020-12-23 RCSB XDD "Modify backbone" 2023-11-03 PDBE #