data_AGD # _chem_comp.id AGD _chem_comp.name "3-(2-amino-6-oxo-1,6-dihydro-9H-purin-9-yl)-D-alanine" _chem_comp.type "D-PEPTIDE LINKING" _chem_comp.pdbx_type ATOMP _chem_comp.formula "C8 H10 N6 O3" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2008-02-12 _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 238.203 _chem_comp.one_letter_code ? _chem_comp.three_letter_code AGD _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 3C1P _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 AGD C2 C2 C 0 1 N N N N N N -6.706 -15.194 5.481 -2.237 -1.698 -0.028 C2 AGD 1 AGD C4 C4 C 0 1 Y N N N N N -8.091 -16.883 5.702 -0.809 0.086 0.318 C4 AGD 2 AGD C5 C5 C 0 1 Y N N N N N -7.574 -17.612 4.635 -1.857 0.985 0.090 C5 AGD 3 AGD C6 C6 C 0 1 N N N N N N -6.532 -17.071 3.901 -3.141 0.470 -0.203 C6 AGD 4 AGD N N N 0 1 N N N Y Y N -8.043 -18.015 8.941 2.592 1.339 -1.151 N AGD 5 AGD CA CA C 0 1 N N R Y N N -9.431 -18.196 8.577 2.387 0.076 -0.429 CA AGD 6 AGD CB CB C 0 1 N N N N N N -9.855 -17.310 7.390 1.642 0.350 0.878 CB AGD 7 AGD N9 N9 N 0 1 Y N N N N N -9.059 -17.650 6.212 0.297 0.848 0.578 N9 AGD 8 AGD N3 N3 N 0 1 N N N N N N -7.719 -15.686 6.155 -1.040 -1.231 0.250 N3 AGD 9 AGD N2 N2 N 0 1 N N N N N N -6.221 -14.024 5.869 -2.425 -3.056 -0.086 N2 AGD 10 AGD N1 N1 N 0 1 N N N N N N -6.127 -15.820 4.391 -3.297 -0.872 -0.254 N1 AGD 11 AGD O6 O6 O 0 1 N N N N N N -5.933 -17.563 2.944 -4.082 1.217 -0.408 O6 AGD 12 AGD N7 N7 N 0 1 Y N N N N N -8.246 -18.805 4.459 -1.349 2.235 0.220 N7 AGD 13 AGD C8 C8 C 0 1 Y N N N N N -9.114 -18.799 5.428 -0.082 2.158 0.508 C8 AGD 14 AGD C C C 0 1 N N N Y N Y -10.356 -17.947 9.762 3.723 -0.551 -0.124 C AGD 15 AGD O O O 0 1 N N N Y N Y -11.570 -17.789 9.543 4.724 0.126 -0.132 O AGD 16 AGD OXT OXT O 0 1 N Y N Y N Y -9.864 -17.931 10.996 3.801 -1.861 0.157 OXT AGD 17 AGD HN1 HN1 H 0 1 N N N N N N -5.375 -15.353 3.925 -4.168 -1.249 -0.453 HN1 AGD 18 AGD H HN H 0 1 N N N Y Y N -7.484 -17.973 8.113 1.710 1.747 -1.424 HN AGD 19 AGD HA HA H 0 1 N N N Y N N -9.525 -19.246 8.262 1.799 -0.604 -1.046 HA AGD 20 AGD HB HB H 0 1 N N N N N N -10.920 -17.477 7.172 1.568 -0.572 1.455 HB AGD 21 AGD HBA HBA H 0 1 N N N N N N -9.691 -16.253 7.648 2.185 1.098 1.456 HBA AGD 22 AGD HN2 HN2 H 0 1 N N N N N N -5.458 -13.544 5.435 -1.681 -3.656 0.077 HN2 AGD 23 AGD HN2A HN2A H 0 0 N N N N N N -6.733 -13.693 6.662 -3.303 -3.415 -0.290 HN2A AGD 24 AGD H8 H8 H 0 1 N N N N N N -9.809 -19.606 5.607 0.572 3.003 0.666 H8 AGD 25 AGD H2 HNA H 0 1 N Y N Y Y N -7.942 -17.163 9.455 3.135 1.986 -0.599 HNA AGD 26 AGD HXT HXT H 0 1 N Y N Y N Y -10.569 -17.787 11.617 4.680 -2.218 0.346 HXT AGD 27 # 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 AGD N1 C2 SING N N 1 AGD C2 N2 SING N N 2 AGD C2 N3 DOUB N N 3 AGD C5 C4 DOUB Y N 4 AGD C4 N3 SING N N 5 AGD C4 N9 SING Y N 6 AGD C6 C5 SING N N 7 AGD N7 C5 SING Y N 8 AGD O6 C6 DOUB N N 9 AGD C6 N1 SING N N 10 AGD CA N SING N N 11 AGD N H SING N N 12 AGD N H2 SING N N 13 AGD CB CA SING N N 14 AGD HA CA SING N N 15 AGD CA C SING N N 16 AGD N9 CB SING N N 17 AGD HB CB SING N N 18 AGD CB HBA SING N N 19 AGD C8 N9 SING Y N 20 AGD HN2A N2 SING N N 21 AGD N2 HN2 SING N N 22 AGD HN1 N1 SING N N 23 AGD N7 C8 DOUB Y N 24 AGD C8 H8 SING N N 25 AGD O C DOUB N N 26 AGD C OXT SING N N 27 AGD OXT HXT SING N N 28 # 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 AGD SMILES ACDLabs 10.04 "O=C(O)C(N)Cn1c2N=C(NC(=O)c2nc1)N" AGD SMILES_CANONICAL CACTVS 3.341 "N[C@H](Cn1cnc2C(=O)NC(=Nc12)N)C(O)=O" AGD SMILES CACTVS 3.341 "N[CH](Cn1cnc2C(=O)NC(=Nc12)N)C(O)=O" AGD SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "c1nc2c(n1C[C@H](C(=O)O)N)N=C(NC2=O)N" AGD SMILES "OpenEye OEToolkits" 1.5.0 "c1nc2c(n1CC(C(=O)O)N)N=C(NC2=O)N" AGD InChI InChI 1.03 "InChI=1S/C8H10N6O3/c9-3(7(16)17)1-14-2-11-4-5(14)12-8(10)13-6(4)15/h2-3H,1,9H2,(H,16,17)(H3,10,12,13,15)/t3-/m1/s1" AGD InChIKey InChI 1.03 BYXRWAYRLQEIRT-GSVOUGTGSA-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 AGD "SYSTEMATIC NAME" ACDLabs 10.04 "3-(2-amino-6-oxo-1,6-dihydro-9H-purin-9-yl)-D-alanine" AGD "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "(2R)-2-amino-3-(2-amino-6-oxo-1H-purin-9-yl)propanoic 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 AGD "Create component" 2008-02-12 RCSB AGD "Modify aromatic_flag" 2011-06-04 RCSB AGD "Modify descriptor" 2011-06-04 RCSB AGD "Modify backbone" 2023-11-03 PDBE #