data_GD1 # _chem_comp.id GD1 _chem_comp.name "2-amino-5-[(Z)-iminomethyl]-3,7-dihydro-4H-pyrrolo[2,3-d]pyrimidin-4-one" _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C7 H7 N5 O" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms "7-cyano-7-deazaguanine, bound form" _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2012-05-25 _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 177.163 _chem_comp.one_letter_code ? _chem_comp.three_letter_code GD1 _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 4F8B _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 GD1 O6 O6 O 0 1 N N N N N N 4.022 19.055 14.065 -0.474 -2.188 -0.002 O6 GD1 1 GD1 C6 C6 C 0 1 N N N N N N 3.000 19.784 14.616 0.216 -1.184 -0.003 C6 GD1 2 GD1 C5 C5 C 0 1 Y N N N N N 1.673 19.938 14.089 -0.371 0.097 -0.001 C5 GD1 3 GD1 C7 C7 C 0 1 Y N N N N N 0.825 19.550 13.003 -1.754 0.600 0.001 C7 GD1 4 GD1 C77 C77 C 0 1 N N N N N N 1.061 18.705 11.818 -2.985 -0.205 0.002 C77 GD1 5 GD1 N77 N77 N 0 1 N N N N N N 2.191 18.331 11.523 -2.913 -1.499 0.002 N77 GD1 6 GD1 N1 N1 N 0 1 N N N N N N 3.298 20.404 15.796 1.566 -1.269 0.000 N1 GD1 7 GD1 C2 C2 C 0 1 N N N N N N 2.387 21.178 16.482 2.323 -0.135 0.000 C2 GD1 8 GD1 N2 N2 N 0 1 N N N N N N 2.745 21.792 17.623 3.690 -0.250 0.004 N2 GD1 9 GD1 N3 N3 N 0 1 N N N N N N 1.125 21.350 16.025 1.785 1.063 -0.003 N3 GD1 10 GD1 C4 C4 C 0 1 Y N N N N N 0.795 20.744 14.852 0.454 1.227 -0.002 C4 GD1 11 GD1 N9 N9 N 0 1 Y N N N N N -0.431 20.855 14.290 -0.355 2.329 -0.000 N9 GD1 12 GD1 C8 C8 C 0 1 Y N N N N N -0.443 20.112 13.141 -1.666 1.959 0.001 C8 GD1 13 GD1 H1 H1 H 0 1 N N N N N N 0.226 18.411 11.200 -3.948 0.283 0.004 H1 GD1 14 GD1 H2 H2 H 0 1 N N N N N N 2.195 17.767 10.697 -3.725 -2.030 0.003 H2 GD1 15 GD1 H3 H3 H 0 1 N N N N N N 4.215 20.292 16.178 1.996 -2.138 0.003 H3 GD1 16 GD1 H4 H4 H 0 1 N N N N N N 2.084 22.360 18.114 4.104 -1.127 0.006 H4 GD1 17 GD1 H5 H5 H 0 1 N N N N N N 3.672 21.680 17.981 4.244 0.547 0.004 H5 GD1 18 GD1 H6 H6 H 0 1 N N N N N N -1.196 21.388 14.652 -0.040 3.246 0.000 H6 GD1 19 GD1 H7 H7 H 0 1 N N N N N N -1.278 19.985 12.468 -2.505 2.639 0.002 H7 GD1 20 # 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 GD1 N77 C77 DOUB N N 1 GD1 C77 C7 SING N N 2 GD1 C7 C8 DOUB Y N 3 GD1 C7 C5 SING Y N 4 GD1 C8 N9 SING Y N 5 GD1 O6 C6 DOUB N N 6 GD1 C5 C6 SING N N 7 GD1 C5 C4 DOUB Y N 8 GD1 N9 C4 SING Y N 9 GD1 C6 N1 SING N N 10 GD1 C4 N3 SING N N 11 GD1 N1 C2 SING N N 12 GD1 N3 C2 DOUB N N 13 GD1 C2 N2 SING N N 14 GD1 C77 H1 SING N N 15 GD1 N77 H2 SING N N 16 GD1 N1 H3 SING N N 17 GD1 N2 H4 SING N N 18 GD1 N2 H5 SING N N 19 GD1 N9 H6 SING N N 20 GD1 C8 H7 SING N N 21 # 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 GD1 SMILES ACDLabs 12.01 "O=C1c2c(cnc2N=C(N)N1)C=[N@H]" GD1 InChI InChI 1.03 "InChI=1S/C7H7N5O/c8-1-3-2-10-5-4(3)6(13)12-7(9)11-5/h1-2,8H,(H4,9,10,11,12,13)/b8-1-" GD1 InChIKey InChI 1.03 BETPBINTBSWYLZ-QPIMQUGISA-N GD1 SMILES_CANONICAL CACTVS 3.370 "NC1=Nc2[nH]cc(C=N)c2C(=O)N1" GD1 SMILES CACTVS 3.370 "NC1=Nc2[nH]cc(C=N)c2C(=O)N1" GD1 SMILES_CANONICAL "OpenEye OEToolkits" 1.7.6 "[H]/N=C\c1c[nH]c2c1C(=O)NC(=N2)N" GD1 SMILES "OpenEye OEToolkits" 1.7.6 "c1c(c2c([nH]1)N=C(NC2=O)N)C=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 GD1 "SYSTEMATIC NAME" ACDLabs 12.01 "2-amino-5-[(Z)-iminomethyl]-3,7-dihydro-4H-pyrrolo[2,3-d]pyrimidin-4-one" GD1 "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.7.6 "2-azanyl-5-(iminomethyl)-3,7-dihydropyrrolo[2,3-d]pyrimidin-4-one" # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site GD1 "Create component" 2012-05-25 RCSB GD1 "Modify synonyms" 2021-03-13 RCSB GD1 "Modify PCM" 2024-09-27 PDBE # _pdbx_chem_comp_synonyms.ordinal 1 _pdbx_chem_comp_synonyms.comp_id GD1 _pdbx_chem_comp_synonyms.name "7-cyano-7-deazaguanine, bound form" _pdbx_chem_comp_synonyms.provenance PDB _pdbx_chem_comp_synonyms.type ? # _pdbx_chem_comp_pcm.pcm_id 1 _pdbx_chem_comp_pcm.comp_id GD1 _pdbx_chem_comp_pcm.modified_residue_id CYS _pdbx_chem_comp_pcm.type None _pdbx_chem_comp_pcm.category "Covalent chemical modification" _pdbx_chem_comp_pcm.position "Amino-acid side chain" _pdbx_chem_comp_pcm.polypeptide_position "Any position" _pdbx_chem_comp_pcm.comp_id_linking_atom C77 _pdbx_chem_comp_pcm.modified_residue_id_linking_atom SG _pdbx_chem_comp_pcm.uniprot_specific_ptm_accession ? _pdbx_chem_comp_pcm.uniprot_generic_ptm_accession ? #