data_DF8 # _chem_comp.id DF8 _chem_comp.name "(2~{R},3~{R},4~{S},5~{R})-2-(6-azanyl-8-diazanyl-purin-9-yl)-5-(hydroxymethyl)oxolane-3,4-diol" _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C10 H15 N7 O4" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms "NEOMYCIN A; NEAMINE" _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2018-01-17 _chem_comp.pdbx_modified_date 2020-05-27 _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 297.271 _chem_comp.one_letter_code ? _chem_comp.three_letter_code DF8 _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 6FI6 _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.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 DF8 O3 O1 O 0 1 N N N -15.137 15.682 44.617 1.028 -2.315 -1.481 O3 DF8 1 DF8 C4 C1 C 0 1 Y N N -16.683 13.771 41.684 -1.678 -0.567 0.326 C4 DF8 2 DF8 C5 C2 C 0 1 N N R -15.577 15.969 42.257 0.855 -0.655 0.319 C5 DF8 3 DF8 C6 C3 C 0 1 N N R -14.519 18.010 41.858 3.118 -0.244 0.594 C6 DF8 4 DF8 N1 N1 N 0 1 N N N -13.346 14.476 40.884 0.354 2.174 -0.643 N1 DF8 5 DF8 C7 C4 C 0 1 N N N -13.217 18.287 41.124 4.093 0.913 0.367 C7 DF8 6 DF8 C8 C5 C 0 1 N N S -14.388 17.687 43.352 3.000 -1.089 -0.689 C8 DF8 7 DF8 N2 N2 N 0 1 Y N N -14.909 12.742 40.681 -1.929 1.528 -0.377 N2 DF8 8 DF8 C9 C6 C 0 1 N N R -14.583 16.165 43.398 1.493 -1.037 -1.041 C9 DF8 9 DF8 N3 N3 N 0 1 N N N -16.867 10.380 40.362 -4.956 1.051 -0.164 N3 DF8 10 DF8 N4 N4 N 0 1 Y N N -18.370 11.717 41.515 -4.317 -1.105 0.554 N4 DF8 11 DF8 N N5 N 0 1 N N N -12.538 13.953 39.851 0.032 3.435 -1.058 N DF8 12 DF8 C C7 C 0 1 Y N N -14.592 13.954 41.078 -0.644 1.277 -0.321 C DF8 13 DF8 O O2 O 0 1 N N N -15.170 16.870 41.250 1.807 0.268 0.890 O DF8 14 DF8 C1 C8 C 0 1 Y N N -16.243 12.616 41.053 -2.620 0.425 0.007 C1 DF8 15 DF8 C2 C9 C 0 1 Y N N -17.149 11.549 40.962 -3.982 0.112 0.137 C2 DF8 16 DF8 C3 C10 C 0 1 Y N N -18.657 12.884 42.104 -3.395 -2.005 0.844 C3 DF8 17 DF8 N5 N6 N 0 1 Y N N -17.891 13.967 42.237 -2.106 -1.755 0.739 N5 DF8 18 DF8 N6 N7 N 0 1 Y N N -15.612 14.634 41.689 -0.441 -0.003 0.115 N6 DF8 19 DF8 O1 O3 O 0 1 N N N -12.284 17.225 41.276 4.285 1.622 1.593 O1 DF8 20 DF8 O2 O4 O 0 1 N N N -15.402 18.352 44.092 3.409 -2.436 -0.440 O2 DF8 21 DF8 H1 H1 H 0 1 N N N -14.512 15.808 45.321 1.399 -2.598 -2.328 H1 DF8 22 DF8 H2 H2 H 0 1 N N N -16.580 16.238 42.620 0.746 -1.535 0.953 H2 DF8 23 DF8 H3 H3 H 0 1 N N N -15.167 18.893 41.756 3.467 -0.867 1.418 H3 DF8 24 DF8 H4 H4 H 0 1 N N N -12.842 14.357 41.739 1.285 1.909 -0.575 H4 DF8 25 DF8 H5 H5 H 0 1 N N N -12.773 19.210 41.525 5.049 0.520 0.021 H5 DF8 26 DF8 H6 H6 H 0 1 N N N -13.434 18.419 40.054 3.685 1.590 -0.384 H6 DF8 27 DF8 H7 H7 H 0 1 N N N -13.382 17.950 43.709 3.595 -0.651 -1.490 H7 DF8 28 DF8 H8 H8 H 0 1 N N N -13.635 15.661 43.160 1.296 -0.273 -1.792 H8 DF8 29 DF8 H9 H9 H 0 1 N N N -17.660 9.774 40.422 -4.700 1.936 -0.468 H9 DF8 30 DF8 H10 H10 H 0 1 N N N -16.645 10.544 39.401 -5.895 0.823 -0.071 H10 DF8 31 DF8 H11 H11 H 0 1 N N N -11.662 14.435 39.836 -0.548 3.902 -0.377 H11 DF8 32 DF8 H12 H12 H 0 1 N N N -12.380 12.979 40.013 0.862 3.973 -1.256 H12 DF8 33 DF8 H13 H13 H 0 1 N N N -19.646 12.959 42.531 -3.710 -2.982 1.179 H13 DF8 34 DF8 H14 H14 H 0 1 N N N -11.486 17.434 40.805 4.893 2.371 1.523 H14 DF8 35 DF8 H15 H15 H 0 1 N N N -15.310 18.144 45.014 4.330 -2.521 -0.158 H15 DF8 36 # 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 DF8 N N1 SING N N 1 DF8 N3 C2 SING N N 2 DF8 N2 C1 SING Y N 3 DF8 N2 C DOUB Y N 4 DF8 N1 C SING N N 5 DF8 C2 C1 DOUB Y N 6 DF8 C2 N4 SING Y N 7 DF8 C1 C4 SING Y N 8 DF8 C N6 SING Y N 9 DF8 C7 O1 SING N N 10 DF8 C7 C6 SING N N 11 DF8 O C6 SING N N 12 DF8 O C5 SING N N 13 DF8 N4 C3 DOUB Y N 14 DF8 C4 N6 SING Y N 15 DF8 C4 N5 DOUB Y N 16 DF8 N6 C5 SING N N 17 DF8 C6 C8 SING N N 18 DF8 C3 N5 SING Y N 19 DF8 C5 C9 SING N N 20 DF8 C8 C9 SING N N 21 DF8 C8 O2 SING N N 22 DF8 C9 O3 SING N N 23 DF8 O3 H1 SING N N 24 DF8 C5 H2 SING N N 25 DF8 C6 H3 SING N N 26 DF8 N1 H4 SING N N 27 DF8 C7 H5 SING N N 28 DF8 C7 H6 SING N N 29 DF8 C8 H7 SING N N 30 DF8 C9 H8 SING N N 31 DF8 N3 H9 SING N N 32 DF8 N3 H10 SING N N 33 DF8 N H11 SING N N 34 DF8 N H12 SING N N 35 DF8 C3 H13 SING N N 36 DF8 O1 H14 SING N N 37 DF8 O2 H15 SING N N 38 # 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 DF8 InChI InChI 1.03 "InChI=1S/C10H15N7O4/c11-7-4-8(14-2-13-7)17(10(15-4)16-12)9-6(20)5(19)3(1-18)21-9/h2-3,5-6,9,18-20H,1,12H2,(H,15,16)(H2,11,13,14)/t3-,5-,6-,9-/m1/s1" DF8 InChIKey InChI 1.03 XMRQUQWRGIIBTK-UUOKFMHZSA-N DF8 SMILES_CANONICAL CACTVS 3.385 "NNc1nc2c(N)ncnc2n1[C@@H]3O[C@H](CO)[C@@H](O)[C@H]3O" DF8 SMILES CACTVS 3.385 "NNc1nc2c(N)ncnc2n1[CH]3O[CH](CO)[CH](O)[CH]3O" DF8 SMILES_CANONICAL "OpenEye OEToolkits" 2.0.6 "c1nc(c2c(n1)n(c(n2)NN)[C@H]3[C@@H]([C@@H]([C@H](O3)CO)O)O)N" DF8 SMILES "OpenEye OEToolkits" 2.0.6 "c1nc(c2c(n1)n(c(n2)NN)C3C(C(C(O3)CO)O)O)N" # _pdbx_chem_comp_identifier.comp_id DF8 _pdbx_chem_comp_identifier.type "SYSTEMATIC NAME" _pdbx_chem_comp_identifier.program "OpenEye OEToolkits" _pdbx_chem_comp_identifier.program_version 2.0.6 _pdbx_chem_comp_identifier.identifier "(2~{R},3~{R},4~{S},5~{R})-2-(6-azanyl-8-diazanyl-purin-9-yl)-5-(hydroxymethyl)oxolane-3,4-diol" # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site DF8 "Create component" 2018-01-17 RCSB DF8 "Initial release" 2019-01-30 RCSB DF8 "Modify synonyms" 2020-05-27 PDBE # loop_ _pdbx_chem_comp_synonyms.ordinal _pdbx_chem_comp_synonyms.comp_id _pdbx_chem_comp_synonyms.name _pdbx_chem_comp_synonyms.provenance _pdbx_chem_comp_synonyms.type 1 DF8 "NEOMYCIN A" ? ? 2 DF8 NEAMINE ? ? #