data_EDI # _chem_comp.id EDI _chem_comp.name "2'-deoxy-1-(2-iodoethyl)inosine" _chem_comp.type "DNA LINKING" _chem_comp.pdbx_type ATOMN _chem_comp.formula "C12 H16 I N4 O7 P" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2014-05-19 _chem_comp.pdbx_modified_date 2014-06-27 _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 486.156 _chem_comp.one_letter_code ? _chem_comp.three_letter_code EDI _chem_comp.pdbx_model_coordinates_details ? _chem_comp.pdbx_model_coordinates_missing_flag Y _chem_comp.pdbx_ideal_coordinates_details Corina _chem_comp.pdbx_ideal_coordinates_missing_flag N _chem_comp.pdbx_model_coordinates_db_code 2MH6 _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 EDI P P P 0 1 N N N 7.485 4.709 -2.121 7.832 0.873 0.169 P EDI 1 EDI OP1 OP1 O 0 1 N N N 8.509 5.444 -2.907 8.849 -0.096 -0.298 OP1 EDI 2 EDI OP2 OP2 O 0 1 N N N 7.906 3.878 -0.965 7.563 1.965 -0.983 OP2 EDI 3 EDI "O5'" "O5'" O 0 1 N N N 6.408 5.765 -1.606 6.463 0.095 0.501 "O5'" EDI 4 EDI "C5'" "C5'" C 0 1 N N N 5.870 6.757 -2.484 5.795 -0.744 -0.444 "C5'" EDI 5 EDI "C4'" "C4'" C 0 1 N N R 4.651 7.400 -1.866 4.531 -1.325 0.193 "C4'" EDI 6 EDI "O4'" "O4'" O 0 1 N N N 3.676 6.373 -1.570 3.570 -0.281 0.459 "O4'" EDI 7 EDI "C3'" "C3'" C 0 1 N N S 4.898 8.131 -0.546 3.792 -2.251 -0.806 "C3'" EDI 8 EDI "O3'" "O3'" O 0 1 N N N 4.041 9.274 -0.444 4.313 -3.581 -0.749 "O3'" EDI 9 EDI "C2'" "C2'" C 0 1 N N N 4.554 7.094 0.501 2.338 -2.204 -0.277 "C2'" EDI 10 EDI "C1'" "C1'" C 0 1 N N R 3.501 6.234 -0.167 2.283 -0.912 0.561 "C1'" EDI 11 EDI N9 N9 N 0 1 Y N N 3.630 4.822 0.166 1.247 -0.020 0.032 N9 EDI 12 EDI C8 C8 C 0 1 Y N N 4.798 4.126 0.321 1.434 0.989 -0.865 C8 EDI 13 EDI N7 N7 N 0 1 Y N N 4.614 2.871 0.625 0.298 1.575 -1.112 N7 EDI 14 EDI C5 C5 C 0 1 Y N N 3.234 2.732 0.674 -0.679 0.979 -0.390 C5 EDI 15 EDI C6 C6 C 0 1 N N N 2.435 1.597 0.956 -2.075 1.185 -0.255 C6 EDI 16 EDI O6 O6 O 0 1 N N N 2.802 0.448 1.229 -2.641 2.066 -0.878 O6 EDI 17 EDI N1 N1 N 0 1 N N N 1.075 1.901 0.897 -2.761 0.376 0.584 N1 EDI 18 EDI C2 C2 C 0 1 N N N 0.560 3.140 0.606 -2.120 -0.601 1.273 C2 EDI 19 EDI N3 N3 N 0 1 N N N 1.295 4.204 0.341 -0.837 -0.803 1.160 N3 EDI 20 EDI C4 C4 C 0 1 Y N N 2.613 3.930 0.392 -0.084 -0.050 0.345 C4 EDI 21 EDI C11 C11 C 0 1 N N N 0.057 -0.034 2.411 -4.948 -0.301 -0.276 C11 EDI 22 EDI C12 C12 C 0 1 N N N 0.123 0.825 1.160 -4.205 0.557 0.750 C12 EDI 23 EDI OP3 OP3 O 0 1 N Y N 6.666 3.789 -3.155 8.365 1.612 1.496 OP3 EDI 24 EDI H1 H1 H 0 1 N N N 8.850 3.926 -0.867 6.906 2.634 -0.745 H1 EDI 25 EDI "H5'" "H5'" H 0 1 N N N 5.587 6.284 -3.436 5.523 -0.158 -1.321 "H5'" EDI 26 EDI "H5''" "H5''" H 0 0 N N N 6.632 7.528 -2.670 6.459 -1.557 -0.741 "H5''" EDI 27 EDI "H4'" "H4'" H 0 1 N N N 4.226 8.115 -2.586 4.777 -1.863 1.109 "H4'" EDI 28 EDI "H3'" "H3'" H 0 1 N N N 5.958 8.415 -0.466 3.851 -1.855 -1.820 "H3'" EDI 29 EDI H3 H3 H 0 1 N Y N 4.203 9.720 0.379 3.882 -4.198 -1.356 H3 EDI 30 EDI "H2'" "H2'" H 0 1 N N N 5.439 6.495 0.764 1.632 -2.152 -1.106 "H2'" EDI 31 EDI "H2''" "H2''" H 0 0 N N N 4.152 7.571 1.407 2.130 -3.074 0.346 "H2''" EDI 32 EDI "H1'" "H1'" H 0 1 N N N 2.505 6.595 0.129 2.068 -1.152 1.602 "H1'" EDI 33 EDI H8 H8 H 0 1 N N N 5.775 4.571 0.203 2.382 1.261 -1.306 H8 EDI 34 EDI H2 H2 H 0 1 N N N -0.514 3.251 0.593 -2.691 -1.233 1.936 H2 EDI 35 EDI H11 H11 H 0 1 N N N 0.943 -0.328 2.994 -4.657 0.003 -1.282 H11 EDI 36 EDI H12 H12 H 0 1 N N N -0.842 -0.125 3.039 -4.693 -1.350 -0.125 H12 EDI 37 EDI H15 H15 H 0 1 N N N -0.869 1.295 1.082 -4.496 0.254 1.756 H15 EDI 38 EDI H14 H14 H 0 1 N N N 0.258 0.114 0.331 -4.460 1.606 0.599 H14 EDI 39 EDI H5 H5 H 0 1 N Y N 7.010 3.914 -4.032 9.189 2.102 1.369 H5 EDI 40 EDI I1 I1 I 0 1 N Y N ? ? ? -7.079 -0.034 -0.031 I1 EDI 41 # 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 EDI OP1 P DOUB N N 1 EDI "C5'" "C4'" SING N N 2 EDI "C5'" "O5'" SING N N 3 EDI P "O5'" SING N N 4 EDI P OP2 SING N N 5 EDI "C4'" "O4'" SING N N 6 EDI "C4'" "C3'" SING N N 7 EDI "O4'" "C1'" SING N N 8 EDI "C3'" "O3'" SING N N 9 EDI "C3'" "C2'" SING N N 10 EDI "C1'" N9 SING N N 11 EDI "C1'" "C2'" SING N N 12 EDI N9 C8 SING Y N 13 EDI N9 C4 SING Y N 14 EDI C8 N7 DOUB Y N 15 EDI N3 C4 SING N N 16 EDI N3 C2 DOUB N N 17 EDI C4 C5 DOUB Y N 18 EDI C2 N1 SING N N 19 EDI N7 C5 SING Y N 20 EDI C5 C6 SING N N 21 EDI N1 C6 SING N N 22 EDI N1 C12 SING N N 23 EDI C6 O6 DOUB N N 24 EDI C12 C11 SING N N 25 EDI P OP3 SING N N 26 EDI OP2 H1 SING N N 27 EDI "C5'" "H5'" SING N N 28 EDI "C5'" "H5''" SING N N 29 EDI "C4'" "H4'" SING N N 30 EDI "C3'" "H3'" SING N N 31 EDI "O3'" H3 SING N N 32 EDI "C2'" "H2'" SING N N 33 EDI "C2'" "H2''" SING N N 34 EDI "C1'" "H1'" SING N N 35 EDI C8 H8 SING N N 36 EDI C2 H2 SING N N 37 EDI C11 H11 SING N N 38 EDI C11 H12 SING N N 39 EDI C12 H15 SING N N 40 EDI C12 H14 SING N N 41 EDI OP3 H5 SING N N 42 EDI C11 I1 SING N N 43 # 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 EDI SMILES ACDLabs 12.01 "O=P(O)(O)OCC3OC(n2cnc1c2N=CN(C1=O)CCI)CC3O" EDI InChI InChI 1.03 "InChI=1S/C12H16IN4O7P/c13-1-2-16-5-15-11-10(12(16)19)14-6-17(11)9-3-7(18)8(24-9)4-23-25(20,21)22/h5-9,18H,1-4H2,(H2,20,21,22)/t7-,8+,9+/m0/s1" EDI InChIKey InChI 1.03 VZODOTFJXVCKSN-DJLDLDEBSA-N EDI SMILES_CANONICAL CACTVS 3.385 "O[C@H]1C[C@@H](O[C@@H]1CO[P](O)(O)=O)n2cnc3C(=O)N(CCI)C=Nc23" EDI SMILES CACTVS 3.385 "O[CH]1C[CH](O[CH]1CO[P](O)(O)=O)n2cnc3C(=O)N(CCI)C=Nc23" EDI SMILES_CANONICAL "OpenEye OEToolkits" 1.7.6 "c1nc2c(n1[C@H]3C[C@@H]([C@H](O3)COP(=O)(O)O)O)N=CN(C2=O)CCI" EDI SMILES "OpenEye OEToolkits" 1.7.6 "c1nc2c(n1C3CC(C(O3)COP(=O)(O)O)O)N=CN(C2=O)CCI" # 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 EDI "SYSTEMATIC NAME" ACDLabs 12.01 ;2'-deoxy-1-(2-iodoethyl)inosine 5'-(dihydrogen phosphate) ; EDI "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.7.6 "[(2R,3S,5R)-5-[1-(2-iodanylethyl)-6-oxidanylidene-purin-9-yl]-3-oxidanyl-oxolan-2-yl]methyl dihydrogen phosphate" # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site EDI "Create component" 2014-05-19 RCSB EDI "Initial release" 2014-07-02 RCSB #