data_4DU # _chem_comp.id 4DU _chem_comp.name "1-(2-deoxy-5-O-phosphono-beta-D-erythro-pentofuranosyl)-1H-imidazo[4,5-c]pyridin-4-amine" _chem_comp.type "DNA LINKING" _chem_comp.pdbx_type ATOMN _chem_comp.formula "C11 H15 N4 O6 P" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2012-03-28 _chem_comp.pdbx_modified_date 2025-07-21 _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 330.234 _chem_comp.one_letter_code ? _chem_comp.three_letter_code 4DU _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 4DU3 _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site RCSB _chem_comp.pdbx_pcm ? # 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_n_terminal_atom_flag _chem_comp_atom.pdbx_backbone_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 4DU OP2 OP2 O 0 1 N N N N N N 1.183 0.320 35.319 5.900 -0.094 -0.120 OP2 4DU 1 4DU P P P 0 1 N N N N N N 1.611 -1.039 36.164 4.709 0.952 0.163 P 4DU 2 4DU OP1 OP1 O 0 1 N N N N N N 1.875 -2.518 35.475 4.502 1.799 -1.032 OP1 4DU 3 4DU "O5'" "O5'" O 0 1 N N N N N N 1.328 -1.046 37.847 3.354 0.145 0.490 "O5'" 4DU 4 4DU "C5'" "C5'" C 0 1 N N N N N N 1.531 -2.193 38.649 2.693 -0.686 -0.466 "C5'" 4DU 5 4DU "C4'" "C4'" C 0 1 N N R N N N 1.009 -1.763 40.010 1.443 -1.299 0.169 "C4'" 4DU 6 4DU "C3'" "C3'" C 0 1 N N S N N N -0.495 -1.602 39.985 0.711 -2.217 -0.842 "C3'" 4DU 7 4DU "O3'" "O3'" O 0 1 N N N N N N -1.109 -2.874 40.145 1.253 -3.539 -0.816 "O3'" 4DU 8 4DU "C2'" "C2'" C 0 1 N N N N N N -0.765 -0.649 41.134 -0.739 -2.203 -0.302 "C2'" 4DU 9 4DU "C1'" "C1'" C 0 1 N N R N N N 0.475 0.216 41.135 -0.809 -0.929 0.562 "C1'" 4DU 10 4DU "O4'" "O4'" O 0 1 N N N N N N 1.472 -0.458 40.347 0.468 -0.276 0.463 "O4'" 4DU 11 4DU N9 N9 N 0 1 Y N N N N N 0.179 1.547 40.544 -1.865 -0.045 0.061 N9 4DU 12 4DU C4 C4 C 0 1 Y N N N N N -0.458 2.554 41.146 -3.200 -0.109 0.380 C4 4DU 13 4DU C3 C3 C 0 1 Y N N N N N -0.986 2.695 42.329 -3.984 -0.924 1.193 C3 4DU 14 4DU C2 C2 C 0 1 Y N N N N N -1.562 3.802 42.696 -5.327 -0.687 1.273 C2 4DU 15 4DU N1 N1 N 0 1 Y N N N N N -1.637 4.869 41.865 -5.898 0.296 0.595 N1 4DU 16 4DU C6 C6 C 0 1 Y N N N N N -1.106 4.797 40.617 -5.207 1.103 -0.193 C6 4DU 17 4DU N6 N6 N 0 1 N N N N N N -1.171 5.842 39.746 -5.853 2.121 -0.883 N6 4DU 18 4DU C5 C5 C 0 1 Y N N N N N -0.499 3.605 40.232 -3.822 0.931 -0.333 C5 4DU 19 4DU N7 N7 N 0 1 Y N N N N N 0.112 3.203 39.094 -2.851 1.564 -1.036 N7 4DU 20 4DU C8 C8 C 0 1 Y N N N N N 0.522 1.936 39.301 -1.703 0.997 -0.803 C8 4DU 21 4DU OP3 O1 O 0 1 N Y N N N N 3.193 -0.765 36.364 5.097 1.881 1.419 OP3 4DU 22 4DU H2 H2 H 0 1 N N N N N N 0.962 -3.051 38.261 2.405 -0.087 -1.330 H2 4DU 23 4DU H3 H3 H 0 1 N N N N N N 2.598 -2.454 38.701 3.366 -1.481 -0.784 H3 4DU 24 4DU H4 H4 H 0 1 N N N N N N 1.297 -2.500 40.774 1.704 -1.850 1.073 H4 4DU 25 4DU H5 H5 H 0 1 N N N N N N -0.801 -1.134 39.038 0.756 -1.801 -1.849 H5 4DU 26 4DU H6 H6 H 0 1 N N N N N N -2.054 -2.774 40.129 0.827 -4.151 -1.432 H6 4DU 27 4DU H7 H7 H 0 1 N N N N N N -1.669 -0.049 40.950 -1.452 -2.146 -1.124 H7 4DU 28 4DU H8 H8 H 0 1 N N N N N N -0.873 -1.192 42.085 -0.928 -3.088 0.307 H8 4DU 29 4DU H9 H9 H 0 1 N N N N N N 0.828 0.342 42.169 -1.010 -1.195 1.599 H9 4DU 30 4DU H10 H10 H 0 1 N N N N N N -0.944 1.870 43.024 -3.536 -1.731 1.753 H10 4DU 31 4DU H11 H11 H 0 1 N N N N N N -1.990 3.872 43.685 -5.938 -1.318 1.902 H11 4DU 32 4DU H12 H12 H 0 1 N N N N N N -1.649 6.607 40.178 -6.811 2.240 -0.787 H12 4DU 33 4DU H13 H13 H 0 1 N N N N N N -0.245 6.126 39.496 -5.347 2.713 -1.461 H13 4DU 34 4DU H14 H14 H 0 1 N N N N N N 1.046 1.326 38.580 -0.762 1.303 -1.235 H14 4DU 35 4DU HOP3 H15 H 0 1 N Y N N N N 3.687 -1.506 36.035 5.905 2.397 1.292 H15 4DU 36 4DU HOP2 H1 H 0 1 N N N N N N 1.117 0.111 34.395 6.091 -0.683 0.622 H1 4DU 37 # 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 4DU OP2 P SING N N 1 4DU OP1 P DOUB N N 2 4DU P "O5'" SING N N 3 4DU "O5'" "C5'" SING N N 4 4DU "C5'" "C4'" SING N N 5 4DU N7 C8 DOUB Y N 6 4DU N7 C5 SING Y N 7 4DU C8 N9 SING Y N 8 4DU N6 C6 SING N N 9 4DU "C3'" "C4'" SING N N 10 4DU "C3'" "O3'" SING N N 11 4DU "C3'" "C2'" SING N N 12 4DU "C4'" "O4'" SING N N 13 4DU C5 C6 DOUB Y N 14 4DU C5 C4 SING Y N 15 4DU "O4'" "C1'" SING N N 16 4DU N9 "C1'" SING N N 17 4DU N9 C4 SING Y N 18 4DU C6 N1 SING Y N 19 4DU "C2'" "C1'" SING N N 20 4DU C4 C3 DOUB Y N 21 4DU N1 C2 DOUB Y N 22 4DU C3 C2 SING Y N 23 4DU P OP3 SING N N 24 4DU "C5'" H2 SING N N 25 4DU "C5'" H3 SING N N 26 4DU "C4'" H4 SING N N 27 4DU "C3'" H5 SING N N 28 4DU "O3'" H6 SING N N 29 4DU "C2'" H7 SING N N 30 4DU "C2'" H8 SING N N 31 4DU "C1'" H9 SING N N 32 4DU C3 H10 SING N N 33 4DU C2 H11 SING N N 34 4DU N6 H12 SING N N 35 4DU N6 H13 SING N N 36 4DU C8 H14 SING N N 37 4DU OP3 HOP3 SING N N 38 4DU OP2 HOP2 SING N N 39 # 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 4DU SMILES ACDLabs 14.52 "O=P(O)(O)OCC1OC(CC1O)n1cnc2c1ccnc2N" 4DU InChI InChI 1.06 "InChI=1S/C11H15N4O6P/c12-11-10-6(1-2-13-11)15(5-14-10)9-3-7(16)8(21-9)4-20-22(17,18)19/h1-2,5,7-9,16H,3-4H2,(H2,12,13)(H2,17,18,19)/t7-,8+,9+/m0/s1" 4DU InChIKey InChI 1.06 IOMKKLVSDVQOGL-DJLDLDEBSA-N 4DU SMILES_CANONICAL CACTVS 3.385 "Nc1nccc2n(cnc12)[C@H]3C[C@H](O)[C@@H](CO[P](O)(O)=O)O3" 4DU SMILES CACTVS 3.385 "Nc1nccc2n(cnc12)[CH]3C[CH](O)[CH](CO[P](O)(O)=O)O3" 4DU SMILES_CANONICAL "OpenEye OEToolkits" 3.1.0.0 "c1cnc(c2c1n(cn2)[C@H]3C[C@@H]([C@H](O3)COP(=O)(O)O)O)N" 4DU SMILES "OpenEye OEToolkits" 3.1.0.0 "c1cnc(c2c1n(cn2)C3CC(C(O3)COP(=O)(O)O)O)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 4DU "SYSTEMATIC NAME" ACDLabs 14.52 "1-(2-deoxy-5-O-phosphono-beta-D-erythro-pentofuranosyl)-1H-imidazo[4,5-c]pyridin-4-amine" 4DU "SYSTEMATIC NAME" "OpenEye OEToolkits" 3.1.0.0 "[(2~{R},3~{S},5~{R})-5-(4-azanylimidazo[4,5-c]pyridin-1-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 4DU "Create component" 2012-03-28 RCSB 4DU "Other modification" 2025-07-21 RCSB #