data_D3 # _chem_comp.id D3 _chem_comp.name "1-(2-DEOXY-BETA-D-RIBOFURANOSYL)-4-(3-BENZAMIDO)PHENYLIMIDAZOLE" _chem_comp.type "DNA LINKING" _chem_comp.pdbx_type HETAIN _chem_comp.formula "C21 H22 N3 O7 P" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 1999-07-08 _chem_comp.pdbx_modified_date 2011-06-04 _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 459.389 _chem_comp.one_letter_code N _chem_comp.three_letter_code D3 _chem_comp.pdbx_model_coordinates_details ? _chem_comp.pdbx_model_coordinates_missing_flag N _chem_comp.pdbx_ideal_coordinates_details ? _chem_comp.pdbx_ideal_coordinates_missing_flag N _chem_comp.pdbx_model_coordinates_db_code 1WAN _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 D3 P P P 0 1 N N N -10.037 2.022 -9.988 -1.567 -0.326 -6.763 P D3 1 D3 OP1 O1P O 0 1 N N N -9.856 1.452 -8.634 -2.286 -1.305 -5.918 OP1 D3 2 D3 OP2 O2P O 0 1 N N N -11.133 1.533 -10.855 -2.606 0.775 -7.309 OP2 D3 3 D3 OP3 O3P O 0 1 N Y N -10.184 3.619 -9.850 -0.888 -1.087 -8.008 OP3 D3 4 D3 "O5'" O5* O 0 1 N N N -8.651 1.864 -10.793 -0.425 0.399 -5.890 "O5'" D3 5 D3 "C5'" C5* C 0 1 N N N -8.166 0.570 -11.164 0.460 -0.625 -5.436 "C5'" D3 6 D3 "C4'" C4* C 0 1 N N R -6.866 0.665 -11.955 1.575 0.000 -4.595 "C4'" D3 7 D3 "O4'" O4* O 0 1 N N N -5.809 1.257 -11.148 1.021 0.655 -3.431 "O4'" D3 8 D3 "C3'" C3* C 0 1 N N S -6.388 -0.726 -12.387 2.506 -1.092 -4.025 "C3'" D3 9 D3 "O3'" O3* O 0 1 N N N -6.155 -0.796 -13.801 3.681 -1.218 -4.828 "O3'" D3 10 D3 "C2'" C2* C 0 1 N N N -5.111 -0.928 -11.631 2.869 -0.581 -2.612 "C2'" D3 11 D3 "C1'" C1* C 0 1 N N R -4.627 0.462 -11.310 2.115 0.762 -2.495 "C1'" D3 12 D3 N1A N1A N 0 1 Y N N -3.787 0.426 -10.109 1.608 0.945 -1.132 N1A D3 13 D3 C2A C2A C 0 1 Y N N -4.098 0.178 -8.833 2.260 1.541 -0.110 C2A D3 14 D3 N3A N3A N 0 1 Y N N -3.114 0.142 -7.986 1.499 1.520 0.947 N3A D3 15 D3 C4A C4A C 0 1 Y N N -2.003 0.396 -8.775 0.334 0.911 0.644 C4A D3 16 D3 C5A C5A C 0 1 Y N N -2.446 0.568 -10.060 0.387 0.548 -0.664 C5A D3 17 D3 C1B C1B C 0 1 Y N N -0.604 0.398 -8.214 -0.801 0.684 1.570 C1B D3 18 D3 C2B C2B C 0 1 Y N N -0.368 0.415 -6.817 -0.562 0.307 2.889 C2B D3 19 D3 C3B C3B C 0 1 Y N N 0.953 0.374 -6.337 -1.629 0.101 3.751 C3B D3 20 D3 C4B C4B C 0 1 Y N N 2.029 0.316 -7.246 -2.931 0.261 3.294 C4B D3 21 D3 C5B C5B C 0 1 Y N N 1.785 0.300 -8.616 -3.168 0.629 1.983 C5B D3 22 D3 C6B C6B C 0 1 Y N N 0.489 0.339 -9.102 -2.112 0.841 1.120 C6B D3 23 D3 N N N 0 1 N N N 1.187 0.379 -4.946 -1.394 -0.271 5.078 N D3 24 D3 C C C 0 1 N N N 1.849 1.357 -4.357 -0.304 0.187 5.724 C D3 25 D3 O O O 0 1 N N N 2.294 2.303 -4.984 0.420 1.004 5.189 O D3 26 D3 C1C C1C C 0 1 Y N N 2.034 1.256 -2.840 0.010 -0.300 7.083 C1C D3 27 D3 C2C C2C C 0 1 Y N N 3.301 1.431 -2.253 1.138 0.173 7.755 C2C D3 28 D3 C3C C3C C 0 1 Y N N 3.447 1.333 -0.864 1.425 -0.287 9.024 C3C D3 29 D3 C4C C4C C 0 1 Y N N 2.337 1.061 -0.059 0.598 -1.216 9.630 C4C D3 30 D3 C5C C5C C 0 1 Y N N 1.078 0.888 -0.639 -0.520 -1.690 8.969 C5C D3 31 D3 C6C C6C C 0 1 Y N N 0.925 0.985 -2.027 -0.823 -1.233 7.703 C6C D3 32 D3 HOP2 2HOP H 0 0 N N N -11.249 1.898 -11.724 -3.272 0.300 -7.825 HOP2 D3 33 D3 HOP3 3HOP H 0 0 N N N -10.300 3.984 -10.719 -0.431 -0.414 -8.532 HOP3 D3 34 D3 "H5'" 1H5* H 0 1 N N N -8.919 0.069 -11.774 0.896 -1.135 -6.295 "H5'" D3 35 D3 "H5''" 2H5* H 0 0 N N N -7.991 -0.016 -10.261 -0.092 -1.341 -4.829 "H5''" D3 36 D3 "H4'" H4* H 0 1 N N N -7.028 1.279 -12.841 2.147 0.710 -5.193 "H4'" D3 37 D3 "H3'" H3* H 0 1 N N N -7.119 -1.480 -12.091 1.983 -2.046 -3.963 "H3'" D3 38 D3 "HO3'" *HO3 H 0 0 N Y N -5.858 -1.658 -14.068 4.236 -1.890 -4.409 "HO3'" D3 39 D3 "H2'" 1H2* H 0 1 N N N -5.308 -1.478 -10.709 2.522 -1.281 -1.852 "H2'" D3 40 D3 "H2''" 2H2* H 0 0 N N N -4.377 -1.453 -12.241 3.944 -0.424 -2.527 "H2''" D3 41 D3 "H1'" H1* H 0 1 N N N -4.047 0.840 -12.153 2.770 1.589 -2.769 "H1'" D3 42 D3 H2A H2A H 0 1 N N N -5.135 0.007 -8.526 3.252 1.966 -0.161 H2A D3 43 D3 H5A H5A H 0 1 N N N -1.814 0.790 -10.925 -0.383 0.040 -1.223 H5A D3 44 D3 H2B H2B H 0 1 N N N -1.200 0.451 -6.109 0.450 0.183 3.241 H2B D3 45 D3 H4B H4B H 0 1 N N N 3.047 0.277 -6.895 -3.761 0.097 3.966 H4B D3 46 D3 H5B H5B H 0 1 N N N 2.606 0.254 -9.307 -4.182 0.753 1.633 H5B D3 47 D3 H6B H6B H 0 1 N N N 0.331 0.316 -10.174 -2.300 1.130 0.097 H6B D3 48 D3 HN HN H 0 1 N N N 0.846 -0.361 -4.402 -2.015 -0.860 5.534 HN D3 49 D3 H2C H2C H 0 1 N N N 4.162 1.644 -2.866 1.784 0.897 7.283 H2C D3 50 D3 H3C H3C H 0 1 N N N 4.421 1.466 -0.414 2.298 0.078 9.544 H3C D3 51 D3 H4C H4C H 0 1 N N N 2.455 0.987 1.013 0.828 -1.573 10.623 H4C D3 52 D3 H5C H5C H 0 1 N N N 0.221 0.679 -0.016 -1.162 -2.415 9.448 H5C D3 53 D3 H6C H6C H 0 1 N N N -0.050 0.853 -2.472 -1.697 -1.604 7.189 H6C D3 54 # 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 D3 P OP1 DOUB N N 1 D3 P OP2 SING N N 2 D3 P OP3 SING N N 3 D3 P "O5'" SING N N 4 D3 OP2 HOP2 SING N N 5 D3 OP3 HOP3 SING N N 6 D3 "O5'" "C5'" SING N N 7 D3 "C5'" "C4'" SING N N 8 D3 "C5'" "H5'" SING N N 9 D3 "C5'" "H5''" SING N N 10 D3 "C4'" "O4'" SING N N 11 D3 "C4'" "C3'" SING N N 12 D3 "C4'" "H4'" SING N N 13 D3 "O4'" "C1'" SING N N 14 D3 "C3'" "O3'" SING N N 15 D3 "C3'" "C2'" SING N N 16 D3 "C3'" "H3'" SING N N 17 D3 "O3'" "HO3'" SING N N 18 D3 "C2'" "C1'" SING N N 19 D3 "C2'" "H2'" SING N N 20 D3 "C2'" "H2''" SING N N 21 D3 "C1'" N1A SING N N 22 D3 "C1'" "H1'" SING N N 23 D3 N1A C2A SING Y N 24 D3 N1A C5A SING Y N 25 D3 C2A N3A DOUB Y N 26 D3 C2A H2A SING N N 27 D3 N3A C4A SING Y N 28 D3 C4A C5A DOUB Y N 29 D3 C4A C1B SING Y N 30 D3 C5A H5A SING N N 31 D3 C1B C2B DOUB Y N 32 D3 C1B C6B SING Y N 33 D3 C2B C3B SING Y N 34 D3 C2B H2B SING N N 35 D3 C3B C4B DOUB Y N 36 D3 C3B N SING N N 37 D3 C4B C5B SING Y N 38 D3 C4B H4B SING N N 39 D3 C5B C6B DOUB Y N 40 D3 C5B H5B SING N N 41 D3 C6B H6B SING N N 42 D3 N C SING N N 43 D3 N HN SING N N 44 D3 C O DOUB N N 45 D3 C C1C SING N N 46 D3 C1C C2C DOUB Y N 47 D3 C1C C6C SING Y N 48 D3 C2C C3C SING Y N 49 D3 C2C H2C SING N N 50 D3 C3C C4C DOUB Y N 51 D3 C3C H3C SING N N 52 D3 C4C C5C SING Y N 53 D3 C4C H4C SING N N 54 D3 C5C C6C DOUB Y N 55 D3 C5C H5C SING N N 56 D3 C6C H6C SING N N 57 # 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 D3 SMILES ACDLabs 10.04 "O=C(c1ccccc1)Nc4cccc(c2ncn(c2)C3OC(C(O)C3)COP(=O)(O)O)c4" D3 SMILES_CANONICAL CACTVS 3.341 "O[C@H]1C[C@@H](O[C@@H]1CO[P](O)(O)=O)n2cnc(c2)c3cccc(NC(=O)c4ccccc4)c3" D3 SMILES CACTVS 3.341 "O[CH]1C[CH](O[CH]1CO[P](O)(O)=O)n2cnc(c2)c3cccc(NC(=O)c4ccccc4)c3" D3 SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "c1ccc(cc1)C(=O)Nc2cccc(c2)c3cn(cn3)[C@H]4C[C@@H]([C@H](O4)COP(=O)(O)O)O" D3 SMILES "OpenEye OEToolkits" 1.5.0 "c1ccc(cc1)C(=O)Nc2cccc(c2)c3cn(cn3)C4CC(C(O4)COP(=O)(O)O)O" D3 InChI InChI 1.03 "InChI=1S/C21H22N3O7P/c25-18-10-20(31-19(18)12-30-32(27,28)29)24-11-17(22-13-24)15-7-4-8-16(9-15)23-21(26)14-5-2-1-3-6-14/h1-9,11,13,18-20,25H,10,12H2,(H,23,26)(H2,27,28,29)/t18-,19+,20+/m0/s1" D3 InChIKey InChI 1.03 OCVGIISTWVVLJA-XUVXKRRUSA-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 D3 "SYSTEMATIC NAME" ACDLabs 10.04 "1-(2-deoxy-5-O-phosphono-beta-D-erythro-pentofuranosyl)-4-{3-[(phenylcarbonyl)amino]phenyl}-1H-imidazole" D3 "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "[(2R,3S,5R)-5-[4-(3-benzamidophenyl)imidazol-1-yl]-3-hydroxy-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 D3 "Create component" 1999-07-08 RCSB D3 "Modify aromatic_flag" 2011-06-04 RCSB D3 "Modify descriptor" 2011-06-04 RCSB #