data_5D0 # _chem_comp.id 5D0 _chem_comp.name "2,2'-[pentane-1,5-diylbis(oxybenzene-4,1-diyl)]di-1,4,5,6-tetrahydropyrimidine" _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C25 H32 N4 O2" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2015-09-07 _chem_comp.pdbx_modified_date 2016-01-15 _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 420.547 _chem_comp.one_letter_code ? _chem_comp.three_letter_code 5D0 _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 5DKQ _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 5D0 C1 C1 C 0 1 N N N -4.911 -6.692 -24.607 -2.503 1.015 0.000 C1 5D0 1 5D0 C2 C2 C 0 1 N N N -5.492 -5.336 -24.210 -1.252 1.896 -0.013 C2 5D0 2 5D0 C3 C3 C 0 1 N N N -4.604 -4.178 -24.663 -0.004 1.010 0.002 C3 5D0 3 5D0 C8 C4 C 0 1 Y N N -0.121 -3.465 -24.737 4.863 1.193 0.002 C8 5D0 4 5D0 C9 C5 C 0 1 Y N N 0.526 -4.308 -25.629 4.913 -0.196 0.018 C9 5D0 5 5D0 C10 C6 C 0 1 Y N N 1.752 -3.937 -26.160 6.129 -0.842 0.023 C10 5D0 6 5D0 C11 C7 C 0 1 Y N N 2.338 -2.727 -25.816 7.312 -0.102 0.013 C11 5D0 7 5D0 C12 C8 C 0 1 Y N N 1.695 -1.880 -24.914 7.258 1.293 -0.004 C12 5D0 8 5D0 C13 C9 C 0 1 Y N N 0.467 -2.251 -24.375 6.038 1.934 -0.009 C13 5D0 9 5D0 C14 C10 C 0 1 Y N N -5.669 -9.009 -24.727 -4.871 1.213 -0.004 C14 5D0 10 5D0 C15 C11 C 0 1 Y N N -5.554 -9.977 -23.742 -6.043 1.959 -0.017 C15 5D0 11 5D0 C16 C12 C 0 1 Y N N -5.335 -11.305 -24.077 -7.266 1.323 -0.008 C16 5D0 12 5D0 C19 C13 C 0 1 Y N N -5.557 -9.369 -26.061 -4.927 -0.175 0.012 C19 5D0 13 5D0 C20 C14 C 0 1 N N N 3.668 -2.371 -26.414 8.620 -0.793 0.019 C20 5D0 14 5D0 C21 C15 C 0 1 N N N -4.977 -13.098 -25.784 -8.637 -0.756 0.023 C21 5D0 15 5D0 N23 N1 N 0 1 N N N -5.118 -14.064 -24.882 -8.667 -2.134 0.044 N23 5D0 16 5D0 N25 N2 N 0 1 N N N 4.002 -1.169 -26.572 8.643 -2.085 0.034 N25 5D0 17 5D0 C27 C16 C 0 1 N N N -4.308 -15.710 -26.567 -11.042 -2.065 -0.429 C27 5D0 18 5D0 C30 C17 C 0 1 N N N 5.757 -1.641 -28.052 11.054 -2.044 -0.440 C30 5D0 19 5D0 C31 C18 C 0 1 N N N 5.313 -0.669 -26.966 9.870 -2.873 0.062 C31 5D0 20 5D0 C4 C19 C 0 1 N N N -3.644 -3.736 -23.562 1.247 1.890 -0.011 C4 5D0 21 5D0 C5 C20 C 0 1 N N N -2.449 -2.984 -24.141 2.494 1.005 0.004 C5 5D0 22 5D0 O6 O1 O 0 1 N N N -1.330 -3.864 -24.218 3.663 1.827 -0.009 O6 5D0 23 5D0 O7 O2 O 0 1 N N N -5.893 -7.703 -24.371 -3.668 1.842 -0.013 O7 5D0 24 5D0 C17 C21 C 0 1 Y N N -5.226 -11.666 -25.412 -7.326 -0.071 0.014 C17 5D0 25 5D0 C18 C22 C 0 1 Y N N -5.328 -10.696 -26.399 -6.146 -0.817 0.020 C18 5D0 26 5D0 N22 N3 N 0 1 N N N -4.606 -13.390 -26.950 -9.714 -0.043 0.005 N22 5D0 27 5D0 N24 N4 N 0 1 N N N 4.503 -3.338 -26.787 9.772 -0.037 0.002 N24 5D0 28 5D0 C26 C23 C 0 1 N N N -3.774 -14.514 -27.345 -11.059 -0.606 0.032 C26 5D0 29 5D0 C28 C24 C 0 1 N N N -4.552 -15.383 -25.096 -9.941 -2.808 0.340 C28 5D0 30 5D0 C29 C25 C 0 1 N N N 5.734 -3.062 -27.501 11.054 -0.697 0.294 C29 5D0 31 5D0 H1 H1 H 0 1 N N N -4.014 -6.900 -24.005 -2.504 0.372 -0.880 H1 5D0 32 5D0 H2 H2 H 0 1 N N N -4.642 -6.680 -25.673 -2.505 0.400 0.900 H2 5D0 33 5D0 H3 H3 H 0 1 N N N -5.592 -5.299 -23.115 -1.250 2.511 -0.913 H3 5D0 34 5D0 H4 H4 H 0 1 N N N -6.484 -5.225 -24.673 -1.251 2.539 0.867 H4 5D0 35 5D0 H5 H5 H 0 1 N N N -4.019 -4.499 -25.538 -0.006 0.395 0.902 H5 5D0 36 5D0 H6 H6 H 0 1 N N N -5.243 -3.327 -24.941 -0.005 0.367 -0.878 H6 5D0 37 5D0 H7 H7 H 0 1 N N N 0.077 -5.249 -25.909 3.997 -0.768 0.027 H7 5D0 38 5D0 H8 H8 H 0 1 N N N 2.257 -4.597 -26.849 6.168 -1.922 0.036 H8 5D0 39 5D0 H9 H9 H 0 1 N N N 2.148 -0.940 -24.635 8.172 1.869 -0.013 H9 5D0 40 5D0 H10 H10 H 0 1 N N N -0.033 -1.598 -23.675 5.996 3.013 -0.026 H10 5D0 41 5D0 H11 H11 H 0 1 N N N -5.636 -9.694 -22.703 -5.996 3.038 -0.033 H11 5D0 42 5D0 H12 H12 H 0 1 N N N -5.250 -12.054 -23.303 -8.177 1.904 -0.017 H12 5D0 43 5D0 H13 H13 H 0 1 N N N -5.648 -8.620 -26.834 -4.014 -0.751 0.017 H13 5D0 44 5D0 H15 H15 H 0 1 N N N -5.624 -13.878 -24.040 -7.864 -2.649 -0.133 H15 5D0 45 5D0 H17 H17 H 0 1 N N N -5.258 -16.031 -27.020 -12.007 -2.527 -0.223 H17 5D0 46 5D0 H18 H18 H 0 1 N N N -3.576 -16.529 -26.631 -10.835 -2.109 -1.498 H18 5D0 47 5D0 H19 H19 H 0 1 N N N 6.778 -1.389 -28.375 11.985 -2.573 -0.235 H19 5D0 48 5D0 H20 H20 H 0 1 N N N 5.073 -1.569 -28.910 10.952 -1.877 -1.512 H20 5D0 49 5D0 H21 H21 H 0 1 N N N 6.011 -0.685 -26.116 10.065 -3.198 1.084 H21 5D0 50 5D0 H22 H22 H 0 1 N N N 5.240 0.355 -27.362 9.748 -3.749 -0.576 H22 5D0 51 5D0 H23 H23 H 0 1 N N N -4.179 -3.076 -22.863 1.249 2.506 -0.911 H23 5D0 52 5D0 H24 H24 H 0 1 N N N -3.282 -4.624 -23.023 1.247 2.534 0.869 H24 5D0 53 5D0 H25 H25 H 0 1 N N N -2.202 -2.131 -23.491 2.492 0.389 0.903 H25 5D0 54 5D0 H26 H26 H 0 1 N N N -2.698 -2.618 -25.148 2.493 0.361 -0.876 H26 5D0 55 5D0 H27 H27 H 0 1 N N N -5.229 -10.975 -27.438 -6.189 -1.896 0.032 H27 5D0 56 5D0 H30 H30 H 0 1 N N N 4.274 -4.286 -26.567 9.739 0.911 -0.199 H30 5D0 57 5D0 H31 H31 H 0 1 N N N -3.857 -14.692 -28.427 -11.704 -0.028 -0.630 H31 5D0 58 5D0 H32 H32 H 0 1 N N N -2.722 -14.324 -27.084 -11.450 -0.555 1.048 H32 5D0 59 5D0 H33 H33 H 0 1 N N N -5.246 -16.131 -24.684 -9.897 -3.847 0.013 H33 5D0 60 5D0 H34 H34 H 0 1 N N N -3.592 -15.440 -24.563 -10.141 -2.763 1.410 H34 5D0 61 5D0 H35 H35 H 0 1 N N N 5.828 -3.771 -28.337 11.148 -0.860 1.368 H35 5D0 62 5D0 H36 H36 H 0 1 N N N 6.582 -3.192 -26.813 11.880 -0.081 -0.061 H36 5D0 63 # 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 5D0 C30 C29 SING N N 1 5D0 C30 C31 SING N N 2 5D0 C29 N24 SING N N 3 5D0 C26 N22 SING N N 4 5D0 C26 C27 SING N N 5 5D0 C31 N25 SING N N 6 5D0 N22 C21 DOUB N N 7 5D0 N24 C20 SING N N 8 5D0 N25 C20 DOUB N N 9 5D0 C27 C28 SING N N 10 5D0 C20 C11 SING N N 11 5D0 C18 C19 DOUB Y N 12 5D0 C18 C17 SING Y N 13 5D0 C10 C11 DOUB Y N 14 5D0 C10 C9 SING Y N 15 5D0 C19 C14 SING Y N 16 5D0 C11 C12 SING Y N 17 5D0 C21 C17 SING N N 18 5D0 C21 N23 SING N N 19 5D0 C9 C8 DOUB Y N 20 5D0 C17 C16 DOUB Y N 21 5D0 C28 N23 SING N N 22 5D0 C12 C13 DOUB Y N 23 5D0 C8 C13 SING Y N 24 5D0 C8 O6 SING N N 25 5D0 C14 O7 SING N N 26 5D0 C14 C15 DOUB Y N 27 5D0 C3 C2 SING N N 28 5D0 C3 C4 SING N N 29 5D0 C1 O7 SING N N 30 5D0 C1 C2 SING N N 31 5D0 O6 C5 SING N N 32 5D0 C5 C4 SING N N 33 5D0 C16 C15 SING Y N 34 5D0 C1 H1 SING N N 35 5D0 C1 H2 SING N N 36 5D0 C2 H3 SING N N 37 5D0 C2 H4 SING N N 38 5D0 C3 H5 SING N N 39 5D0 C3 H6 SING N N 40 5D0 C9 H7 SING N N 41 5D0 C10 H8 SING N N 42 5D0 C12 H9 SING N N 43 5D0 C13 H10 SING N N 44 5D0 C15 H11 SING N N 45 5D0 C16 H12 SING N N 46 5D0 C19 H13 SING N N 47 5D0 N23 H15 SING N N 48 5D0 C27 H17 SING N N 49 5D0 C27 H18 SING N N 50 5D0 C30 H19 SING N N 51 5D0 C30 H20 SING N N 52 5D0 C31 H21 SING N N 53 5D0 C31 H22 SING N N 54 5D0 C4 H23 SING N N 55 5D0 C4 H24 SING N N 56 5D0 C5 H25 SING N N 57 5D0 C5 H26 SING N N 58 5D0 C18 H27 SING N N 59 5D0 N24 H30 SING N N 60 5D0 C26 H31 SING N N 61 5D0 C26 H32 SING N N 62 5D0 C28 H33 SING N N 63 5D0 C28 H34 SING N N 64 5D0 C29 H35 SING N N 65 5D0 C29 H36 SING N N 66 # 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 5D0 SMILES ACDLabs 12.01 "C(Oc2ccc(C=1NCCCN=1)cc2)CCCCOc3ccc(cc3)C4=NCCCN4" 5D0 InChI InChI 1.03 "InChI=1S/C25H32N4O2/c1(2-18-30-22-10-6-20(7-11-22)24-26-14-4-15-27-24)3-19-31-23-12-8-21(9-13-23)25-28-16-5-17-29-25/h6-13H,1-5,14-19H2,(H,26,27)(H,28,29)" 5D0 InChIKey InChI 1.03 KPYLNHFSSDNDFO-UHFFFAOYSA-N 5D0 SMILES_CANONICAL CACTVS 3.385 "C(CCOc1ccc(cc1)C2=NCCCN2)CCOc3ccc(cc3)C4=NCCCN4" 5D0 SMILES CACTVS 3.385 "C(CCOc1ccc(cc1)C2=NCCCN2)CCOc3ccc(cc3)C4=NCCCN4" 5D0 SMILES_CANONICAL "OpenEye OEToolkits" 1.9.2 "c1cc(ccc1C2=NCCCN2)OCCCCCOc3ccc(cc3)C4=NCCCN4" 5D0 SMILES "OpenEye OEToolkits" 1.9.2 "c1cc(ccc1C2=NCCCN2)OCCCCCOc3ccc(cc3)C4=NCCCN4" # 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 5D0 "SYSTEMATIC NAME" ACDLabs 12.01 "2,2'-[pentane-1,5-diylbis(oxybenzene-4,1-diyl)]di-1,4,5,6-tetrahydropyrimidine" 5D0 "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.9.2 "2-[4-[5-[4-(1,4,5,6-tetrahydropyrimidin-2-yl)phenoxy]pentoxy]phenyl]-1,4,5,6-tetrahydropyrimidine" # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site 5D0 "Create component" 2015-09-07 RCSB 5D0 "Initial release" 2016-01-20 RCSB #