data_D4B # _chem_comp.id D4B _chem_comp.name "[(2~{R},3~{S},5~{R})-5-[4-azanyl-5-[2-(4-ethynylphenyl)ethynyl]-2-oxidanylidene-pyrimidin-1-yl]-3-oxidanyl-oxolan-2-yl]methyl dihydrogen phosphate" _chem_comp.type "DNA LINKING" _chem_comp.pdbx_type ATOMN _chem_comp.formula "C19 H18 N3 O7 P" _chem_comp.mon_nstd_parent_comp_id DC _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2017-12-19 _chem_comp.pdbx_modified_date 2018-09-21 _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 431.336 _chem_comp.one_letter_code C _chem_comp.three_letter_code D4B _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 6FBF _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site EBI # 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 D4B O O1 O 0 1 N N N 32.389 -14.632 3.438 -2.536 0.109 0.469 O D4B 1 D4B "C1'" C1 C 0 1 N N R 31.502 -14.983 2.418 -1.391 0.758 1.065 "C1'" D4B 2 D4B C10 C2 C 0 1 Y N N 28.639 -18.518 8.564 6.081 -0.942 1.227 C10 D4B 3 D4B C11 C3 C 0 1 Y N N 28.074 -18.821 9.785 7.375 -1.321 1.445 C11 D4B 4 D4B C12 C4 C 0 1 Y N N 26.744 -19.534 7.433 6.698 -0.108 -0.963 C12 D4B 5 D4B C13 C5 C 0 1 Y N N 26.182 -19.834 8.670 7.994 -0.477 -0.738 C13 D4B 6 D4B C14 C6 C 0 1 Y N N 26.847 -19.486 9.848 8.346 -1.093 0.466 C14 D4B 7 D4B C15 C7 C 0 1 N N N 26.365 -19.785 11.138 9.702 -1.491 0.697 C15 D4B 8 D4B C16 C8 C 0 1 N N N 25.853 -20.097 12.155 10.814 -1.817 0.886 C16 D4B 9 D4B C2 C9 C 0 1 N N N 31.522 -17.507 1.817 -0.665 1.560 -1.106 C2 D4B 10 D4B "C2'" C10 C 0 1 N N N 30.269 -14.030 2.639 -1.930 2.111 1.581 "C2'" D4B 11 D4B "C3'" C11 C 0 1 N N S 31.013 -12.716 2.892 -3.442 1.862 1.779 "C3'" D4B 12 D4B C4 C12 C 0 1 N N N 30.348 -16.735 3.772 0.927 0.580 0.325 C4 D4B 13 D4B "C4'" C13 C 0 1 N N R 32.304 -13.219 3.626 -3.638 0.389 1.359 "C4'" D4B 14 D4B C5 C14 C 0 1 N N N 29.962 -18.054 4.050 1.902 0.790 -0.631 C5 D4B 15 D4B "C5'" C15 C 0 1 N N N 32.131 -12.834 5.141 -4.970 0.217 0.627 "C5'" D4B 16 D4B C6 C16 C 0 1 N N N 30.389 -19.071 3.137 1.506 1.433 -1.890 C6 D4B 17 D4B C7 C17 C 0 1 N N N 29.227 -18.337 5.192 3.258 0.393 -0.401 C7 D4B 18 D4B C8 C18 C 0 1 N N N 28.613 -18.595 6.171 4.370 0.067 -0.212 C8 D4B 19 D4B C9 C19 C 0 1 Y N N 27.974 -18.882 7.381 5.727 -0.330 0.019 C9 D4B 20 D4B N1 N1 N 0 1 N N N 31.143 -18.837 2.060 0.239 1.783 -2.057 N1 D4B 21 D4B N3 N2 N 0 1 N N N 31.097 -16.441 2.700 -0.347 0.975 0.060 N3 D4B 22 D4B N6 N3 N 0 1 N N N 30.010 -20.379 3.328 2.433 1.667 -2.876 N6 D4B 23 D4B O1 O2 O 0 1 N N N 31.029 -13.396 5.677 -5.152 -1.159 0.285 O1 D4B 24 D4B O2 O3 O 0 1 N N N 32.230 -17.238 0.859 -1.819 1.903 -1.298 O2 D4B 25 D4B OP1 O4 O 0 1 N N N 29.218 -13.676 7.501 -6.619 -0.951 -1.758 OP1 D4B 26 D4B "O3'" O5 O 0 1 N N N 31.313 -12.027 1.721 -3.804 2.045 3.149 "O3'" D4B 27 D4B P P1 P 0 1 N N N 30.657 -13.236 7.430 -6.450 -1.705 -0.496 P D4B 28 D4B OP2 O6 O 0 1 N N N 30.815 -11.702 7.499 -6.259 -3.269 -0.827 OP2 D4B 29 D4B "H1'" H1 H 0 1 N N N 31.917 -14.866 1.406 -1.005 0.163 1.893 "H1'" D4B 30 D4B H2 H2 H 0 1 N N N 29.588 -18.004 8.517 5.331 -1.118 1.984 H2 D4B 31 D4B H11 H3 H 0 1 N N N 28.582 -18.543 10.696 7.648 -1.796 2.376 H11 D4B 32 D4B H14 H4 H 0 1 N N N 26.231 -19.804 6.522 6.426 0.368 -1.894 H14 D4B 33 D4B H15 H5 H 0 1 N N N 25.228 -20.338 8.720 8.746 -0.294 -1.491 H15 D4B 34 D4B H16 H6 H 0 1 N N N 25.393 -20.377 13.068 11.808 -2.108 1.054 H16 D4B 35 D4B "H2'A" H7 H 0 0 N N N 29.628 -13.974 1.747 -1.459 2.373 2.529 "H2'A" D4B 36 D4B "H2'B" H8 H 0 0 N N N 29.665 -14.334 3.507 -1.765 2.895 0.842 "H2'B" D4B 37 D4B "H3'" H9 H 0 1 N N N 30.429 -12.094 3.586 -4.025 2.523 1.137 "H3'" D4B 38 D4B H4 H10 H 0 1 N N N 30.036 -15.941 4.434 1.172 0.111 1.266 H4 D4B 39 D4B "H4'" H11 H 0 1 N N N 33.185 -12.704 3.215 -3.597 -0.263 2.231 "H4'" D4B 40 D4B "H5'B" H12 H 0 0 N N N 33.014 -13.179 5.699 -5.785 0.541 1.274 "H5'B" D4B 41 D4B "H5'A" H13 H 0 0 N N N 32.049 -11.740 5.223 -4.966 0.819 -0.282 "H5'A" D4B 42 D4B HN2 H14 H 0 1 N N N 30.300 -21.083 2.680 3.358 1.408 -2.744 HN2 D4B 43 D4B HN1 H15 H 0 1 N N N 29.444 -20.626 4.115 2.162 2.093 -3.705 HN1 D4B 44 D4B H3 H17 H 0 1 N N N 31.772 -11.223 1.935 -3.644 2.938 3.483 H3 D4B 45 D4B HP2 HP2 H 0 1 N N N 29.959 -11.298 7.576 -7.005 -3.665 -1.298 HP2 D4B 46 D4B OP3 OP3 O 0 1 N Y N 31.909 -13.926 8.142 -7.754 -1.507 0.427 OP3 D4B 47 D4B HP3 HP3 H 0 1 N N N 31.615 -14.682 8.637 -7.712 -1.974 1.272 HP3 D4B 48 # 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 D4B O2 C2 DOUB N N 1 D4B "O3'" "C3'" SING N N 2 D4B C2 N1 SING N N 3 D4B C2 N3 SING N N 4 D4B N1 C6 DOUB N N 5 D4B "C1'" "C2'" SING N N 6 D4B "C1'" N3 SING N N 7 D4B "C1'" O SING N N 8 D4B "C2'" "C3'" SING N N 9 D4B N3 C4 SING N N 10 D4B "C3'" "C4'" SING N N 11 D4B C6 N6 SING N N 12 D4B C6 C5 SING N N 13 D4B O "C4'" SING N N 14 D4B "C4'" "C5'" SING N N 15 D4B C4 C5 DOUB N N 16 D4B C5 C7 SING N N 17 D4B "C5'" O1 SING N N 18 D4B C7 C8 TRIP N N 19 D4B O1 P SING N N 20 D4B C8 C9 SING N N 21 D4B C9 C12 DOUB Y N 22 D4B C9 C10 SING Y N 23 D4B P OP2 SING N N 24 D4B P OP1 DOUB N N 25 D4B C12 C13 SING Y N 26 D4B C10 C11 DOUB Y N 27 D4B C13 C14 DOUB Y N 28 D4B C11 C14 SING Y N 29 D4B C14 C15 SING N N 30 D4B C15 C16 TRIP N N 31 D4B "C1'" "H1'" SING N N 32 D4B C10 H2 SING N N 33 D4B C11 H11 SING N N 34 D4B C12 H14 SING N N 35 D4B C13 H15 SING N N 36 D4B C16 H16 SING N N 37 D4B "C2'" "H2'A" SING N N 38 D4B "C2'" "H2'B" SING N N 39 D4B "C3'" "H3'" SING N N 40 D4B C4 H4 SING N N 41 D4B "C4'" "H4'" SING N N 42 D4B "C5'" "H5'B" SING N N 43 D4B "C5'" "H5'A" SING N N 44 D4B N6 HN2 SING N N 45 D4B N6 HN1 SING N N 46 D4B "O3'" H3 SING N N 47 D4B OP2 HP2 SING N N 48 D4B P OP3 SING N N 49 D4B OP3 HP3 SING N N 50 # 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 D4B InChI InChI 1.03 "InChI=1S/C19H18N3O7P/c1-2-12-3-5-13(6-4-12)7-8-14-10-22(19(24)21-18(14)20)17-9-15(23)16(29-17)11-28-30(25,26)27/h1,3-6,10,15-17,23H,9,11H2,(H2,20,21,24)(H2,25,26,27)/t15-,16+,17+/m0/s1" D4B InChIKey InChI 1.03 JCGCLKWMRGKZTM-GVDBMIGSSA-N D4B SMILES_CANONICAL CACTVS 3.385 "NC1=NC(=O)N(C=C1C#Cc2ccc(cc2)C#C)[C@H]3C[C@H](O)[C@@H](CO[P](O)(O)=O)O3" D4B SMILES CACTVS 3.385 "NC1=NC(=O)N(C=C1C#Cc2ccc(cc2)C#C)[CH]3C[CH](O)[CH](CO[P](O)(O)=O)O3" D4B SMILES_CANONICAL "OpenEye OEToolkits" 2.0.6 "C#Cc1ccc(cc1)C#CC2=CN(C(=O)N=C2N)[C@H]3C[C@@H]([C@H](O3)COP(=O)(O)O)O" D4B SMILES "OpenEye OEToolkits" 2.0.6 "C#Cc1ccc(cc1)C#CC2=CN(C(=O)N=C2N)C3CC(C(O3)COP(=O)(O)O)O" # 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 D4B "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.6 "[(2~{R},3~{S},5~{R})-5-[4-azanyl-5-[2-(4-ethynylphenyl)ethynyl]-2-oxidanylidene-pyrimidin-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 D4B "Create component" 2017-12-19 RCSB D4B "Other modification" 2018-01-18 EBI D4B "Initial release" 2018-09-26 RCSB #