data_8PY # _chem_comp.id 8PY _chem_comp.name "[(2~{R},3~{S},5~{R})-5-[2-azanyl-8-[ethanoyl(pyren-2-yl)amino]-6-oxidanylidene-1~{H}-purin-9-yl]-3-oxidanyl-oxolan-2-yl]methyl dihydrogen phosphate" _chem_comp.type "DNA linking" _chem_comp.pdbx_type ATOMN _chem_comp.formula "C28 H25 N6 O8 P" _chem_comp.mon_nstd_parent_comp_id DG _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2016-04-22 _chem_comp.pdbx_modified_date 2019-05-07 _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 604.507 _chem_comp.one_letter_code G _chem_comp.three_letter_code 8PY _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 5g35 _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 8PY P P1 P 0 1 N N N 24.144 59.534 -22.951 6.899 -1.826 0.380 P 8PY 1 8PY OP1 O1 O 0 1 N N N 24.063 60.090 -21.536 7.430 -0.613 -0.281 OP1 8PY 2 8PY "O5'" O2 O 0 1 N N N 22.842 59.903 -23.821 5.290 -1.814 0.312 "O5'" 8PY 3 8PY "C5'" C1 C 0 1 N N N 21.772 58.978 -23.779 4.564 -1.689 -0.913 "C5'" 8PY 4 8PY "C4'" C2 C 0 1 N N R 21.275 58.713 -25.198 3.063 -1.713 -0.620 "C4'" 8PY 5 8PY "C3'" C3 C 0 1 N N S 20.635 57.346 -25.260 2.257 -1.666 -1.937 "C3'" 8PY 6 8PY "O3'" O3 O 0 1 N N N 19.239 57.373 -24.894 1.837 -2.979 -2.314 "O3'" 8PY 7 8PY "C2'" C4 C 0 1 N N N 20.869 56.902 -26.684 1.035 -0.783 -1.599 "C2'" 8PY 8 8PY "C1'" C5 C 0 1 N N R 21.723 57.985 -27.323 1.247 -0.401 -0.117 "C1'" 8PY 9 8PY "O4'" O4 O 0 1 N N N 22.285 58.656 -26.184 2.671 -0.522 0.097 "O4'" 8PY 10 8PY N9 N1 N 0 1 Y N N 22.611 57.200 -28.225 0.810 0.977 0.122 N9 8PY 11 8PY C4 C6 C 0 1 Y N N 23.217 56.083 -27.834 1.360 2.108 -0.424 C4 8PY 12 8PY C5 C7 C 0 1 Y N N 23.938 55.561 -29.013 0.625 3.184 0.083 C5 8PY 13 8PY N7 N2 N 0 1 Y N N 23.710 56.374 -30.056 -0.328 2.673 0.904 N7 8PY 14 8PY C8 C8 C 0 1 Y N N 22.897 57.286 -29.523 -0.226 1.370 0.925 C8 8PY 15 8PY N3 N3 N 0 1 N N N 23.298 55.438 -26.655 2.373 2.337 -1.268 N3 8PY 16 8PY C2 C9 C 0 1 N N N 24.063 54.347 -26.629 2.692 3.559 -1.632 C2 8PY 17 8PY N2 N4 N 0 1 N N N 24.132 53.702 -25.481 3.739 3.744 -2.501 N2 8PY 18 8PY N1 N5 N 0 1 N N N 24.742 53.813 -27.659 2.012 4.647 -1.172 N1 8PY 19 8PY C6 C10 C 0 1 N N N 24.743 54.344 -28.873 0.977 4.494 -0.317 C6 8PY 20 8PY O6 O5 O 0 1 N N N 25.389 53.887 -29.853 0.363 5.461 0.101 O6 8PY 21 8PY OP2 O6 O 0 1 N Y N 24.451 58.042 -22.950 7.458 -3.135 -0.371 OP2 8PY 22 8PY N8 N6 N 0 1 N N N 22.559 58.255 -30.379 -1.037 0.516 1.658 N8 8PY 23 8PY C7 C11 C 0 1 N N N 23.145 59.469 -30.408 -0.621 0.050 2.852 C7 8PY 24 8PY C9 C12 C 0 1 N N N 22.480 60.522 -31.250 0.645 0.586 3.470 C9 8PY 25 8PY O10 O7 O 0 1 N N N 24.178 59.720 -29.798 -1.265 -0.800 3.430 O10 8PY 26 8PY C11 C13 C 0 1 Y N N 21.698 57.984 -31.364 -2.248 0.149 1.173 C11 8PY 27 8PY C12 C14 C 0 1 Y N N 22.392 57.858 -32.525 -3.258 1.106 1.111 C12 8PY 28 8PY C13 C15 C 0 1 Y N N 21.735 57.627 -33.673 -4.517 0.777 0.615 C13 8PY 29 8PY C14 C16 C 0 1 Y N N 20.365 57.539 -33.555 -4.751 -0.605 0.158 C14 8PY 30 8PY C15 C17 C 0 1 Y N N 19.640 57.668 -32.359 -3.653 -1.586 0.241 C15 8PY 31 8PY C16 C18 C 0 1 Y N N 20.325 57.910 -31.202 -2.428 -1.165 0.752 C16 8PY 32 8PY C23 C19 C 0 1 Y N N 19.674 57.276 -34.794 -5.916 -0.957 -0.314 C23 8PY 33 8PY C24 C20 C 0 1 Y N N 18.233 57.163 -34.747 -6.150 -2.339 -0.770 C24 8PY 34 8PY C25 C21 C 0 1 Y N N 17.586 57.308 -33.524 -5.117 -3.269 -0.694 C25 8PY 35 8PY C26 C22 C 0 1 Y N N 18.275 57.564 -32.335 -3.868 -2.892 -0.190 C26 8PY 36 8PY C27 C23 C 0 1 Y N N 20.426 57.117 -36.035 -7.014 0.024 -0.396 C27 8PY 37 8PY C28 C24 C 0 1 Y N N 21.817 57.237 -36.048 -6.799 1.331 0.033 C28 8PY 38 8PY C29 C25 C 0 1 Y N N 22.473 57.489 -34.862 -5.550 1.707 0.539 C29 8PY 39 8PY C30 C26 C 0 1 Y N N 17.588 56.915 -35.946 -7.411 -2.668 -1.264 C30 8PY 40 8PY C31 C27 C 0 1 Y N N 18.294 56.773 -37.122 -8.421 -1.712 -1.325 C31 8PY 41 8PY C32 C28 C 0 1 Y N N 19.693 56.874 -37.182 -8.241 -0.397 -0.905 C32 8PY 42 8PY H2 H2 H 0 1 N N N 20.952 59.393 -23.174 4.825 -0.747 -1.395 H2 8PY 43 8PY H3 H3 H 0 1 N N N 22.119 58.036 -23.330 4.819 -2.518 -1.572 H3 8PY 44 8PY H4 H4 H 0 1 N N N 20.525 59.473 -25.460 2.803 -2.604 -0.047 H4 8PY 45 8PY H5 H5 H 0 1 N N N 21.181 56.670 -24.585 2.850 -1.213 -2.731 H5 8PY 46 8PY H6 H6 H 0 1 N N N 19.153 57.658 -23.992 1.327 -3.008 -3.135 H6 8PY 47 8PY H7 H7 H 0 1 N N N 19.912 56.805 -27.217 1.023 0.109 -2.225 H7 8PY 48 8PY H8 H8 H 0 1 N N N 21.398 55.937 -26.702 0.111 -1.347 -1.722 H8 8PY 49 8PY H9 H9 H 0 1 N N N 21.088 58.665 -27.910 0.707 -1.089 0.533 H9 8PY 50 8PY H10 H10 H 0 1 N N N 23.625 54.038 -24.687 4.232 2.980 -2.837 H10 8PY 51 8PY H11 H11 H 0 1 N N N 24.691 52.877 -25.404 3.986 4.641 -2.778 H11 8PY 52 8PY H12 H12 H 0 1 N N N 25.270 52.978 -27.502 2.273 5.536 -1.460 H12 8PY 53 8PY H13 H13 H 0 1 N N N 24.535 57.736 -22.055 7.150 -3.969 0.009 H13 8PY 54 8PY H14 H14 H 0 1 N N N 23.062 61.454 -31.199 0.424 1.507 4.010 H14 8PY 55 8PY H15 H15 H 0 1 N N N 22.429 60.178 -32.294 1.051 -0.152 4.162 H15 8PY 56 8PY H16 H16 H 0 1 N N N 21.463 60.704 -30.874 1.374 0.789 2.686 H16 8PY 57 8PY H17 H17 H 0 1 N N N 23.469 57.943 -32.525 -3.063 2.112 1.451 H17 8PY 58 8PY H18 H18 H 0 1 N N N 19.839 58.033 -30.246 -1.607 -1.865 0.818 H18 8PY 59 8PY H19 H19 H 0 1 N N N 16.510 57.219 -33.492 -5.281 -4.284 -1.026 H19 8PY 60 8PY H20 H20 H 0 1 N N N 17.736 57.679 -31.406 -3.069 -3.616 -0.134 H20 8PY 61 8PY H21 H21 H 0 1 N N N 22.369 57.134 -36.971 -7.598 2.055 -0.024 H21 8PY 62 8PY H22 H22 H 0 1 N N N 23.549 57.580 -34.846 -5.387 2.722 0.872 H22 8PY 63 8PY H23 H23 H 0 1 N N N 16.511 56.831 -35.961 -7.606 -3.674 -1.604 H23 8PY 64 8PY H24 H24 H 0 1 N N N 17.749 56.576 -38.033 -9.385 -2.003 -1.714 H24 8PY 65 8PY H25 H25 H 0 1 N N N 20.199 56.761 -38.129 -9.060 0.303 -0.975 H25 8PY 66 8PY O1 O8 O 0 1 N Y N ? ? ? 7.371 -1.849 1.920 O1 8PY 67 8PY H1 H1 H 0 1 N N N ? ? ? 8.330 -1.857 2.037 H1 8PY 68 # # 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 8PY C32 C31 DOUB Y N 1 8PY C32 C27 SING Y N 2 8PY C31 C30 SING Y N 3 8PY C28 C27 DOUB Y N 4 8PY C28 C29 SING Y N 5 8PY C27 C23 SING Y N 6 8PY C30 C24 DOUB Y N 7 8PY C29 C13 DOUB Y N 8 8PY C23 C24 SING Y N 9 8PY C23 C14 DOUB Y N 10 8PY C24 C25 SING Y N 11 8PY C13 C14 SING Y N 12 8PY C13 C12 SING Y N 13 8PY C14 C15 SING Y N 14 8PY C25 C26 DOUB Y N 15 8PY C12 C11 DOUB Y N 16 8PY C15 C26 SING Y N 17 8PY C15 C16 DOUB Y N 18 8PY C11 C16 SING Y N 19 8PY C11 N8 SING N N 20 8PY C9 C7 SING N N 21 8PY C7 N8 SING N N 22 8PY C7 O10 DOUB N N 23 8PY N8 C8 SING N N 24 8PY N7 C8 DOUB Y N 25 8PY N7 C5 SING Y N 26 8PY O6 C6 DOUB N N 27 8PY C8 N9 SING Y N 28 8PY C5 C6 SING N N 29 8PY C5 C4 DOUB Y N 30 8PY C6 N1 SING N N 31 8PY N9 C4 SING Y N 32 8PY N9 "C1'" SING N N 33 8PY C4 N3 SING N N 34 8PY N1 C2 SING N N 35 8PY "C1'" "C2'" SING N N 36 8PY "C1'" "O4'" SING N N 37 8PY "C2'" "C3'" SING N N 38 8PY N3 C2 DOUB N N 39 8PY C2 N2 SING N N 40 8PY "O4'" "C4'" SING N N 41 8PY "C3'" "C4'" SING N N 42 8PY "C3'" "O3'" SING N N 43 8PY "C4'" "C5'" SING N N 44 8PY "O5'" "C5'" SING N N 45 8PY "O5'" P SING N N 46 8PY P OP2 SING N N 47 8PY P OP1 DOUB N N 48 8PY "C5'" H2 SING N N 49 8PY "C5'" H3 SING N N 50 8PY "C4'" H4 SING N N 51 8PY "C3'" H5 SING N N 52 8PY "O3'" H6 SING N N 53 8PY "C2'" H7 SING N N 54 8PY "C2'" H8 SING N N 55 8PY "C1'" H9 SING N N 56 8PY N2 H10 SING N N 57 8PY N2 H11 SING N N 58 8PY N1 H12 SING N N 59 8PY OP2 H13 SING N N 60 8PY C9 H14 SING N N 61 8PY C9 H15 SING N N 62 8PY C9 H16 SING N N 63 8PY C12 H17 SING N N 64 8PY C16 H18 SING N N 65 8PY C25 H19 SING N N 66 8PY C26 H20 SING N N 67 8PY C28 H21 SING N N 68 8PY C29 H22 SING N N 69 8PY C30 H23 SING N N 70 8PY C31 H24 SING N N 71 8PY C32 H25 SING N N 72 8PY P O1 SING N N 73 8PY O1 H1 SING N N 74 # # 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 8PY InChI InChI 1.03 "InChI=1S/C28H25N6O8P/c1-13(35)33(18-9-16-7-5-14-3-2-4-15-6-8-17(10-18)23(16)22(14)15)28-30-24-25(31-27(29)32-26(24)37)34(28)21-11-19(36)20(42-21)12-41-43(38,39)40/h2-10,19-21,36H,11-12H2,1H3,(H2,38,39,40)(H3,29,31,32,37)/t19-,20+,21+/m0/s1" 8PY InChIKey InChI 1.03 SOPYCICHZOSXGU-PWRODBHTSA-N 8PY SMILES_CANONICAL CACTVS 3.385 "CC(=O)N(c1cc2ccc3cccc4ccc(c1)c2c34)c5nc6C(=O)NC(=Nc6n5[C@H]7C[C@H](O)[C@@H](CO[P](O)(O)=O)O7)N" 8PY SMILES CACTVS 3.385 "CC(=O)N(c1cc2ccc3cccc4ccc(c1)c2c34)c5nc6C(=O)NC(=Nc6n5[CH]7C[CH](O)[CH](CO[P](O)(O)=O)O7)N" 8PY SMILES_CANONICAL "OpenEye OEToolkits" 2.0.5 "CC(=O)N(c1cc2ccc3cccc4c3c2c(c1)cc4)c5nc6c(n5[C@H]7C[C@@H]([C@H](O7)COP(=O)(O)O)O)N=C(NC6=O)N" 8PY SMILES "OpenEye OEToolkits" 2.0.5 "CC(=O)N(c1cc2ccc3cccc4c3c2c(c1)cc4)c5nc6c(n5C7CC(C(O7)COP(=O)(O)O)O)N=C(NC6=O)N" # _pdbx_chem_comp_identifier.comp_id 8PY _pdbx_chem_comp_identifier.type "SYSTEMATIC NAME" _pdbx_chem_comp_identifier.program "OpenEye OEToolkits" _pdbx_chem_comp_identifier.program_version 2.0.5 _pdbx_chem_comp_identifier.identifier "[(2~{R},3~{S},5~{R})-5-[2-azanyl-8-[ethanoyl(pyren-2-yl)amino]-6-oxidanylidene-1~{H}-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 8PY "Create component" 2016-04-22 EBI 8PY "Initial release" 2016-06-01 RCSB 8PY "Other modification" 2016-06-02 RCSB 8PY "Modify one letter code" 2019-05-07 EBI ##