data_LDG # _chem_comp.id LDG _chem_comp.name ;2'-deoxy-N-[(1,3-dimethoxy-9,10-dioxo-9,10-dihydroanthracen-2-yl)methyl]guanosine 5'-(dihydrogen phosphate) ; _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C27 H26 N5 O11 P" _chem_comp.mon_nstd_parent_comp_id DG _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2017-06-15 _chem_comp.pdbx_modified_date 2017-10-13 _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 627.496 _chem_comp.one_letter_code ? _chem_comp.three_letter_code LDG _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 5W2A _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 LDG O19 O1 O 0 1 N N N -12.000 -31.220 30.069 -5.676 1.054 2.391 O19 LDG 1 LDG C19 C1 C 0 1 N N N -12.142 -31.201 31.292 -6.109 0.882 1.268 C19 LDG 2 LDG C18 C2 C 0 1 Y N N -13.471 -31.120 31.880 -5.188 0.620 0.148 C18 LDG 3 LDG C17 C3 C 0 1 Y N N -14.640 -31.074 31.007 -3.853 0.279 0.390 C17 LDG 4 LDG O17 O2 O 0 1 N N N -14.495 -31.069 29.664 -3.394 0.187 1.662 O17 LDG 5 LDG C16 C4 C 0 1 Y N N -15.939 -30.966 31.677 -2.999 0.035 -0.679 C16 LDG 6 LDG C9 C5 C 0 1 Y N N -15.970 -30.960 33.145 -3.464 0.128 -1.981 C9 LDG 7 LDG C81 C6 C 0 1 Y N N -14.835 -31.018 33.906 -4.792 0.466 -2.235 C81 LDG 8 LDG C7 C7 C 0 1 Y N N -13.615 -31.086 33.335 -5.657 0.711 -1.179 C7 LDG 9 LDG C61 C8 C 0 1 N N N -12.460 -31.140 34.206 -7.070 1.068 -1.432 C61 LDG 10 LDG O61 O3 O 0 1 N N N -12.600 -31.127 35.422 -7.433 1.392 -2.546 O61 LDG 11 LDG C20 C9 C 0 1 Y N N -10.966 -31.241 32.177 -7.565 0.928 1.011 C20 LDG 12 LDG C1 C10 C 0 1 Y N N -9.710 -31.311 31.640 -8.471 0.882 2.065 C1 LDG 13 LDG C51 C11 C 0 1 Y N N -11.128 -31.222 33.624 -8.036 1.025 -0.312 C51 LDG 14 LDG C41 C12 C 0 1 Y N N -10.029 -31.279 34.426 -9.405 1.068 -0.557 C41 LDG 15 LDG C3 C13 C 0 1 Y N N -8.789 -31.333 33.848 -10.295 1.015 0.503 C3 LDG 16 LDG C71 C14 C 0 1 Y N N -8.630 -31.367 32.483 -9.830 0.926 1.807 C71 LDG 17 LDG O1 O4 O 0 1 N N N -17.191 -30.906 33.710 -2.620 -0.112 -3.016 O1 LDG 18 LDG C14 C15 C 0 1 N N N -17.386 -30.481 35.044 -3.161 -0.000 -4.334 C14 LDG 19 LDG C15 C16 C 0 1 N N N -14.251 -32.290 29.029 -2.855 1.375 2.245 C15 LDG 20 LDG C2R C17 C 0 1 N N N -17.270 -30.940 30.985 -1.561 -0.332 -0.421 C2R LDG 21 LDG P P1 P 0 1 N N N -22.308 -23.293 34.840 9.117 1.606 -0.734 P LDG 22 LDG OP1 O5 O 0 1 N N N -22.262 -23.017 36.249 9.469 1.693 -2.302 OP1 LDG 23 LDG "O5'" O6 O 0 1 N N N -21.641 -24.690 34.590 7.523 1.488 -0.547 "O5'" LDG 24 LDG "C5'" C18 C 0 1 N N N -21.577 -25.577 35.705 6.886 1.497 0.733 "C5'" LDG 25 LDG "C4'" C19 C 0 1 N N R -20.437 -26.547 35.550 5.373 1.368 0.551 "C4'" LDG 26 LDG "C3'" C20 C 0 1 N N S -19.056 -25.985 35.843 4.654 1.502 1.912 "C3'" LDG 27 LDG "O3'" O7 O 0 1 N N N -18.374 -26.793 36.793 4.155 2.829 2.086 "O3'" LDG 28 LDG "C2'" C21 C 0 1 N N N -18.337 -26.038 34.513 3.487 0.493 1.821 "C2'" LDG 29 LDG "C1'" C22 C 0 1 N N R -19.164 -26.931 33.628 3.639 -0.131 0.416 "C1'" LDG 30 LDG "O4'" O8 O 0 1 N N N -20.446 -26.885 34.160 5.034 0.045 0.083 "O4'" LDG 31 LDG N9 N1 N 0 1 Y N N -19.215 -26.480 32.261 3.299 -1.556 0.451 N9 LDG 32 LDG C4 C23 C 0 1 Y N N -18.782 -27.173 31.179 2.052 -2.094 0.281 C4 LDG 33 LDG C5 C24 C 0 1 Y N N -18.971 -26.335 30.128 2.210 -3.480 0.395 C5 LDG 34 LDG N7 N2 N 0 1 Y N N -19.488 -25.143 30.562 3.524 -3.718 0.624 N7 LDG 35 LDG C8 C25 C 0 1 Y N N -19.613 -25.250 31.849 4.168 -2.588 0.652 C8 LDG 36 LDG N3 N3 N 0 1 N N N -18.307 -28.426 31.188 0.838 -1.582 0.051 N3 LDG 37 LDG C2 C26 C 0 1 N N N -17.999 -28.868 29.986 -0.215 -2.359 -0.072 C2 LDG 38 LDG N2 N4 N 0 1 N N N -17.492 -30.116 29.846 -1.440 -1.787 -0.308 N2 LDG 39 LDG N1 N5 N 0 1 N N N -18.138 -28.077 28.864 -0.126 -3.715 0.029 N1 LDG 40 LDG C6 C27 C 0 1 N N N -18.633 -26.771 28.829 1.067 -4.304 0.266 C6 LDG 41 LDG O6 O9 O 0 1 N N N -18.723 -26.133 27.747 1.158 -5.517 0.357 O6 LDG 42 LDG OP2 O10 O 0 1 N N N -21.866 -22.250 33.977 9.830 0.311 -0.095 OP2 LDG 43 LDG H1 H1 H 0 1 N N N -14.917 -31.009 34.983 -5.147 0.537 -3.252 H1 LDG 44 LDG H2 H2 H 0 1 N N N -9.571 -31.322 30.569 -8.115 0.813 3.082 H2 LDG 45 LDG H3 H3 H 0 1 N N N -10.134 -31.282 35.501 -9.772 1.142 -1.569 H3 LDG 46 LDG H4 H4 H 0 1 N N N -7.914 -31.349 34.480 -11.357 1.049 0.313 H4 LDG 47 LDG H5 H5 H 0 1 N N N -7.636 -31.439 32.067 -10.533 0.890 2.626 H5 LDG 48 LDG H6 H6 H 0 1 N N N -18.458 -30.518 35.288 -2.383 -0.217 -5.066 H6 LDG 49 LDG H7 H7 H 0 1 N N N -16.832 -31.144 35.725 -3.979 -0.711 -4.452 H7 LDG 50 LDG H8 H8 H 0 1 N N N -17.019 -29.450 35.158 -3.534 1.013 -4.489 H8 LDG 51 LDG H9 H9 H 0 1 N N N -14.157 -32.128 27.945 -2.525 1.163 3.262 H9 LDG 52 LDG H10 H10 H 0 1 N N N -13.318 -32.725 29.417 -2.007 1.718 1.652 H10 LDG 53 LDG H11 H11 H 0 1 N N N -15.086 -32.979 29.225 -3.621 2.150 2.266 H11 LDG 54 LDG H12 H12 H 0 1 N N N -18.008 -30.633 31.740 -0.942 0.021 -1.246 H12 LDG 55 LDG H13 H13 H 0 1 N N N -17.477 -31.973 30.668 -1.228 0.133 0.508 H13 LDG 56 LDG H14 H14 H 0 1 N N N -23.139 -23.067 36.611 10.414 1.766 -2.490 H14 LDG 57 LDG H15 H15 H 0 1 N N N -21.430 -24.991 36.624 7.253 0.661 1.328 H15 LDG 58 LDG H16 H16 H 0 1 N N N -22.521 -26.138 35.775 7.112 2.433 1.244 H16 LDG 59 LDG H17 H17 H 0 1 N N N -20.615 -27.436 36.173 5.009 2.124 -0.146 H17 LDG 60 LDG H18 H18 H 0 1 N N N -19.139 -24.943 36.187 5.327 1.238 2.727 H18 LDG 61 LDG H19 H19 H 0 1 N N N -18.829 -26.756 37.626 3.694 2.969 2.925 H19 LDG 62 LDG H20 H20 H 0 1 N N N -17.328 -26.456 34.641 3.583 -0.273 2.591 H20 LDG 63 LDG H21 H21 H 0 1 N N N -18.264 -25.030 34.078 2.530 1.006 1.911 H21 LDG 64 LDG H22 H22 H 0 1 N N N -18.761 -27.953 33.671 3.009 0.393 -0.303 H22 LDG 65 LDG H23 H23 H 0 1 N N N -19.981 -24.471 32.500 5.230 -2.483 0.816 H23 LDG 66 LDG H24 H24 H 0 1 N N N -17.272 -30.462 28.934 -2.227 -2.348 -0.401 H24 LDG 67 LDG H25 H25 H 0 1 N N N -17.857 -28.477 27.992 -0.923 -4.260 -0.066 H25 LDG 68 LDG H26 H26 H 0 1 N N N -22.576 -21.993 33.400 9.557 -0.525 -0.495 H26 LDG 69 LDG OP3 OP3 O 0 1 N Y N -23.801 -23.569 34.456 9.605 2.825 -0.050 OP3 LDG 70 # 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 LDG O6 C6 DOUB N N 1 LDG C6 N1 SING N N 2 LDG C6 C5 SING N N 3 LDG N1 C2 SING N N 4 LDG C15 O17 SING N N 5 LDG O17 C17 SING N N 6 LDG N2 C2 SING N N 7 LDG N2 C2R SING N N 8 LDG C2 N3 DOUB N N 9 LDG O19 C19 DOUB N N 10 LDG C5 N7 SING Y N 11 LDG C5 C4 DOUB Y N 12 LDG N7 C8 DOUB Y N 13 LDG C2R C16 SING N N 14 LDG C17 C16 DOUB Y N 15 LDG C17 C18 SING Y N 16 LDG C4 N3 SING N N 17 LDG C4 N9 SING Y N 18 LDG C19 C18 SING N N 19 LDG C19 C20 SING N N 20 LDG C1 C20 DOUB Y N 21 LDG C1 C71 SING Y N 22 LDG C16 C9 SING Y N 23 LDG C8 N9 SING Y N 24 LDG C18 C7 DOUB Y N 25 LDG C20 C51 SING Y N 26 LDG N9 "C1'" SING N N 27 LDG C71 C3 DOUB Y N 28 LDG C9 O1 SING N N 29 LDG C9 C81 DOUB Y N 30 LDG C7 C81 SING Y N 31 LDG C7 C61 SING N N 32 LDG C51 C61 SING N N 33 LDG C51 C41 DOUB Y N 34 LDG "C1'" "O4'" SING N N 35 LDG "C1'" "C2'" SING N N 36 LDG O1 C14 SING N N 37 LDG C3 C41 SING Y N 38 LDG OP2 P SING N N 39 LDG "O4'" "C4'" SING N N 40 LDG C61 O61 DOUB N N 41 LDG "C2'" "C3'" SING N N 42 LDG "O5'" P SING N N 43 LDG "O5'" "C5'" SING N N 44 LDG P OP1 SING N N 45 LDG "C4'" "C5'" SING N N 46 LDG "C4'" "C3'" SING N N 47 LDG "C3'" "O3'" SING N N 48 LDG C81 H1 SING N N 49 LDG C1 H2 SING N N 50 LDG C41 H3 SING N N 51 LDG C3 H4 SING N N 52 LDG C71 H5 SING N N 53 LDG C14 H6 SING N N 54 LDG C14 H7 SING N N 55 LDG C14 H8 SING N N 56 LDG C15 H9 SING N N 57 LDG C15 H10 SING N N 58 LDG C15 H11 SING N N 59 LDG C2R H12 SING N N 60 LDG C2R H13 SING N N 61 LDG OP1 H14 SING N N 62 LDG "C5'" H15 SING N N 63 LDG "C5'" H16 SING N N 64 LDG "C4'" H17 SING N N 65 LDG "C3'" H18 SING N N 66 LDG "O3'" H19 SING N N 67 LDG "C2'" H20 SING N N 68 LDG "C2'" H21 SING N N 69 LDG "C1'" H22 SING N N 70 LDG C8 H23 SING N N 71 LDG N2 H24 SING N N 72 LDG N1 H25 SING N N 73 LDG OP2 H26 SING N N 74 LDG P OP3 DOUB N N 75 # 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 LDG SMILES ACDLabs 12.01 "O=C5c1c(cc(c(c1OC)CNC4=Nc3n(C2CC(C(COP(O)(=O)O)O2)O)cnc3C(N4)=O)OC)C(=O)c6c5cccc6" LDG InChI InChI 1.03 "InChI=1S/C27H26N5O11P/c1-40-17-7-14-20(23(35)13-6-4-3-5-12(13)22(14)34)24(41-2)15(17)9-28-27-30-25-21(26(36)31-27)29-11-32(25)19-8-16(33)18(43-19)10-42-44(37,38)39/h3-7,11,16,18-19,33H,8-10H2,1-2H3,(H2,37,38,39)(H2,28,30,31,36)/t16-,18+,19+/m0/s1" LDG InChIKey InChI 1.03 DZJXUNLGRPPLSY-QXAKKESOSA-N LDG SMILES_CANONICAL CACTVS 3.385 "COc1cc2C(=O)c3ccccc3C(=O)c2c(OC)c1CNC4=Nc5n(cnc5C(=O)N4)[C@H]6C[C@H](O)[C@@H](CO[P](O)(O)=O)O6" LDG SMILES CACTVS 3.385 "COc1cc2C(=O)c3ccccc3C(=O)c2c(OC)c1CNC4=Nc5n(cnc5C(=O)N4)[CH]6C[CH](O)[CH](CO[P](O)(O)=O)O6" LDG SMILES_CANONICAL "OpenEye OEToolkits" 2.0.6 "COc1cc2c(c(c1CNC3=Nc4c(ncn4[C@H]5C[C@@H]([C@H](O5)COP(=O)(O)O)O)C(=O)N3)OC)C(=O)c6ccccc6C2=O" LDG SMILES "OpenEye OEToolkits" 2.0.6 "COc1cc2c(c(c1CNC3=Nc4c(ncn4C5CC(C(O5)COP(=O)(O)O)O)C(=O)N3)OC)C(=O)c6ccccc6C2=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 LDG "SYSTEMATIC NAME" ACDLabs 12.01 ;2'-deoxy-N-[(1,3-dimethoxy-9,10-dioxo-9,10-dihydroanthracen-2-yl)methyl]guanosine 5'-(dihydrogen phosphate) ; LDG "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.6 "[(2~{R},3~{S},5~{R})-5-[2-[[1,3-dimethoxy-9,10-bis(oxidanylidene)anthracen-2-yl]methylamino]-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 LDG "Create component" 2017-06-15 RCSB LDG "Initial release" 2017-10-18 RCSB #