data_DG8 # _chem_comp.id DG8 _chem_comp.name ;2'-deoxy-8-(pyren-1-ylamino)guanosine 5'-(dihydrogen phosphate) ; _chem_comp.type "DNA LINKING" _chem_comp.pdbx_type ATOMN _chem_comp.formula "C26 H23 N6 O7 P" _chem_comp.mon_nstd_parent_comp_id DG _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2012-05-15 _chem_comp.pdbx_modified_date 2013-01-04 _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 562.471 _chem_comp.one_letter_code ? _chem_comp.three_letter_code DG8 _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 4EYH _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 DG8 P P P 0 1 N N N 11.161 35.042 -25.556 -1.995 4.321 1.396 P NPG 1 DG8 O1P O1P O 0 1 N N N 10.931 34.746 -27.027 -2.835 3.112 1.548 O1P NPG 2 DG8 O2P O2P O 0 1 N N N 12.353 34.474 -24.805 -1.681 4.943 2.847 O2P NPG 3 DG8 "O5'" "O5'" O 0 1 N N N 9.789 34.729 -24.760 -0.613 3.927 0.671 "O5'" NPG 4 DG8 "C5'" "C5'" C 0 1 N N N 8.520 34.838 -25.408 -0.559 3.254 -0.589 "C5'" NPG 5 DG8 "C4'" "C4'" C 0 1 N N R 7.898 33.446 -25.440 0.902 3.033 -0.987 "C4'" NPG 6 DG8 "C3'" "C3'" C 0 1 N N S 6.391 33.362 -25.672 0.991 2.294 -2.347 "C3'" NPG 7 DG8 "C2'" "C2'" C 0 1 N N N 5.956 32.161 -24.838 2.384 1.623 -2.260 "C2'" NPG 8 DG8 "C1'" "C1'" C 0 1 N N R 7.113 31.905 -23.878 2.688 1.579 -0.750 "C1'" NPG 9 DG8 "O4'" "O4'" O 0 1 N N N 8.193 32.798 -24.195 1.548 2.127 -0.068 "O4'" NPG 10 DG8 N9 N9 N 0 1 Y N N 6.582 32.082 -22.503 2.905 0.194 -0.326 N9 NPG 11 DG8 C8 C8 C 0 1 Y N N 6.973 32.951 -21.506 1.947 -0.777 -0.214 C8 NPG 12 DG8 N7 N7 N 0 1 Y N N 6.235 32.769 -20.387 2.498 -1.893 0.191 N7 NPG 13 DG8 C5 C5 C 0 1 Y N N 5.367 31.749 -20.664 3.833 -1.699 0.359 C5 NPG 14 DG8 C6 C6 C 0 1 N N N 4.382 31.120 -19.915 4.902 -2.527 0.770 C6 NPG 15 DG8 O6 O6 O 0 1 N N N 4.184 31.498 -18.740 4.709 -3.694 1.065 O6 NPG 16 DG8 N1 N1 N 0 1 N N N 3.644 30.092 -20.475 6.142 -1.994 0.828 N1 NPG 17 DG8 C2 C2 C 0 1 N N N 3.883 29.681 -21.774 6.346 -0.688 0.496 C2 NPG 18 DG8 N2 N2 N 0 1 N N N 3.135 28.615 -22.376 7.617 -0.172 0.563 N2 NPG 19 DG8 N3 N3 N 0 1 N N N 4.842 30.295 -22.500 5.360 0.092 0.112 N3 NPG 20 DG8 C4 C4 C 0 1 Y N N 5.577 31.310 -21.971 4.107 -0.369 0.026 C4 NPG 21 DG8 N24 N24 N 0 1 N N N 8.050 33.966 -21.717 0.603 -0.605 -0.486 N24 NPG 22 DG8 C25 C25 C 0 1 Y N N 8.183 35.055 -20.702 -0.273 -1.608 -0.233 C25 NPG 23 DG8 C30 C30 C 0 1 Y N N 8.983 36.167 -20.998 -1.559 -1.376 -0.358 C30 NPG 24 DG8 C35 C35 C 0 1 Y N N 9.141 37.196 -20.060 -2.513 -2.466 -0.083 C35 NPG 25 DG8 C34 C34 C 0 1 Y N N 9.936 38.304 -20.382 -3.797 -2.268 -0.199 C34 NPG 26 DG8 C38 C38 C 0 1 Y N N 10.093 39.328 -19.447 -4.745 -3.364 0.078 C38 NPG 27 DG8 C37 C37 C 0 1 Y N N 9.463 39.242 -18.202 -4.292 -4.540 0.441 C37 NPG 28 DG8 C36 C36 C 0 1 Y N N 8.669 38.136 -17.877 -2.837 -4.764 0.572 C36 NPG 29 DG8 C28 C28 C 0 1 Y N N 8.507 37.113 -18.810 -1.998 -3.786 0.325 C28 NPG 30 DG8 C27 C27 C 0 1 Y N N 7.722 36.003 -18.508 -0.538 -3.945 0.437 C27 NPG 31 DG8 C26 C26 C 0 1 Y N N 7.571 34.983 -19.449 0.245 -2.922 0.168 C26 NPG 32 DG8 C39 C39 C 0 1 Y N N 10.879 40.433 -19.760 -6.183 -3.078 -0.072 C39 NPG 33 DG8 C40 C40 C 0 1 Y N N 11.502 40.509 -21.003 -6.566 -1.874 -0.440 C40 NPG 34 DG8 C41 C41 C 0 1 Y N N 11.348 39.486 -21.935 -5.617 -0.786 -0.714 C41 NPG 35 DG8 C33 C33 C 0 1 Y N N 10.566 38.384 -21.625 -4.320 -0.952 -0.606 C33 NPG 36 DG8 C32 C32 C 0 1 Y N N 10.410 37.365 -22.560 -3.373 0.142 -0.882 C32 NPG 37 DG8 C31 C31 C 0 1 Y N N 9.614 36.263 -22.245 -2.074 -0.058 -0.765 C31 NPG 38 DG8 "O3'" "O3'" O 0 1 N N N 6.083 33.066 -27.043 0.938 3.219 -3.435 "O3'" NPG 39 DG8 H2 H2 H 0 1 N N N 12.876 33.944 -25.395 -2.470 5.204 3.342 H2 NPG 40 DG8 H3 H3 H 0 1 N N N 8.653 35.213 -26.433 -1.063 2.292 -0.509 H3 NPG 41 DG8 H4 H4 H 0 1 N N N 7.870 35.526 -24.847 -1.054 3.862 -1.347 H4 NPG 42 DG8 H5 H5 H 0 1 N N N 8.387 32.886 -26.251 1.435 3.983 -1.028 H5 NPG 43 DG8 H6 H6 H 0 1 N N N 5.892 34.279 -25.324 0.204 1.546 -2.435 H6 NPG 44 DG8 H7 H7 H 0 1 N N N 5.036 32.390 -24.281 2.347 0.614 -2.672 H7 NPG 45 DG8 H8 H8 H 0 1 N N N 5.787 31.285 -25.481 3.129 2.223 -2.783 H8 NPG 46 DG8 H9 H9 H 0 1 N N N 7.445 30.864 -24.002 3.575 2.176 -0.534 H9 NPG 47 DG8 H10 H10 H 0 1 N N N 2.932 29.642 -19.936 6.891 -2.543 1.107 H10 NPG 48 DG8 H11 H11 H 0 1 N N N 3.328 28.339 -23.318 8.354 -0.736 0.845 H11 NPG 49 DG8 H12 H12 H 0 1 N N N 2.421 28.148 -21.854 7.777 0.755 0.330 H12 NPG 50 DG8 H13 H13 H 0 1 N N N 8.659 33.918 -22.508 0.286 0.233 -0.858 H13 NPG 51 DG8 H14 H14 H 0 1 N N N 9.590 40.038 -17.483 -4.983 -5.346 0.644 H14 NPG 52 DG8 H15 H15 H 0 1 N N N 8.187 38.076 -16.913 -2.464 -5.732 0.872 H15 NPG 53 DG8 H16 H16 H 0 1 N N N 7.231 35.932 -17.548 -0.113 -4.893 0.732 H16 NPG 54 DG8 H17 H17 H 0 1 N N N 6.969 34.121 -19.203 1.314 -3.053 0.250 H17 NPG 55 DG8 H18 H18 H 0 1 N N N 11.005 41.229 -19.041 -6.915 -3.848 0.119 H18 NPG 56 DG8 H19 H19 H 0 1 N N N 12.109 41.368 -21.246 -7.622 -1.677 -0.546 H19 NPG 57 DG8 H20 H20 H 0 1 N N N 11.836 39.551 -22.896 -5.999 0.179 -1.013 H20 NPG 58 DG8 H21 H21 H 0 1 N N N 10.900 37.427 -23.520 -3.743 1.111 -1.181 H21 NPG 59 DG8 H22 H22 H 0 1 N N N 9.483 35.475 -22.971 -1.385 0.749 -0.969 H22 NPG 60 DG8 H23 H23 H 0 1 N N N 5.141 33.021 -27.154 0.990 2.804 -4.307 H23 NPG 61 DG8 O3P O3P O 0 1 N Y N ? ? ? -2.777 5.409 0.503 O3P NPG 62 DG8 H25 H25 H 0 1 N Y N ? ? ? -2.285 6.229 0.362 H25 NPG 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 DG8 "O3'" "C3'" SING N N 1 DG8 O1P P DOUB N N 2 DG8 "C3'" "C4'" SING N N 3 DG8 "C3'" "C2'" SING N N 4 DG8 P O2P SING N N 5 DG8 P "O5'" SING N N 6 DG8 "C4'" "C5'" SING N N 7 DG8 "C4'" "O4'" SING N N 8 DG8 "C5'" "O5'" SING N N 9 DG8 "C2'" "C1'" SING N N 10 DG8 "O4'" "C1'" SING N N 11 DG8 "C1'" N9 SING N N 12 DG8 C32 C31 DOUB Y N 13 DG8 C32 C33 SING Y N 14 DG8 N9 C4 SING Y N 15 DG8 N9 C8 SING Y N 16 DG8 N3 C4 SING N N 17 DG8 N3 C2 DOUB N N 18 DG8 N2 C2 SING N N 19 DG8 C31 C30 SING Y N 20 DG8 C4 C5 DOUB Y N 21 DG8 C41 C33 DOUB Y N 22 DG8 C41 C40 SING Y N 23 DG8 C2 N1 SING N N 24 DG8 N24 C8 SING N N 25 DG8 N24 C25 SING N N 26 DG8 C33 C34 SING Y N 27 DG8 C8 N7 DOUB Y N 28 DG8 C40 C39 DOUB Y N 29 DG8 C30 C25 DOUB Y N 30 DG8 C30 C35 SING Y N 31 DG8 C25 C26 SING Y N 32 DG8 C5 N7 SING Y N 33 DG8 C5 C6 SING N N 34 DG8 N1 C6 SING N N 35 DG8 C34 C35 DOUB Y N 36 DG8 C34 C38 SING Y N 37 DG8 C35 C28 SING Y N 38 DG8 C6 O6 DOUB N N 39 DG8 C39 C38 SING Y N 40 DG8 C26 C27 DOUB Y N 41 DG8 C38 C37 DOUB Y N 42 DG8 C28 C27 SING Y N 43 DG8 C28 C36 DOUB Y N 44 DG8 C37 C36 SING Y N 45 DG8 O2P H2 SING N N 46 DG8 "C5'" H3 SING N N 47 DG8 "C5'" H4 SING N N 48 DG8 "C4'" H5 SING N N 49 DG8 "C3'" H6 SING N N 50 DG8 "C2'" H7 SING N N 51 DG8 "C2'" H8 SING N N 52 DG8 "C1'" H9 SING N N 53 DG8 N1 H10 SING N N 54 DG8 N2 H11 SING N N 55 DG8 N2 H12 SING N N 56 DG8 N24 H13 SING N N 57 DG8 C37 H14 SING N N 58 DG8 C36 H15 SING N N 59 DG8 C27 H16 SING N N 60 DG8 C26 H17 SING N N 61 DG8 C39 H18 SING N N 62 DG8 C40 H19 SING N N 63 DG8 C41 H20 SING N N 64 DG8 C32 H21 SING N N 65 DG8 C31 H22 SING N N 66 DG8 "O3'" H23 SING N N 67 DG8 P O3P SING N N 68 DG8 O3P H25 SING N N 69 # 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 DG8 SMILES ACDLabs 12.01 "O=P(O)(O)OCC7OC(n2c(nc1c2N=C(N)NC1=O)Nc6c3c5c4c(cc3)cccc4ccc5cc6)CC7O" DG8 InChI InChI 1.03 "InChI=1S/C26H23N6O7P/c27-25-30-23-22(24(34)31-25)29-26(32(23)19-10-17(33)18(39-19)11-38-40(35,36)37)28-16-9-7-14-5-4-12-2-1-3-13-6-8-15(16)21(14)20(12)13/h1-9,17-19,33H,10-11H2,(H,28,29)(H2,35,36,37)(H3,27,30,31,34)/t17-,18+,19+/m0/s1" DG8 InChIKey InChI 1.03 OMTGOBLIMHUJJK-IPMKNSEASA-N DG8 SMILES_CANONICAL CACTVS 3.370 "NC1=Nc2n([C@H]3C[C@H](O)[C@@H](CO[P](O)(O)=O)O3)c(Nc4ccc5ccc6cccc7ccc4c5c67)nc2C(=O)N1" DG8 SMILES CACTVS 3.370 "NC1=Nc2n([CH]3C[CH](O)[CH](CO[P](O)(O)=O)O3)c(Nc4ccc5ccc6cccc7ccc4c5c67)nc2C(=O)N1" DG8 SMILES_CANONICAL "OpenEye OEToolkits" 1.7.6 "c1cc2ccc3ccc(c4c3c2c(c1)cc4)Nc5nc6c(n5[C@H]7C[C@@H]([C@H](O7)COP(=O)(O)O)O)N=C(NC6=O)N" DG8 SMILES "OpenEye OEToolkits" 1.7.6 "c1cc2ccc3ccc(c4c3c2c(c1)cc4)Nc5nc6c(n5C7CC(C(O7)COP(=O)(O)O)O)N=C(NC6=O)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 DG8 "SYSTEMATIC NAME" ACDLabs 12.01 ;2'-deoxy-8-(pyren-1-ylamino)guanosine 5'-(dihydrogen phosphate) ; DG8 "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.7.6 "[(2R,3S,5R)-5-[2-azanyl-6-oxidanylidene-8-(pyren-1-ylamino)-1H-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 DG8 "Create component" 2012-05-15 RCSB DG8 "Initial release" 2013-01-04 RCSB #