data_4E9 # _chem_comp.id 4E9 _chem_comp.name ;2'-deoxy-8-[(7-oxo-7H-benzo[de]anthracen-3-yl)amino]guanosine 5'-(dihydrogen phosphate) ; _chem_comp.type "DNA LINKING" _chem_comp.pdbx_type ATOMN _chem_comp.formula "C27 H23 N6 O8 P" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2015-07-16 _chem_comp.pdbx_modified_date 2016-07-01 _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 590.481 _chem_comp.one_letter_code ? _chem_comp.three_letter_code 4E9 _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 2N4M _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 4E9 "O5'" "O5'" O 0 1 N N N 0.137 -7.792 26.226 -2.245 3.852 -0.909 "O5'" 4E9 1 4E9 "C5'" "C5'" C 0 1 N N N -0.623 -6.596 26.364 -1.959 3.328 0.389 "C5'" 4E9 2 4E9 "C4'" "C4'" C 0 1 N N R -0.841 -5.883 25.016 -3.023 2.296 0.769 "C4'" 4E9 3 4E9 "O4'" "O4'" O 0 1 N N N 0.406 -5.410 24.514 -2.939 1.139 -0.090 "O4'" 4E9 4 4E9 "C1'" "C1'" C 0 1 N N R 0.465 -5.677 23.135 -3.572 0.052 0.606 "C1'" 4E9 5 4E9 N9 N9 N 0 1 Y N N 1.889 -5.604 22.674 -2.892 -1.206 0.288 N9 4E9 6 4E9 C4 C4 C 0 1 Y N N 2.829 -6.616 22.575 -3.495 -2.403 -0.003 C4 4E9 7 4E9 N3 N3 N 0 1 N N N 2.675 -7.925 22.925 -4.768 -2.806 -0.091 N3 4E9 8 4E9 C2 C2 C 0 1 N N N 3.796 -8.630 22.890 -5.068 -4.049 -0.396 C2 4E9 9 4E9 N1 N1 N 0 1 N N N 4.988 -8.152 22.471 -4.104 -4.983 -0.636 N1 4E9 10 4E9 C6 C6 C 0 1 N N N 5.183 -6.856 22.041 -2.797 -4.649 -0.565 C6 4E9 11 4E9 C5 C5 C 0 1 Y N N 4.001 -6.033 22.138 -2.461 -3.315 -0.239 C5 4E9 12 4E9 N7 N7 N 0 1 Y N N 3.816 -4.665 21.950 -1.289 -2.648 -0.085 N7 4E9 13 4E9 C8 C8 C 0 1 Y N N 2.594 -4.470 22.342 -1.538 -1.400 0.221 C8 4E9 14 4E9 "C2'" "C2'" C 0 1 N N N -0.298 -6.996 22.988 -3.454 0.345 2.115 "C2'" 4E9 15 4E9 "C3'" "C3'" C 0 1 N N S -1.468 -6.793 23.943 -2.744 1.719 2.180 "C3'" 4E9 16 4E9 "O3'" "O3'" O 0 1 N N N -2.536 -6.195 23.213 -3.325 2.544 3.193 "O3'" 4E9 17 4E9 P P P 0 1 N N N 0.774 -8.552 27.497 -1.329 4.964 -1.627 P 4E9 18 4E9 OP1 OP1 O 0 1 N N N -0.135 -8.405 28.655 -1.871 5.222 -3.121 OP1 4E9 19 4E9 OP2 OP2 O 0 1 N N N 1.186 -9.907 27.067 -1.394 6.337 -0.788 OP2 4E9 20 4E9 O6 O6 O 0 1 N N N 6.313 -6.553 21.661 -1.928 -5.478 -0.777 O6 4E9 21 4E9 N24 N24 N 0 1 N N N 3.779 -9.831 23.392 -6.388 -4.417 -0.475 N24 4E9 22 4E9 N8 N8 N 0 1 N N N 2.048 -3.210 22.493 -0.581 -0.427 0.445 N8 4E9 23 4E9 C10 C10 C 0 1 Y N N 2.658 -2.016 22.272 0.759 -0.710 0.229 C10 4E9 24 4E9 C11 C11 C 0 1 Y N N 2.447 -0.897 23.155 1.758 0.144 0.750 C11 4E9 25 4E9 C12 C12 C 0 1 Y N N 1.619 -1.002 24.287 1.419 1.286 1.489 C12 4E9 26 4E9 C13 C13 C 0 1 Y N N 1.421 0.093 25.133 2.405 2.106 1.988 C13 4E9 27 4E9 C14 C14 C 0 1 Y N N 2.044 1.317 24.869 3.744 1.823 1.772 C14 4E9 28 4E9 C15 C15 C 0 1 Y N N 2.884 1.480 23.757 4.117 0.697 1.042 C15 4E9 29 4E9 C16 C16 C 0 1 N N N 3.481 2.677 23.521 5.537 0.394 0.811 C16 4E9 30 4E9 O27 O27 O 0 1 N N N 3.270 3.614 24.302 6.405 1.124 1.256 O27 4E9 31 4E9 C17 C17 C 0 1 Y N N 4.302 2.874 22.454 5.894 -0.804 0.036 C17 4E9 32 4E9 C18 C18 C 0 1 Y N N 4.897 4.135 22.260 7.233 -1.122 -0.203 C18 4E9 33 4E9 C19 C19 C 0 1 Y N N 5.748 4.380 21.176 7.549 -2.247 -0.932 C19 4E9 34 4E9 C20 C20 C 0 1 Y N N 6.011 3.356 20.264 6.547 -3.068 -1.431 C20 4E9 35 4E9 C21 C21 C 0 1 Y N N 5.434 2.087 20.435 5.221 -2.771 -1.207 C21 4E9 36 4E9 C22 C22 C 0 1 Y N N 4.573 1.807 21.521 4.877 -1.636 -0.471 C22 4E9 37 4E9 C23 C23 C 0 1 Y N N 3.952 0.518 21.741 3.463 -1.307 -0.223 C23 4E9 38 4E9 C24 C24 C 0 1 Y N N 4.130 -0.602 20.908 2.454 -2.130 -0.723 C24 4E9 39 4E9 C26 C26 C 0 1 Y N N 3.094 0.363 22.882 3.120 -0.159 0.520 C26 4E9 40 4E9 C25 C25 C 0 1 Y N N 3.498 -1.830 21.171 1.124 -1.834 -0.494 C25 4E9 41 4E9 "H5'" "H5'" H 0 1 N N N -1.604 -6.848 26.794 -0.978 2.852 0.380 "H5'" 4E9 42 4E9 "H5''" "H5''" H 0 0 N N N -0.089 -5.914 27.043 -1.962 4.139 1.118 "H5''" 4E9 43 4E9 "H4'" "H4'" H 0 1 N N N -1.519 -5.033 25.184 -4.018 2.738 0.722 "H4'" 4E9 44 4E9 "H1'" "H1'" H 0 1 N N N -0.104 -4.905 22.595 -4.621 -0.011 0.319 "H1'" 4E9 45 4E9 H1 H1 H 0 1 N N N 5.772 -8.772 22.473 -4.359 -5.892 -0.859 H1 4E9 46 4E9 "H2'" "H2'" H 0 1 N N N -0.646 -7.143 21.955 -4.442 0.403 2.570 "H2'" 4E9 47 4E9 "H2''" "H2''" H 0 0 N N N 0.322 -7.852 23.292 -2.851 -0.420 2.605 "H2''" 4E9 48 4E9 "H3'" "H3'" H 0 1 N N N -1.767 -7.753 24.390 -1.674 1.597 2.346 "H3'" 4E9 49 4E9 H2 H2 H 0 1 N N N -2.869 -6.814 22.574 -3.178 2.225 4.093 H2 4E9 50 4E9 H3 H3 H 0 1 N N N 0.235 -8.851 29.408 -1.365 5.883 -3.614 H3 4E9 51 4E9 H4 H4 H 0 1 N N N 1.565 -10.372 27.804 -2.284 6.707 -0.709 H4 4E9 52 4E9 H21 H21 H 0 1 N N N 2.936 -10.195 23.788 -7.084 -3.763 -0.306 H21 4E9 53 4E9 H22 H22 H 0 1 N N N 4.609 -10.389 23.381 -6.624 -5.331 -0.699 H22 4E9 54 4E9 H10 H10 H 0 1 N N N 1.097 -3.172 22.799 -0.847 0.453 0.753 H10 4E9 55 4E9 H12 H12 H 0 1 N N N 1.130 -1.940 24.505 0.380 1.524 1.667 H12 4E9 56 4E9 H13 H13 H 0 1 N N N 0.782 -0.007 25.998 2.132 2.984 2.556 H13 4E9 57 4E9 H14 H14 H 0 1 N N N 1.875 2.152 25.533 4.503 2.479 2.172 H14 4E9 58 4E9 H18 H18 H 0 1 N N N 4.693 4.930 22.962 8.018 -0.488 0.182 H18 4E9 59 4E9 H19 H19 H 0 1 N N N 6.198 5.353 21.046 8.585 -2.493 -1.116 H19 4E9 60 4E9 H20 H20 H 0 1 N N N 6.662 3.541 19.422 6.810 -3.947 -2.001 H20 4E9 61 4E9 H23 H23 H 0 1 N N N 5.653 1.307 19.721 4.448 -3.415 -1.600 H23 4E9 62 4E9 H24 H24 H 0 1 N N N 4.770 -0.516 20.042 2.716 -3.009 -1.293 H24 4E9 63 4E9 H25 H25 H 0 1 N N N 3.668 -2.658 20.499 0.358 -2.487 -0.887 H25 4E9 64 4E9 OP3 OP3 O 0 1 N N N ? ? ? 0.071 4.487 -1.686 OP3 4E9 65 # 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 4E9 "O5'" "C5'" SING N N 1 4E9 "O5'" P SING N N 2 4E9 "C5'" "C4'" SING N N 3 4E9 "C4'" "O4'" SING N N 4 4E9 "C4'" "C3'" SING N N 5 4E9 "O4'" "C1'" SING N N 6 4E9 "C1'" N9 SING N N 7 4E9 "C1'" "C2'" SING N N 8 4E9 N9 C4 SING Y N 9 4E9 N9 C8 SING Y N 10 4E9 C4 N3 SING N N 11 4E9 C4 C5 DOUB Y N 12 4E9 N3 C2 DOUB N N 13 4E9 C2 N1 SING N N 14 4E9 C2 N24 SING N N 15 4E9 N1 C6 SING N N 16 4E9 C6 C5 SING N N 17 4E9 C6 O6 DOUB N N 18 4E9 C5 N7 SING Y N 19 4E9 N7 C8 DOUB Y N 20 4E9 C8 N8 SING N N 21 4E9 "C2'" "C3'" SING N N 22 4E9 "C3'" "O3'" SING N N 23 4E9 P OP1 SING N N 24 4E9 P OP2 SING N N 25 4E9 N8 C10 SING N N 26 4E9 C10 C11 DOUB Y N 27 4E9 C10 C25 SING Y N 28 4E9 C11 C12 SING Y N 29 4E9 C11 C26 SING Y N 30 4E9 C12 C13 DOUB Y N 31 4E9 C13 C14 SING Y N 32 4E9 C14 C15 DOUB Y N 33 4E9 C15 C16 SING N N 34 4E9 C15 C26 SING Y N 35 4E9 C16 O27 DOUB N N 36 4E9 C16 C17 SING N N 37 4E9 C17 C18 DOUB Y N 38 4E9 C17 C22 SING Y N 39 4E9 C18 C19 SING Y N 40 4E9 C19 C20 DOUB Y N 41 4E9 C20 C21 SING Y N 42 4E9 C21 C22 DOUB Y N 43 4E9 C22 C23 SING N N 44 4E9 C23 C24 SING Y N 45 4E9 C23 C26 DOUB Y N 46 4E9 C24 C25 DOUB Y N 47 4E9 "C5'" "H5'" SING N N 48 4E9 "C5'" "H5''" SING N N 49 4E9 "C4'" "H4'" SING N N 50 4E9 "C1'" "H1'" SING N N 51 4E9 N1 H1 SING N N 52 4E9 "C2'" "H2'" SING N N 53 4E9 "C2'" "H2''" SING N N 54 4E9 "C3'" "H3'" SING N N 55 4E9 "O3'" H2 SING N N 56 4E9 OP1 H3 SING N N 57 4E9 OP2 H4 SING N N 58 4E9 N24 H21 SING N N 59 4E9 N24 H22 SING N N 60 4E9 N8 H10 SING N N 61 4E9 C12 H12 SING N N 62 4E9 C13 H13 SING N N 63 4E9 C14 H14 SING N N 64 4E9 C18 H18 SING N N 65 4E9 C19 H19 SING N N 66 4E9 C20 H20 SING N N 67 4E9 C21 H23 SING N N 68 4E9 C24 H24 SING N N 69 4E9 C25 H25 SING N N 70 4E9 P OP3 DOUB N N 71 # 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 4E9 SMILES ACDLabs 12.01 "O(CC7OC(n2c1N=C(NC(c1nc2Nc4c5cccc6C(=O)c3ccccc3c(cc4)c56)=O)N)CC7O)P(O)(O)=O" 4E9 InChI InChI 1.03 "InChI=1S/C27H23N6O8P/c28-26-31-24-22(25(36)32-26)30-27(33(24)20-10-18(34)19(41-20)11-40-42(37,38)39)29-17-9-8-13-12-4-1-2-5-14(12)23(35)16-7-3-6-15(17)21(13)16/h1-9,18-20,34H,10-11H2,(H,29,30)(H2,37,38,39)(H3,28,31,32,36)/t18-,19+,20+/m0/s1" 4E9 InChIKey InChI 1.03 JKGHGBFHLIPVJU-XUVXKRRUSA-N 4E9 SMILES_CANONICAL CACTVS 3.385 "NC1=Nc2n([C@H]3C[C@H](O)[C@@H](CO[P](O)(O)=O)O3)c(Nc4ccc5c6ccccc6C(=O)c7cccc4c57)nc2C(=O)N1" 4E9 SMILES CACTVS 3.385 "NC1=Nc2n([CH]3C[CH](O)[CH](CO[P](O)(O)=O)O3)c(Nc4ccc5c6ccccc6C(=O)c7cccc4c57)nc2C(=O)N1" 4E9 SMILES_CANONICAL "OpenEye OEToolkits" 1.7.6 "c1ccc2c(c1)-c3ccc(c4c3c(ccc4)C2=O)Nc5nc6c(n5[C@H]7C[C@@H]([C@H](O7)COP(=O)(O)O)O)N=C(NC6=O)N" 4E9 SMILES "OpenEye OEToolkits" 1.7.6 "c1ccc2c(c1)-c3ccc(c4c3c(ccc4)C2=O)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 4E9 "SYSTEMATIC NAME" ACDLabs 12.01 ;2'-deoxy-8-[(7-oxo-7H-benzo[de]anthracen-3-yl)amino]guanosine 5'-(dihydrogen phosphate) ; 4E9 "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.7.6 "[(2R,3S,5R)-5-[2-azanyl-6-oxidanylidene-8-[(7-oxidanylidenebenzo[a]phenalen-3-yl)amino]-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 4E9 "Create component" 2015-07-16 RCSB 4E9 "Initial release" 2016-07-06 RCSB #