data_5J9 # _chem_comp.id 5J9 _chem_comp.name "3'-{4-[(4-amino-2-oxopyrimidin-1(2H)-yl)methyl]-1H-1,2,3-triazol-1-yl}-3'-deoxyadenosine" _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C17 H19 N11 O4" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2015-09-30 _chem_comp.pdbx_modified_date 2015-11-13 _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 441.404 _chem_comp.one_letter_code ? _chem_comp.three_letter_code 5J9 _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 5E13 _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 5J9 C4 C1 C 0 1 Y N N -8.961 -9.890 21.140 -3.627 1.072 -0.149 C4 5J9 1 5J9 C14 C2 C 0 1 Y N N -8.235 -16.364 19.073 1.812 -1.651 -0.268 C14 5J9 2 5J9 C5 C3 C 0 1 Y N N -9.844 -9.068 21.754 -5.003 1.145 0.125 C5 5J9 3 5J9 C6 C4 C 0 1 Y N N -9.395 -7.904 22.300 -5.600 2.416 0.193 C6 5J9 4 5J9 C8 C5 C 0 1 Y N N -10.891 -10.833 21.031 -4.462 -0.955 0.093 C8 5J9 5 5J9 C13 C6 C 0 1 Y N N -7.207 -16.831 19.775 3.077 -1.496 0.189 C13 5J9 6 5J9 N1 N1 N 0 1 Y N N -8.104 -7.557 22.234 -4.836 3.485 -0.005 N1 5J9 7 5J9 N3 N2 N 0 1 Y N N -7.657 -9.571 21.038 -2.945 2.197 -0.333 N3 5J9 8 5J9 O2T O1 O 0 1 N N N -6.924 -18.890 17.298 5.800 0.092 1.213 O2T 5J9 9 5J9 C2T C7 C 0 1 N N N -5.819 -18.941 17.849 5.291 0.827 0.383 C2T 5J9 10 5J9 N3T N3 N 0 1 N N N -4.747 -19.297 17.106 5.515 2.138 0.445 N3T 5J9 11 5J9 C4T C8 C 0 1 N N N -3.509 -19.385 17.637 4.973 2.961 -0.444 C4T 5J9 12 5J9 N4T N4 N 0 1 N N N -2.497 -19.736 16.858 5.212 4.313 -0.371 N4T 5J9 13 5J9 C5T C9 C 0 1 N N N -3.303 -19.114 18.996 4.153 2.440 -1.466 C5T 5J9 14 5J9 C6T C10 C 0 1 N N N -4.404 -18.754 19.773 3.935 1.104 -1.515 C6T 5J9 15 5J9 N1T N5 N 0 1 N N N -5.684 -18.667 19.169 4.517 0.299 -0.583 N1T 5J9 16 5J9 C15 C11 C 0 1 N N N -6.856 -18.308 19.991 4.295 -1.148 -0.629 C15 5J9 17 5J9 N12 N6 N 0 1 Y N N -6.514 -15.837 20.306 3.034 -1.712 1.508 N12 5J9 18 5J9 N11 N7 N 0 1 Y N N -7.106 -14.710 19.909 1.823 -1.982 1.847 N11 5J9 19 5J9 N10 N8 N 0 1 Y N N -8.168 -15.029 19.151 1.057 -1.956 0.812 N10 5J9 20 5J9 "C3'" C12 C 0 1 N N S -9.076 -14.022 18.547 -0.386 -2.213 0.806 "C3'" 5J9 21 5J9 "C2'" C13 C 0 1 N N R -9.891 -13.280 19.607 -1.172 -0.887 0.900 "C2'" 5J9 22 5J9 "O2'" O2 O 0 1 N N N -10.138 -14.088 20.779 -0.275 0.224 0.968 "O2'" 5J9 23 5J9 "C4'" C14 C 0 1 N N S -8.276 -12.866 17.888 -0.822 -2.813 -0.549 "C4'" 5J9 24 5J9 "C5'" C15 C 0 1 N N N -8.751 -12.352 16.548 -0.944 -4.334 -0.443 "C5'" 5J9 25 5J9 "O5'" O3 O 0 1 N N N -10.142 -12.634 16.320 -1.235 -4.880 -1.732 "O5'" 5J9 26 5J9 "O4'" O4 O 0 1 N N N -8.485 -11.674 18.720 -2.113 -2.223 -0.815 "O4'" 5J9 27 5J9 "C1'" C16 C 0 1 N N R -8.968 -12.120 19.966 -1.991 -0.842 -0.409 "C1'" 5J9 28 5J9 N9 N9 N 0 1 Y N N -9.616 -10.968 20.690 -3.315 -0.264 -0.163 N9 5J9 29 5J9 N7 N10 N 0 1 Y N N -11.029 -9.683 21.671 -5.450 -0.126 0.267 N7 5J9 30 5J9 C2 C17 C 0 1 Y N N -7.192 -8.396 21.595 -3.546 3.366 -0.260 C2 5J9 31 5J9 N6 N11 N 0 1 N N N -10.220 -7.046 22.943 -6.951 2.550 0.459 N6 5J9 32 5J9 H1 H1 H 0 1 N N N -8.976 -16.946 18.545 1.474 -1.546 -1.288 H1 5J9 33 5J9 H2 H2 H 0 1 N N N -11.680 -11.540 20.822 -4.537 -2.030 0.151 H2 5J9 34 5J9 H3 H3 H 0 1 N N N -2.655 -19.932 15.890 5.777 4.669 0.333 H3 5J9 35 5J9 H4 H4 H 0 1 N N N -1.574 -19.805 17.238 4.814 4.912 -1.023 H4 5J9 36 5J9 H5 H5 H 0 1 N N N -2.317 -19.182 19.431 3.704 3.096 -2.197 H5 5J9 37 5J9 H6 H6 H 0 1 N N N -4.283 -18.543 20.825 3.309 0.681 -2.288 H6 5J9 38 5J9 H7 H7 H 0 1 N N N -7.712 -18.934 19.699 5.165 -1.663 -0.221 H7 5J9 39 5J9 H8 H8 H 0 1 N N N -6.623 -18.477 21.053 4.140 -1.460 -1.662 H8 5J9 40 5J9 H9 H9 H 0 1 N N N -9.744 -14.487 17.807 -0.658 -2.878 1.626 H9 5J9 41 5J9 H10 H10 H 0 1 N N N -10.828 -12.902 19.172 -1.835 -0.896 1.765 H10 5J9 42 5J9 H11 H11 H 0 1 N N N -10.645 -13.588 21.408 -0.716 1.082 1.028 H11 5J9 43 5J9 H12 H12 H 0 1 N N N -7.209 -13.131 17.840 -0.113 -2.542 -1.331 H12 5J9 44 5J9 H13 H13 H 0 1 N N N -8.158 -12.830 15.755 -0.005 -4.749 -0.076 H13 5J9 45 5J9 H14 H14 H 0 1 N N N -8.600 -11.263 16.513 -1.748 -4.588 0.248 H14 5J9 46 5J9 H15 H15 H 0 1 N N N -10.399 -12.296 15.470 -1.326 -5.843 -1.740 H15 5J9 47 5J9 H16 H16 H 0 1 N N N -8.140 -12.506 20.579 -1.461 -0.268 -1.169 H16 5J9 48 5J9 H17 H17 H 0 1 N N N -6.146 -8.133 21.537 -2.962 4.262 -0.415 H17 5J9 49 5J9 H18 H18 H 0 1 N N N -9.694 -6.262 23.274 -7.498 1.762 0.602 H18 5J9 50 5J9 H19 H19 H 0 1 N N N -10.929 -6.730 22.313 -7.351 3.433 0.504 H19 5J9 51 # 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 5J9 "O5'" "C5'" SING N N 1 5J9 "C5'" "C4'" SING N N 2 5J9 N4T C4T SING N N 3 5J9 N3T C4T DOUB N N 4 5J9 N3T C2T SING N N 5 5J9 O2T C2T DOUB N N 6 5J9 C4T C5T SING N N 7 5J9 C2T N1T SING N N 8 5J9 "C4'" "C3'" SING N N 9 5J9 "C4'" "O4'" SING N N 10 5J9 "C3'" N10 SING N N 11 5J9 "C3'" "C2'" SING N N 12 5J9 "O4'" "C1'" SING N N 13 5J9 C5T C6T DOUB N N 14 5J9 C14 N10 SING Y N 15 5J9 C14 C13 DOUB Y N 16 5J9 N10 N11 SING Y N 17 5J9 N1T C6T SING N N 18 5J9 N1T C15 SING N N 19 5J9 "C2'" "C1'" SING N N 20 5J9 "C2'" "O2'" SING N N 21 5J9 C13 C15 SING N N 22 5J9 C13 N12 SING Y N 23 5J9 N11 N12 DOUB Y N 24 5J9 "C1'" N9 SING N N 25 5J9 N9 C8 SING Y N 26 5J9 N9 C4 SING Y N 27 5J9 C8 N7 DOUB Y N 28 5J9 N3 C4 DOUB Y N 29 5J9 N3 C2 SING Y N 30 5J9 C4 C5 SING Y N 31 5J9 C2 N1 DOUB Y N 32 5J9 N7 C5 SING Y N 33 5J9 C5 C6 DOUB Y N 34 5J9 N1 C6 SING Y N 35 5J9 C6 N6 SING N N 36 5J9 C14 H1 SING N N 37 5J9 C8 H2 SING N N 38 5J9 N4T H3 SING N N 39 5J9 N4T H4 SING N N 40 5J9 C5T H5 SING N N 41 5J9 C6T H6 SING N N 42 5J9 C15 H7 SING N N 43 5J9 C15 H8 SING N N 44 5J9 "C3'" H9 SING N N 45 5J9 "C2'" H10 SING N N 46 5J9 "O2'" H11 SING N N 47 5J9 "C4'" H12 SING N N 48 5J9 "C5'" H13 SING N N 49 5J9 "C5'" H14 SING N N 50 5J9 "O5'" H15 SING N N 51 5J9 "C1'" H16 SING N N 52 5J9 C2 H17 SING N N 53 5J9 N6 H18 SING N N 54 5J9 N6 H19 SING N N 55 # 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 5J9 SMILES ACDLabs 12.01 "c12c(c(N)ncn1)ncn2C5C(C(n4cc(CN3C(=O)N=C(C=C3)N)nn4)C(O5)CO)O" 5J9 InChI InChI 1.03 "InChI=1S/C17H19N11O4/c18-10-1-2-26(17(31)23-10)3-8-4-28(25-24-8)12-9(5-29)32-16(13(12)30)27-7-22-11-14(19)20-6-21-15(11)27/h1-2,4,6-7,9,12-13,16,29-30H,3,5H2,(H2,18,23,31)(H2,19,20,21)/t9-,12-,13-,16-/m1/s1" 5J9 InChIKey InChI 1.03 RYUXRYKLIYXCJZ-RVXWVPLUSA-N 5J9 SMILES_CANONICAL CACTVS 3.385 "NC1=NC(=O)N(Cc2cn(nn2)[C@H]3[C@@H](O)[C@@H](O[C@@H]3CO)n4cnc5c(N)ncnc45)C=C1" 5J9 SMILES CACTVS 3.385 "NC1=NC(=O)N(Cc2cn(nn2)[CH]3[CH](O)[CH](O[CH]3CO)n4cnc5c(N)ncnc45)C=C1" 5J9 SMILES_CANONICAL "OpenEye OEToolkits" 1.9.2 "c1c(nnn1[C@@H]2[C@H](O[C@H]([C@@H]2O)n3cnc4c3ncnc4N)CO)CN5C=CC(=NC5=O)N" 5J9 SMILES "OpenEye OEToolkits" 1.9.2 "c1c(nnn1C2C(OC(C2O)n3cnc4c3ncnc4N)CO)CN5C=CC(=NC5=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 5J9 "SYSTEMATIC NAME" ACDLabs 12.01 "3'-{4-[(4-amino-2-oxopyrimidin-1(2H)-yl)methyl]-1H-1,2,3-triazol-1-yl}-3'-deoxyadenosine" 5J9 "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.9.2 "1-[[1-[(2S,3S,4R,5R)-5-(6-aminopurin-9-yl)-2-(hydroxymethyl)-4-oxidanyl-oxolan-3-yl]-1,2,3-triazol-4-yl]methyl]-4-azanyl-pyrimidin-2-one" # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site 5J9 "Create component" 2015-09-30 EBI 5J9 "Initial release" 2015-11-18 RCSB #