data_JNT # _chem_comp.id JNT _chem_comp.name "[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2~{R},3~{S},4~{S})-2,3,4,5-tetrakis(oxidanyl)pentyl] hydrogen phosphate" _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C15 H25 N5 O14 P2" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2019-03-13 _chem_comp.pdbx_modified_date 2020-03-27 _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 561.332 _chem_comp.one_letter_code ? _chem_comp.three_letter_code JNT _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 6R0R _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 JNT "O5'" O1 O 0 1 N N N 11.482 7.295 10.123 -0.739 1.996 -0.105 "O5'" JNT 1 JNT "C5'" C1 C 0 1 N N N 12.844 7.010 10.389 -2.030 2.596 0.026 "C5'" JNT 2 JNT "C4'" C2 C 0 1 N N R 13.597 7.017 9.086 -3.013 1.903 -0.918 "C4'" JNT 3 JNT "O4'" O2 O 0 1 N N N 13.102 6.090 8.127 -3.224 0.546 -0.495 "O4'" JNT 4 JNT "C3'" C3 C 0 1 N N S 13.403 8.349 8.465 -4.378 2.618 -0.871 "C3'" JNT 5 JNT "O3'" O3 O 0 1 N N N 14.646 9.028 8.469 -4.726 3.117 -2.164 "O3'" JNT 6 JNT "C2'" C4 C 0 1 N N R 12.827 8.195 7.072 -5.370 1.515 -0.430 "C2'" JNT 7 JNT "O2'" O4 O 0 1 N N N 13.543 8.890 6.048 -6.593 1.607 -1.162 "O2'" JNT 8 JNT "C1'" C5 C 0 1 N N R 12.921 6.711 6.856 -4.597 0.218 -0.799 "C1'" JNT 9 JNT N9 N1 N 0 1 Y N N 11.652 6.123 6.358 -5.054 -0.906 0.022 N9 JNT 10 JNT C8 C6 C 0 1 Y N N 10.410 6.605 6.541 -4.484 -1.344 1.180 C8 JNT 11 JNT N7 N2 N 0 1 Y N N 9.487 5.820 5.986 -5.147 -2.363 1.645 N7 JNT 12 JNT C5 C7 C 0 1 Y N N 10.171 4.781 5.429 -6.182 -2.643 0.817 C5 JNT 13 JNT C4 C8 C 0 1 Y N N 11.588 4.983 5.665 -6.138 -1.708 -0.232 C4 JNT 14 JNT N3 N3 N 0 1 Y N N 12.509 4.088 5.200 -7.058 -1.768 -1.189 N3 JNT 15 JNT C2 C9 C 0 1 Y N N 12.067 3.026 4.509 -7.998 -2.689 -1.160 C2 JNT 16 JNT N1 N4 N 0 1 Y N N 10.756 2.791 4.302 -8.080 -3.588 -0.196 N1 JNT 17 JNT C6 C10 C 0 1 Y N N 9.780 3.619 4.681 -7.210 -3.601 0.809 C6 JNT 18 JNT N6 N5 N 0 1 N N N 8.472 3.377 4.459 -7.303 -4.547 1.814 N6 JNT 19 JNT O1C O5 O 0 1 N N N 4.712 5.445 14.372 9.744 -4.227 -0.550 "O1'A" JNT 20 JNT C1A C11 C 0 1 N N N 4.439 6.394 13.544 9.393 -2.887 -0.201 "C1'A" JNT 21 JNT C2A C12 C 0 1 N N S 5.630 7.245 13.110 7.908 -2.657 -0.491 "C2'A" JNT 22 JNT O2C O6 O 0 1 N N N 6.601 6.389 12.474 7.676 -2.754 -1.897 "O2'A" JNT 23 JNT C3A C13 C 0 1 N N S 6.262 7.947 14.328 7.503 -1.265 -0.002 "C3'A" JNT 24 JNT O3C O7 O 0 1 N N N 5.340 8.834 15.037 7.735 -1.167 1.405 "O3'A" JNT 25 JNT C4A C14 C 0 1 N N R 7.480 8.810 13.994 6.018 -1.035 -0.291 "C4'A" JNT 26 JNT O4C O8 O 0 1 N N N 7.573 9.150 12.613 5.786 -1.132 -1.698 "O4'A" JNT 27 JNT C5A C15 C 0 1 N N N 8.808 8.179 14.393 5.613 0.357 0.197 "C5'A" JNT 28 JNT O5A O9 O 0 1 N N N 9.881 9.133 14.238 4.203 0.528 0.033 "O5'A" JNT 29 JNT PB P1 P 0 1 N N N 11.367 8.653 13.894 3.430 1.879 0.445 PB JNT 30 JNT O2B O10 O 0 1 N N N 11.794 7.633 14.940 3.934 3.091 -0.487 O2B JNT 31 JNT O1B O11 O 0 1 N N N 12.223 9.863 13.705 3.712 2.197 1.862 O1B JNT 32 JNT O3A O12 O 0 1 N N N 11.296 7.829 12.530 1.846 1.672 0.246 O3A JNT 33 JNT PA P2 P 0 1 N N N 10.576 8.155 11.122 0.542 2.476 0.742 PA JNT 34 JNT O1A O13 O 0 1 N N N 10.649 9.616 10.830 0.751 3.927 0.540 O1A JNT 35 JNT O2A O14 O 0 1 N N N 9.234 7.547 11.107 0.293 2.182 2.305 O2A JNT 36 JNT H1 H1 H 0 1 N N N 12.930 6.021 10.862 -2.376 2.490 1.054 H1 JNT 37 JNT H2 H2 H 0 1 N N N 13.259 7.776 11.061 -1.965 3.654 -0.228 H2 JNT 38 JNT H3 H3 H 0 1 N N N 14.667 6.846 9.278 -2.623 1.918 -1.936 H3 JNT 39 JNT H4 H4 H 0 1 N N N 12.679 8.913 9.072 -4.358 3.429 -0.142 H4 JNT 40 JNT H5 H5 H 0 1 N N N 14.965 9.100 9.361 -5.577 3.577 -2.191 H5 JNT 41 JNT H6 H6 H 0 1 N N N 11.770 8.499 7.079 -5.556 1.565 0.643 H6 JNT 42 JNT H7 H7 H 0 1 N N N 13.477 9.826 6.194 -7.067 2.440 -1.033 H7 JNT 43 JNT H8 H8 H 0 1 N N N 13.750 6.477 6.172 -4.711 -0.008 -1.859 H8 JNT 44 JNT H9 H9 H 0 1 N N N 10.187 7.518 7.073 -3.611 -0.909 1.643 H9 JNT 45 JNT H10 H10 H 0 1 N N N 12.789 2.333 4.103 -8.731 -2.710 -1.953 H10 JNT 46 JNT H11 H11 H 0 1 N N N 8.370 2.505 3.981 -8.010 -5.211 1.791 H11 JNT 47 JNT H12 H12 H 0 1 N N N 7.988 3.336 5.333 -6.662 -4.547 2.542 H12 JNT 48 JNT H13 H13 H 0 1 N N N 3.917 4.971 14.585 10.673 -4.444 -0.393 H13 JNT 49 JNT H14 H14 H 0 1 N N N 3.702 7.058 14.019 9.585 -2.725 0.859 H14 JNT 50 JNT H15 H15 H 0 1 N N N 3.998 5.942 12.643 9.990 -2.190 -0.789 H15 JNT 51 JNT H16 H16 H 0 1 N N N 5.281 8.011 12.402 7.316 -3.411 0.029 H16 JNT 52 JNT H17 H17 H 0 1 N N N 7.348 6.907 12.199 8.172 -2.112 -2.423 H17 JNT 53 JNT H18 H18 H 0 1 N N N 6.593 7.163 15.025 8.095 -0.511 -0.521 H18 JNT 54 JNT H19 H19 H 0 1 N N N 5.788 9.234 15.773 7.239 -1.809 1.930 H19 JNT 55 JNT H20 H20 H 0 1 N N N 7.380 9.741 14.571 5.426 -1.788 0.228 H20 JNT 56 JNT H21 H21 H 0 1 N N N 8.346 9.684 12.469 6.282 -0.490 -2.224 H21 JNT 57 JNT H22 H22 H 0 1 N N N 8.756 7.858 15.444 5.872 0.462 1.250 H22 JNT 58 JNT H23 H23 H 0 1 N N N 9.003 7.306 13.752 6.140 1.114 -0.384 H23 JNT 59 JNT H24 H24 H 0 1 N N N 12.597 7.923 15.356 3.781 2.951 -1.432 H24 JNT 60 JNT H25 H25 H 0 1 N N N 8.587 8.212 10.903 0.148 1.248 2.512 H25 JNT 61 # # 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 JNT N1 C2 DOUB Y N 1 JNT N1 C6 SING Y N 2 JNT N6 C6 SING N N 3 JNT C2 N3 SING Y N 4 JNT C6 C5 DOUB Y N 5 JNT N3 C4 DOUB Y N 6 JNT C5 C4 SING Y N 7 JNT C5 N7 SING Y N 8 JNT C4 N9 SING Y N 9 JNT N7 C8 DOUB Y N 10 JNT "O2'" "C2'" SING N N 11 JNT N9 C8 SING Y N 12 JNT N9 "C1'" SING N N 13 JNT "C1'" "C2'" SING N N 14 JNT "C1'" "O4'" SING N N 15 JNT "C2'" "C3'" SING N N 16 JNT "O4'" "C4'" SING N N 17 JNT "C3'" "O3'" SING N N 18 JNT "C3'" "C4'" SING N N 19 JNT "C4'" "C5'" SING N N 20 JNT "O5'" "C5'" SING N N 21 JNT "O5'" PA SING N N 22 JNT O1A PA DOUB N N 23 JNT O2A PA SING N N 24 JNT PA O3A SING N N 25 JNT O2C C2A SING N N 26 JNT O3A PB SING N N 27 JNT O4C C4A SING N N 28 JNT C2A C1A SING N N 29 JNT C2A C3A SING N N 30 JNT C1A O1C SING N N 31 JNT O1B PB DOUB N N 32 JNT PB O5A SING N N 33 JNT PB O2B SING N N 34 JNT C4A C3A SING N N 35 JNT C4A C5A SING N N 36 JNT O5A C5A SING N N 37 JNT "C5'" H1 SING N N 38 JNT "C5'" H2 SING N N 39 JNT "C4'" H3 SING N N 40 JNT "C3'" H4 SING N N 41 JNT "O3'" H5 SING N N 42 JNT "C2'" H6 SING N N 43 JNT "O2'" H7 SING N N 44 JNT "C1'" H8 SING N N 45 JNT C8 H9 SING N N 46 JNT C2 H10 SING N N 47 JNT N6 H11 SING N N 48 JNT N6 H12 SING N N 49 JNT O1C H13 SING N N 50 JNT C1A H14 SING N N 51 JNT C1A H15 SING N N 52 JNT C2A H16 SING N N 53 JNT O2C H17 SING N N 54 JNT C3A H18 SING N N 55 JNT O3C H19 SING N N 56 JNT C4A H20 SING N N 57 JNT O4C H21 SING N N 58 JNT C5A H22 SING N N 59 JNT C5A H23 SING N N 60 JNT O2B H24 SING N N 61 JNT O2A H25 SING N N 62 JNT C3A O3C SING N N 63 # # 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 JNT InChI InChI 1.03 "InChI=1S/C15H25N5O14P2/c16-13-9-14(18-4-17-13)20(5-19-9)15-12(26)11(25)8(33-15)3-32-36(29,30)34-35(27,28)31-2-7(23)10(24)6(22)1-21/h4-8,10-12,15,21-26H,1-3H2,(H,27,28)(H,29,30)(H2,16,17,18)/t6-,7+,8+,10-,11+,12+,15+/m0/s1" JNT InChIKey InChI 1.03 QKJRZYRQRSLXSV-AOOZFPJJSA-N JNT SMILES_CANONICAL CACTVS 3.385 "Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P](O)(=O)O[P](O)(=O)OC[C@@H](O)[C@@H](O)[C@@H](O)CO)[C@@H](O)[C@H]3O" JNT SMILES CACTVS 3.385 "Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(=O)OC[CH](O)[CH](O)[CH](O)CO)[CH](O)[CH]3O" JNT SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)COP(=O)(O)OP(=O)(O)OC[C@H]([C@H]([C@H](CO)O)O)O)O)O)N" JNT SMILES "OpenEye OEToolkits" 2.0.7 "c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OCC(C(C(CO)O)O)O)O)O)N" # _pdbx_chem_comp_identifier.comp_id JNT _pdbx_chem_comp_identifier.type "SYSTEMATIC NAME" _pdbx_chem_comp_identifier.program "OpenEye OEToolkits" _pdbx_chem_comp_identifier.program_version 2.0.7 _pdbx_chem_comp_identifier.identifier "[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2~{R},3~{S},4~{S})-2,3,4,5-tetrakis(oxidanyl)pentyl] hydrogen 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 JNT "Create component" 2019-03-13 RCSB JNT "Initial release" 2020-04-01 RCSB ##