data_X4M # _chem_comp.id X4M _chem_comp.name "(2R,5R,7R,8R,10R,12aR,14R,15aS,16R)-7-(2-amino-6-oxo-1,6-dihydro-9H-purin-9-yl)-16-hydroxy-14-[(pyrimidin-4-yl)oxy]-2,10-disulfanyldecahydro-2H,10H-5,8-methano-2lambda~5~,10lambda~5~-cyclopenta[l][1,3,6,9,11,2,10]pentaoxadiphosphacyclotetradecine-2,10-dione" _chem_comp.type non-polymer _chem_comp.pdbx_type HETAIN _chem_comp.formula "C20 H25 N7 O10 P2 S2" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2020-11-30 _chem_comp.pdbx_modified_date 2021-05-28 _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 649.531 _chem_comp.one_letter_code ? _chem_comp.three_letter_code X4M _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 7KW1 _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 X4M C4 C1 C 0 1 Y N N 40.837 7.895 19.412 1.977 0.183 -2.765 C4 X4M 1 X4M C5 C2 C 0 1 Y N N 39.551 9.458 18.796 1.914 2.341 -2.575 C5 X4M 2 X4M C6 C3 C 0 1 Y N N 45.929 9.401 16.912 -5.656 1.383 0.579 C6 X4M 3 X4M C7 C4 C 0 1 Y N N 38.899 8.297 18.443 2.713 1.857 -1.533 C7 X4M 4 X4M C8 C5 C 0 1 N N N 38.919 10.712 18.509 1.709 3.737 -2.678 C8 X4M 5 X4M C10 C6 C 0 1 N N N 45.556 5.908 15.744 -2.739 0.087 2.287 C10 X4M 6 X4M C13 C7 C 0 1 N N N 41.698 4.222 20.784 1.884 -3.254 -1.699 C13 X4M 7 X4M C15 C8 C 0 1 N N S 44.703 5.845 17.918 -1.860 -1.003 0.248 C15 X4M 8 X4M C17 C9 C 0 1 N N R 40.704 5.297 17.875 2.573 -0.800 0.408 C17 X4M 9 X4M C20 C10 C 0 1 N N R 39.586 5.860 18.704 3.444 -0.453 -0.811 C20 X4M 10 X4M C1 C11 C 0 1 Y N N 45.185 10.533 16.690 -6.184 2.619 0.206 C1 X4M 11 X4M C2 C12 C 0 1 Y N N 45.675 11.736 17.153 -7.521 2.686 -0.135 C2 X4M 12 X4M C3 C13 C 0 1 Y N N 47.545 10.651 17.993 -7.725 0.430 0.262 C3 X4M 13 X4M C9 C14 C 0 1 N N N 37.113 9.306 17.567 3.066 4.009 -0.773 C9 X4M 14 X4M C11 C15 C 0 1 N N N 46.083 6.435 17.995 -3.359 -0.763 0.041 C11 X4M 15 X4M C12 C16 C 0 1 N N N 43.411 4.656 16.179 -0.305 0.288 1.729 C12 X4M 16 X4M C14 C17 C 0 1 N N R 44.789 5.003 16.691 -1.524 -0.635 1.696 C14 X4M 17 X4M C16 C18 C 0 1 N N R 40.499 4.044 19.866 3.102 -2.792 -0.894 C16 X4M 18 X4M C18 C19 C 0 1 N N R 46.238 6.976 16.596 -3.886 -0.035 1.281 C18 X4M 19 X4M C19 C20 C 0 1 N N R 40.869 3.909 18.419 2.640 -2.342 0.507 C19 X4M 20 X4M N21 N1 N 0 1 Y N N 46.849 11.772 17.792 -8.254 1.582 -0.096 N21 X4M 21 X4M N22 N2 N 0 1 Y N N 47.096 9.471 17.556 -6.454 0.322 0.594 N22 X4M 22 X4M N23 N3 N 0 1 Y N N 40.754 9.206 19.403 1.494 1.270 -3.291 N23 X4M 23 X4M N24 N4 N 0 1 N N N 37.695 8.179 17.828 3.263 2.714 -0.665 N24 X4M 24 X4M N25 N5 N 0 1 Y N N 39.750 7.294 18.841 2.735 0.495 -1.673 N25 X4M 25 X4M N26 N6 N 0 1 N N N 37.703 10.509 17.894 2.298 4.541 -1.765 N26 X4M 26 X4M N27 N7 N 0 1 N N N 35.885 9.431 16.954 3.651 4.850 0.140 N27 X4M 27 X4M O28 O1 O 0 1 N N N 39.407 11.804 18.789 1.020 4.203 -3.569 O28 X4M 28 X4M S29 S1 S 0 1 N N N 40.922 5.220 13.647 2.962 -0.187 4.652 S29 X4M 29 X4M S30 S2 S 0 1 N N N 44.895 4.119 21.763 -1.735 -4.527 -2.161 S30 X4M 30 X4M O31 O2 O 0 1 N N N 42.778 5.893 15.896 0.676 -0.248 2.618 O31 X4M 31 X4M O32 O3 O 0 1 N N N 42.476 5.322 20.375 0.749 -3.332 -0.833 O32 X4M 32 X4M O33 O4 O 0 1 N N N 39.668 5.202 19.968 3.701 -1.661 -1.529 O33 X4M 33 X4M O34 O5 O 0 1 N N N 44.547 4.945 19.002 -1.552 -2.378 0.011 O34 X4M 34 X4M O35 O6 O 0 1 N N N 40.331 5.217 16.502 3.097 -0.205 1.594 O35 X4M 35 X4M O36 O7 O 0 1 N N N 39.860 3.102 17.810 3.590 -2.738 1.498 O36 X4M 36 X4M O37 O8 O 0 1 N N N 40.871 7.581 15.552 2.090 1.842 2.677 O37 X4M 37 X4M O38 O9 O 0 1 N N N 44.375 6.958 20.618 -0.633 -1.778 -2.263 O38 X4M 38 X4M O39 O10 O 0 1 N N N 45.472 8.181 16.453 -4.349 1.267 0.916 O39 X4M 39 X4M P40 P1 P 0 1 N N R 41.219 6.007 15.404 2.156 0.367 2.770 P40 X4M 40 X4M P41 P2 P 0 1 N N R 44.106 5.370 20.499 -0.730 -2.881 -1.280 P41 X4M 41 X4M H1 H1 H 0 1 N N N 41.673 7.351 19.826 1.802 -0.817 -3.133 H1 X4M 42 X4M H2 H2 H 0 1 N N N 44.865 6.380 15.030 -3.023 -0.380 3.230 H2 X4M 43 X4M H3 H3 H 0 1 N N N 46.310 5.326 15.194 -2.501 1.138 2.451 H3 X4M 44 X4M H4 H4 H 0 1 N N N 41.344 4.391 21.812 1.684 -2.540 -2.498 H4 X4M 45 X4M H5 H5 H 0 1 N N N 42.315 3.312 20.754 2.082 -4.236 -2.129 H5 X4M 46 X4M H6 H6 H 0 1 N N N 43.917 6.612 17.855 -1.289 -0.375 -0.436 H6 X4M 47 X4M H7 H7 H 0 1 N N N 41.625 5.882 18.016 1.546 -0.481 0.244 H7 X4M 48 X4M H8 H8 H 0 1 N N N 38.625 5.636 18.218 4.386 -0.016 -0.479 H8 X4M 49 X4M H9 H9 H 0 1 N N N 44.241 10.483 16.167 -5.562 3.502 0.183 H9 X4M 50 X4M H10 H10 H 0 1 N N N 45.113 12.645 17.000 -7.964 3.626 -0.429 H10 X4M 51 X4M H11 H11 H 0 1 N N N 48.488 10.699 18.518 -8.349 -0.451 0.284 H11 X4M 52 X4M H12 H12 H 0 1 N N N 46.839 5.668 18.218 -3.515 -0.146 -0.844 H12 X4M 53 X4M H13 H13 H 0 1 N N N 46.139 7.236 18.747 -3.873 -1.716 -0.077 H13 X4M 54 X4M H14 H14 H 0 1 N N N 42.846 4.104 16.945 0.117 0.368 0.728 H14 X4M 55 X4M H15 H15 H 0 1 N N N 43.484 4.046 15.266 -0.608 1.276 2.076 H15 X4M 56 X4M H16 H16 H 0 1 N N N 45.364 4.087 16.890 -1.322 -1.539 2.269 H16 X4M 57 X4M H17 H17 H 0 1 N N N 39.941 3.150 20.180 3.821 -3.603 -0.805 H17 X4M 58 X4M H18 H18 H 0 1 N N N 47.295 7.101 16.319 -4.704 -0.605 1.722 H18 X4M 59 X4M H19 H19 H 0 1 N N N 41.889 3.521 18.280 1.656 -2.752 0.734 H19 X4M 60 X4M H20 H20 H 0 1 N N N 37.187 11.332 17.656 2.173 5.502 -1.816 H20 X4M 61 X4M H21 H21 H 0 1 N N N 35.379 8.614 16.677 4.200 4.486 0.853 H21 X4M 62 X4M H22 H22 H 0 1 N N N 35.500 10.339 16.786 3.516 5.808 0.074 H22 X4M 63 X4M H23 H23 H 0 1 N N N 41.281 3.986 13.840 2.088 0.347 5.524 H23 X4M 64 X4M H24 H24 H 0 1 N N N 44.463 4.576 22.901 -0.950 -4.835 -3.208 H24 X4M 65 X4M H25 H25 H 0 1 N N N 39.931 2.210 18.130 3.673 -3.696 1.602 H25 X4M 66 # # 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 X4M S29 P40 SING N N 1 X4M P40 O37 DOUB N N 2 X4M P40 O31 SING N N 3 X4M P40 O35 SING N N 4 X4M C10 C18 SING N N 5 X4M C10 C14 SING N N 6 X4M O31 C12 SING N N 7 X4M C12 C14 SING N N 8 X4M O39 C18 SING N N 9 X4M O39 C6 SING N N 10 X4M O35 C17 SING N N 11 X4M C18 C11 SING N N 12 X4M C1 C6 SING Y N 13 X4M C1 C2 DOUB Y N 14 X4M C14 C15 SING N N 15 X4M C6 N22 DOUB Y N 16 X4M N27 C9 SING N N 17 X4M C2 N21 SING Y N 18 X4M N22 C3 SING Y N 19 X4M C9 N24 DOUB N N 20 X4M C9 N26 SING N N 21 X4M N21 C3 DOUB Y N 22 X4M O36 C19 SING N N 23 X4M N24 C7 SING N N 24 X4M C17 C19 SING N N 25 X4M C17 C20 SING N N 26 X4M N26 C8 SING N N 27 X4M C15 C11 SING N N 28 X4M C15 O34 SING N N 29 X4M C19 C16 SING N N 30 X4M C7 C5 DOUB Y N 31 X4M C7 N25 SING Y N 32 X4M C8 O28 DOUB N N 33 X4M C8 C5 SING N N 34 X4M C20 N25 SING N N 35 X4M C20 O33 SING N N 36 X4M C5 N23 SING Y N 37 X4M N25 C4 SING Y N 38 X4M O34 P41 SING N N 39 X4M N23 C4 DOUB Y N 40 X4M C16 O33 SING N N 41 X4M C16 C13 SING N N 42 X4M O32 P41 SING N N 43 X4M O32 C13 SING N N 44 X4M P41 O38 DOUB N N 45 X4M P41 S30 SING N N 46 X4M C4 H1 SING N N 47 X4M C10 H2 SING N N 48 X4M C10 H3 SING N N 49 X4M C13 H4 SING N N 50 X4M C13 H5 SING N N 51 X4M C15 H6 SING N N 52 X4M C17 H7 SING N N 53 X4M C20 H8 SING N N 54 X4M C1 H9 SING N N 55 X4M C2 H10 SING N N 56 X4M C3 H11 SING N N 57 X4M C11 H12 SING N N 58 X4M C11 H13 SING N N 59 X4M C12 H14 SING N N 60 X4M C12 H15 SING N N 61 X4M C14 H16 SING N N 62 X4M C16 H17 SING N N 63 X4M C18 H18 SING N N 64 X4M C19 H19 SING N N 65 X4M N26 H20 SING N N 66 X4M N27 H21 SING N N 67 X4M N27 H22 SING N N 68 X4M S29 H23 SING N N 69 X4M S30 H24 SING N N 70 X4M O36 H25 SING 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 X4M SMILES ACDLabs 12.01 "c1nc6c(n1C5C3C(C(COP(S)(OC2CC(CC2COP(S)(O3)=O)Oc4ncncc4)=O)O5)O)N=C(NC6=O)N" X4M InChI InChI 1.03 "InChI=1S/C20H25N7O10P2S2/c21-20-25-17-14(18(29)26-20)24-8-27(17)19-16-15(28)12(35-19)6-33-38(30,40)36-11-4-10(34-13-1-2-22-7-23-13)3-9(11)5-32-39(31,41)37-16/h1-2,7-12,15-16,19,28H,3-6H2,(H,30,40)(H,31,41)(H3,21,25,26,29)/t9-,10-,11+,12-,15-,16-,19-,38-,39-/m1/s1" X4M InChIKey InChI 1.03 OYKBZTYSLUEHAP-FEFYGENMSA-N X4M SMILES_CANONICAL CACTVS 3.385 "NC1=Nc2n(cnc2C(=O)N1)[C@@H]3O[C@@H]4CO[P@](S)(=O)O[C@H]5C[C@@H](C[C@@H]5CO[P@](S)(=O)O[C@@H]3[C@@H]4O)Oc6ccncn6" X4M SMILES CACTVS 3.385 "NC1=Nc2n(cnc2C(=O)N1)[CH]3O[CH]4CO[P](S)(=O)O[CH]5C[CH](C[CH]5CO[P](S)(=O)O[CH]3[CH]4O)Oc6ccncn6" X4M SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "c1cncnc1O[C@@H]2C[C@@H]3CO[P@](=O)(O[C@@H]4[C@@H]([C@@H](CO[P@](=O)(O[C@H]3C2)S)O[C@H]4n5cnc6c5N=C(NC6=O)N)O)S" X4M SMILES "OpenEye OEToolkits" 2.0.7 "c1cncnc1OC2CC3COP(=O)(OC4C(C(COP(=O)(OC3C2)S)OC4n5cnc6c5N=C(NC6=O)N)O)S" # # 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 X4M "SYSTEMATIC NAME" ACDLabs 12.01 "(2R,5R,7R,8R,10R,12aR,14R,15aS,16R)-7-(2-amino-6-oxo-1,6-dihydro-9H-purin-9-yl)-16-hydroxy-14-[(pyrimidin-4-yl)oxy]-2,10-disulfanyldecahydro-2H,10H-5,8-methano-2lambda~5~,10lambda~5~-cyclopenta[l][1,3,6,9,11,2,10]pentaoxadiphosphacyclotetradecine-2,10-dione" X4M "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 "2-azanyl-9-[(1~{R},3~{R},6~{R},8~{R},10~{S},12~{R},15~{R},17~{R},18~{R})-18-oxidanyl-3,12-bis(oxidanylidene)-8-pyrimidin-4-yloxy-3,12-bis(sulfanyl)-2,4,11,13,16-pentaoxa-3$l^{5},12$l^{5}-diphosphatricyclo[13.2.1.0^{6,10}]octadecan-17-yl]-1~{H}-purin-6-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 X4M "Create component" 2020-11-30 RCSB X4M "Initial release" 2021-06-02 RCSB ##