data_X5D # _chem_comp.id X5D _chem_comp.name "(2R,5R,7R,8R,10S,12aR,14R,15aS,16R)-7-(2-amino-6-oxo-1,6-dihydro-9H-purin-9-yl)-2,10,16-trihydroxy-14-[(pyrimidin-4-yl)oxy]decahydro-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 O12 P2" _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 2022-02-04 _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 617.400 _chem_comp.one_letter_code ? _chem_comp.three_letter_code X5D _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 7KVZ _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 X5D C4 C1 C 0 1 Y N N 41.027 7.908 19.421 2.181 0.399 -2.521 C4 X5D 1 X5D C5 C2 C 0 1 Y N N 39.747 9.447 18.737 2.042 2.517 -2.086 C5 X5D 2 X5D C6 C3 C 0 1 Y N N 46.020 9.234 17.006 -5.688 1.031 0.408 C6 X5D 3 X5D C7 C4 C 0 1 Y N N 39.117 8.282 18.388 2.784 1.931 -1.055 C7 X5D 4 X5D C8 C5 C 0 1 N N N 39.124 10.690 18.406 1.803 3.911 -2.040 C8 X5D 5 X5D C10 C6 C 0 1 N N N 45.868 5.762 15.840 -2.852 -0.394 2.150 C10 X5D 6 X5D C13 C7 C 0 1 N N N 41.862 4.068 20.722 2.119 -3.141 -1.871 C13 X5D 7 X5D C15 C8 C 0 1 N N S 44.960 5.648 18.041 -1.809 -1.217 0.063 C15 X5D 8 X5D C17 C9 C 0 1 N N R 40.780 5.172 17.875 2.596 -0.939 0.550 C17 X5D 9 X5D C20 C10 C 0 1 N N R 39.754 5.869 18.724 3.534 -0.432 -0.558 C20 X5D 10 X5D C1 C11 C 0 1 Y N N 45.293 10.352 16.693 -6.226 2.291 0.146 C1 X5D 11 X5D C2 C12 C 0 1 Y N N 45.854 11.532 17.129 -7.540 2.368 -0.275 C2 X5D 12 X5D C3 C13 C 0 1 Y N N 47.613 10.445 18.043 -7.702 0.077 -0.159 C3 X5D 13 X5D C9 C14 C 0 1 N N N 37.366 9.242 17.445 3.023 3.986 -0.028 C9 X5D 14 X5D C11 C15 C 0 1 N N N 46.302 6.328 18.091 -3.298 -0.986 -0.217 C11 X5D 15 X5D C12 C16 C 0 1 N N N 43.670 4.575 16.159 -0.394 -0.077 1.788 C12 X5D 16 X5D C14 C17 C 0 1 N N R 45.019 4.893 16.746 -1.580 -1.015 1.564 C14 X5D 17 X5D C16 C18 C 0 1 N N R 40.578 4.040 19.922 3.267 -2.751 -0.936 C16 X5D 18 X5D C18 C19 C 0 1 N N R 46.408 6.878 16.705 -3.927 -0.421 1.060 C18 X5D 19 X5D C19 C20 C 0 1 N N R 40.780 3.780 18.462 2.701 -2.480 0.473 C19 X5D 20 X5D N21 N1 N 0 1 Y N N 47.009 11.609 17.804 -8.240 1.252 -0.415 N21 X5D 21 X5D N22 N2 N 0 1 Y N N 47.176 9.240 17.674 -6.453 -0.042 0.245 N22 X5D 22 X5D N23 N3 N 0 1 Y N N 40.930 9.214 19.377 1.701 1.530 -2.949 N23 X5D 23 X5D N24 N4 N 0 1 N N N 37.937 8.119 17.747 3.250 2.691 -0.058 N24 X5D 24 X5D N25 N5 N 0 1 Y N N 39.955 7.298 18.836 2.855 0.596 -1.351 N25 X5D 25 X5D N26 N6 N 0 1 N N N 37.931 10.454 17.759 2.306 4.614 -1.002 N26 X5D 26 X5D N27 N7 N 0 1 N N N 36.170 9.345 16.794 3.522 4.726 1.015 N27 X5D 27 X5D O28 O1 O 0 1 N N N 39.607 11.787 18.678 1.160 4.464 -2.916 O28 X5D 28 X5D O29 O2 O 0 1 N N N 41.478 4.901 14.113 2.477 -0.594 4.292 O29 X5D 29 X5D O30 O3 O 0 1 N N N 44.794 4.142 21.589 -1.208 -4.055 -2.452 O30 X5D 30 X5D O31 O4 O 0 1 N N N 42.912 5.780 16.084 0.543 -0.692 2.673 O31 X5D 31 X5D O32 O5 O 0 1 N N N 42.643 5.230 20.513 0.932 -3.346 -1.099 O32 X5D 32 X5D O33 O6 O 0 1 N N N 39.858 5.271 20.006 3.872 -1.540 -1.393 O33 X5D 33 X5D O34 O7 O 0 1 N N N 44.834 4.721 19.100 -1.446 -2.548 -0.310 O34 X5D 34 X5D O35 O8 O 0 1 N N N 40.426 5.145 16.499 3.023 -0.476 1.830 O35 X5D 35 X5D O36 O9 O 0 1 N N N 39.651 3.058 17.965 3.596 -2.970 1.474 O36 X5D 36 X5D O37 O10 O 0 1 N N N 40.952 7.251 15.201 1.878 1.536 3.078 O37 X5D 37 X5D O38 O11 O 0 1 N N N 44.726 6.700 20.723 -0.399 -1.664 -2.430 O38 X5D 38 X5D O39 O12 O 0 1 N N N 45.541 8.016 16.603 -4.403 0.904 0.818 O39 X5D 39 X5D P40 P1 P 0 1 N N N 41.447 5.724 15.380 1.990 -0.068 2.997 P40 X5D 40 X5D P41 P2 P 0 1 N N N 44.277 5.142 20.566 -0.527 -2.877 -1.591 P41 X5D 41 X5D H1 H1 H 0 1 N N N 41.856 7.378 19.867 2.059 -0.554 -3.014 H1 X5D 42 X5D H2 H2 H 0 1 N N N 45.255 6.175 15.025 -3.184 -0.975 3.011 H2 X5D 43 X5D H3 H3 H 0 1 N N N 46.696 5.175 15.416 -2.657 0.635 2.451 H3 X5D 44 X5D H4 H4 H 0 1 N N N 41.606 4.010 21.790 1.950 -2.343 -2.593 H4 X5D 45 X5D H5 H5 H 0 1 N N N 42.464 3.191 20.442 2.373 -4.061 -2.398 H5 X5D 46 X5D H6 H6 H 0 1 N N N 44.145 6.386 18.031 -1.214 -0.501 -0.502 H6 X5D 47 X5D H7 H7 H 0 1 N N N 41.766 5.638 18.021 1.573 -0.625 0.353 H7 X5D 48 X5D H8 H8 H 0 1 N N N 38.757 5.673 18.302 4.439 -0.016 -0.114 H8 X5D 49 X5D H9 H9 H 0 1 N N N 44.360 10.312 16.151 -5.631 3.183 0.269 H9 X5D 50 X5D H10 H10 H 0 1 N N N 45.331 12.452 16.914 -7.990 3.326 -0.488 H10 X5D 51 X5D H11 H11 H 0 1 N N N 48.545 10.481 18.587 -8.301 -0.813 -0.282 H11 X5D 52 X5D H12 H12 H 0 1 N N N 47.109 5.610 18.302 -3.414 -0.273 -1.033 H12 X5D 53 X5D H13 H13 H 0 1 N N N 46.319 7.130 18.844 -3.776 -1.930 -0.480 H13 X5D 54 X5D H14 H14 H 0 1 N N N 43.149 3.848 16.800 0.090 0.130 0.833 H14 X5D 55 X5D H15 H15 H 0 1 N N N 43.795 4.152 15.151 -0.747 0.857 2.225 H15 X5D 56 X5D H16 H16 H 0 1 N N N 45.554 3.948 16.918 -1.389 -1.976 2.040 H16 X5D 57 X5D H17 H17 H 0 1 N N N 39.949 3.233 20.326 4.003 -3.551 -0.893 H17 X5D 58 X5D H18 H18 H 0 1 N N N 47.449 7.117 16.444 -4.755 -1.057 1.375 H18 X5D 59 X5D H19 H19 H 0 1 N N N 41.732 3.263 18.270 1.717 -2.935 0.583 H19 X5D 60 X5D H20 H20 H 0 1 N N N 37.413 11.264 17.484 2.157 5.571 -0.950 H20 X5D 61 X5D H21 H21 H 0 1 N N N 35.678 8.519 16.519 4.033 4.292 1.716 H21 X5D 62 X5D H22 H22 H 0 1 N N N 35.786 10.246 16.592 3.363 5.682 1.051 H22 X5D 63 X5D H23 H23 H 0 1 N N N 45.344 4.590 22.221 -0.707 -4.305 -3.240 H23 X5D 64 X5D H24 H24 H 0 1 N N N 39.648 2.182 18.332 3.700 -3.931 1.472 H24 X5D 65 X5D H25 H25 H 0 1 N N N 40.745 7.412 14.288 1.271 1.854 3.761 H25 X5D 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 X5D O29 P40 DOUB N N 1 X5D O37 P40 SING N N 2 X5D P40 O31 SING N N 3 X5D P40 O35 SING N N 4 X5D C10 C18 SING N N 5 X5D C10 C14 SING N N 6 X5D O31 C12 SING N N 7 X5D C12 C14 SING N N 8 X5D O35 C17 SING N N 9 X5D O39 C18 SING N N 10 X5D O39 C6 SING N N 11 X5D C1 C6 SING Y N 12 X5D C1 C2 DOUB Y N 13 X5D C18 C11 SING N N 14 X5D C14 C15 SING N N 15 X5D N27 C9 SING N N 16 X5D C6 N22 DOUB Y N 17 X5D C2 N21 SING Y N 18 X5D C9 N24 DOUB N N 19 X5D C9 N26 SING N N 20 X5D N22 C3 SING Y N 21 X5D N24 C7 SING N N 22 X5D N26 C8 SING N N 23 X5D N21 C3 DOUB Y N 24 X5D C17 C19 SING N N 25 X5D C17 C20 SING N N 26 X5D O36 C19 SING N N 27 X5D C15 C11 SING N N 28 X5D C15 O34 SING N N 29 X5D C7 C5 DOUB Y N 30 X5D C7 N25 SING Y N 31 X5D C8 O28 DOUB N N 32 X5D C8 C5 SING N N 33 X5D C19 C16 SING N N 34 X5D C20 N25 SING N N 35 X5D C20 O33 SING N N 36 X5D C5 N23 SING Y N 37 X5D N25 C4 SING Y N 38 X5D O34 P41 SING N N 39 X5D N23 C4 DOUB Y N 40 X5D C16 O33 SING N N 41 X5D C16 C13 SING N N 42 X5D O32 P41 SING N N 43 X5D O32 C13 SING N N 44 X5D P41 O38 DOUB N N 45 X5D P41 O30 SING N N 46 X5D C4 H1 SING N N 47 X5D C10 H2 SING N N 48 X5D C10 H3 SING N N 49 X5D C13 H4 SING N N 50 X5D C13 H5 SING N N 51 X5D C15 H6 SING N N 52 X5D C17 H7 SING N N 53 X5D C20 H8 SING N N 54 X5D C1 H9 SING N N 55 X5D C2 H10 SING N N 56 X5D C3 H11 SING N N 57 X5D C11 H12 SING N N 58 X5D C11 H13 SING N N 59 X5D C12 H14 SING N N 60 X5D C12 H15 SING N N 61 X5D C14 H16 SING N N 62 X5D C16 H17 SING N N 63 X5D C18 H18 SING N N 64 X5D C19 H19 SING N N 65 X5D N26 H20 SING N N 66 X5D N27 H21 SING N N 67 X5D N27 H22 SING N N 68 X5D O30 H23 SING N N 69 X5D O36 H24 SING N N 70 X5D O37 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 X5D SMILES ACDLabs 12.01 "c1nc6c(n1C5C3C(C(COP(O)(OC2CC(CC2COP(=O)(O3)O)Oc4ncncc4)=O)O5)O)N=C(NC6=O)N" X5D InChI InChI 1.03 "InChI=1S/C20H25N7O12P2/c21-20-25-17-14(18(29)26-20)24-8-27(17)19-16-15(28)12(37-19)6-35-40(30,31)38-11-4-10(36-13-1-2-22-7-23-13)3-9(11)5-34-41(32,33)39-16/h1-2,7-12,15-16,19,28H,3-6H2,(H,30,31)(H,32,33)(H3,21,25,26,29)/t9-,10-,11+,12-,15-,16-,19-/m1/s1" X5D InChIKey InChI 1.03 IQDCEFNXFAZHCY-SECPXAEJSA-N X5D SMILES_CANONICAL CACTVS 3.385 "NC1=Nc2n(cnc2C(=O)N1)[C@@H]3O[C@@H]4CO[P](O)(=O)O[C@H]5C[C@@H](C[C@@H]5CO[P](O)(=O)O[C@@H]3[C@@H]4O)Oc6ccncn6" X5D SMILES CACTVS 3.385 "NC1=Nc2n(cnc2C(=O)N1)[CH]3O[CH]4CO[P](O)(=O)O[CH]5C[CH](C[CH]5CO[P](O)(=O)O[CH]3[CH]4O)Oc6ccncn6" X5D SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "c1cncnc1O[C@@H]2C[C@@H]3COP(=O)(O[C@@H]4[C@@H]([C@@H](COP(=O)(O[C@H]3C2)O)O[C@H]4n5cnc6c5N=C(NC6=O)N)O)O" X5D SMILES "OpenEye OEToolkits" 2.0.7 "c1cncnc1OC2CC3COP(=O)(OC4C(C(COP(=O)(OC3C2)O)OC4n5cnc6c5N=C(NC6=O)N)O)O" # # 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 X5D "SYSTEMATIC NAME" ACDLabs 12.01 "(2R,5R,7R,8R,10S,12aR,14R,15aS,16R)-7-(2-amino-6-oxo-1,6-dihydro-9H-purin-9-yl)-2,10,16-trihydroxy-14-[(pyrimidin-4-yl)oxy]decahydro-2H,10H-5,8-methano-2lambda~5~,10lambda~5~-cyclopenta[l][1,3,6,9,11,2,10]pentaoxadiphosphacyclotetradecine-2,10-dione" X5D "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 "2-azanyl-9-[(1~{R},6~{R},8~{R},10~{S},15~{R},17~{R},18~{R})-3,12,18-tris(oxidanyl)-3,12-bis(oxidanylidene)-8-pyrimidin-4-yloxy-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 X5D "Create component" 2020-11-30 RCSB X5D "Initial release" 2022-02-09 RCSB ##