data_Y4F # _chem_comp.id Y4F _chem_comp.name ;Cyclic (adenosine-(2'-5')-monophosphate-adenosine-(3'-5')-monophosphate ; _chem_comp.type non-polymer _chem_comp.pdbx_type HETAIN _chem_comp.formula "C20 H24 N10 O12 P2" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2023-01-04 _chem_comp.pdbx_modified_date 2024-02-02 _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 658.412 _chem_comp.one_letter_code ? _chem_comp.three_letter_code Y4F _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 8FMF _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.pdbx_backbone_atom_flag _chem_comp_atom.pdbx_n_terminal_atom_flag _chem_comp_atom.pdbx_c_terminal_atom_flag _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 Y4F C4 C1 C 0 1 Y N N N N N -51.209 39.677 54.436 5.640 -0.163 -0.109 C4 Y4F 1 Y4F C8 C2 C 0 1 Y N N N N N -51.973 37.843 53.494 4.220 1.243 -1.041 C8 Y4F 2 Y4F "C1'" C3 C 0 1 N N R N N N -49.716 38.683 52.675 3.283 -1.021 -0.442 "C1'" Y4F 3 Y4F C16 C4 C 0 1 N N N N N N -47.077 40.223 54.049 -0.027 -0.039 -1.320 C16 Y4F 4 Y4F C2 C5 C 0 1 Y N N N N N -51.047 41.453 55.717 7.608 -0.976 0.755 C2 Y4F 5 Y4F "C2'" C6 C 0 1 N N R N N N -49.368 39.950 51.892 2.610 -0.957 0.939 "C2'" Y4F 6 Y4F C21 C7 C 0 1 N N R N N N -44.355 39.400 51.647 -3.346 -0.538 -0.450 C21 Y4F 7 Y4F C22 C8 C 0 1 N N R N N N -44.570 37.976 51.146 -3.887 -1.984 -0.344 C22 Y4F 8 Y4F C24 C9 C 0 1 N N R N N N -44.141 38.067 49.678 -4.348 -2.059 1.129 C24 Y4F 9 Y4F C25 C10 C 0 1 N N N N N N -45.245 38.370 48.699 -3.204 -2.589 1.992 C25 Y4F 10 Y4F "C3'" C11 C 0 1 N N S N N N -47.867 39.746 51.674 1.103 -1.122 0.641 "C3'" Y4F 11 Y4F C32 C12 C 0 1 N N R N N N -43.074 39.749 50.910 -4.220 0.228 0.559 C32 Y4F 12 Y4F C34 C13 C 0 1 Y N N N N N -43.876 42.026 50.120 -2.785 1.151 2.416 C34 Y4F 13 Y4F C36 C14 C 0 1 Y N N N N N -41.883 41.994 51.055 -3.191 2.531 0.745 C36 Y4F 14 Y4F C37 C15 C 0 1 Y N N N N N -42.218 43.285 50.663 -2.393 3.165 1.712 C37 Y4F 15 Y4F C38 C16 C 0 1 Y N N N N N -41.323 44.307 50.894 -2.003 4.495 1.483 C38 Y4F 16 Y4F "C4'" C17 C 0 1 N N R N N N -47.453 39.177 53.026 0.996 -1.096 -0.890 "C4'" Y4F 17 Y4F C40 C18 C 0 1 Y N N N N N -39.839 42.794 51.872 -3.156 4.453 -0.516 C40 Y4F 18 Y4F C5 C19 C 0 1 Y N N N N N -52.444 39.343 54.946 6.280 1.057 -0.389 C5 Y4F 19 Y4F C6 C20 C 0 1 Y N N N N N -52.980 40.190 55.933 7.638 1.186 -0.054 C6 Y4F 20 Y4F N01 N1 N 0 1 N N N N N N -54.164 40.001 56.506 8.321 2.363 -0.306 N01 Y4F 21 Y4F N1 N2 N 0 1 Y N N N N N -52.238 41.264 56.300 8.252 0.151 0.511 N1 Y4F 22 Y4F N3 N3 N 0 1 Y N N N N N -50.447 40.728 54.778 6.337 -1.142 0.458 N3 Y4F 23 Y4F N33 N4 N 0 1 Y N N N N N -42.946 41.191 50.707 -3.426 1.265 1.218 N33 Y4F 24 Y4F N35 N5 N 0 1 Y N N N N N -43.481 43.278 50.073 -2.179 2.266 2.704 N35 Y4F 25 Y4F N39 N6 N 0 1 Y N N N N N -40.126 44.041 51.507 -2.406 5.089 0.365 N39 Y4F 26 Y4F N42 N7 N 0 1 Y N N N N N -40.697 41.758 51.657 -3.547 3.208 -0.343 N42 Y4F 27 Y4F N64 N8 N 0 1 N N N N N N -41.567 45.567 50.546 -1.217 5.170 2.400 N64 Y4F 28 Y4F N7 N9 N 0 1 Y N N N N N -52.917 38.183 54.342 5.357 1.870 -0.957 N7 Y4F 29 Y4F N9 N10 N 0 1 Y N N N N N -50.912 38.722 53.506 4.341 -0.013 -0.526 N9 Y4F 30 Y4F O17 O1 O 0 1 N N N N N N -46.040 41.094 53.525 -0.985 -0.640 -2.196 O17 Y4F 31 Y4F O19 O2 O 0 1 N N N N N N -43.665 41.818 53.157 -1.934 1.592 -2.910 O19 Y4F 32 Y4F "O2'" O3 O 0 1 N N N N N N -50.139 39.988 50.712 3.071 -2.024 1.767 "O2'" Y4F 33 Y4F O20 O4 O 0 1 N N N N N N -44.274 39.341 53.071 -3.503 -0.027 -1.768 O20 Y4F 34 Y4F O23 O5 O 0 1 N N N N N N -43.710 37.065 51.823 -4.997 -2.166 -1.223 O23 Y4F 35 Y4F O26 O6 O 0 1 N N N N N N -45.885 39.612 49.069 -1.961 -2.069 1.514 O26 Y4F 36 Y4F O28 O7 O 0 1 N N N N N N -47.689 38.838 50.596 0.638 -2.361 1.176 O28 Y4F 37 Y4F O29 O8 O 0 1 N N N N N N -48.058 38.759 48.096 -1.012 -3.141 -0.567 O29 Y4F 38 Y4F O30 O9 O 0 1 N N N N N N -47.914 41.047 49.267 -0.878 -4.463 1.574 O30 Y4F 39 Y4F O31 O10 O 0 1 N N N N N N -43.167 39.139 49.641 -4.672 -0.723 1.526 O31 Y4F 40 Y4F "O4'" O11 O 0 1 N N N N N N -48.607 38.439 53.512 2.281 -0.755 -1.422 "O4'" Y4F 41 Y4F O44 O12 O 0 1 N N N N N N -44.316 40.547 55.289 -2.651 -0.443 -4.224 O44 Y4F 42 Y4F P18 P1 P 0 1 N N N N N N -44.496 40.750 53.811 -2.260 0.155 -2.781 P18 Y4F 43 Y4F P27 P2 P 0 1 N N N N N N -47.485 39.607 49.196 -0.806 -3.003 0.893 P27 Y4F 44 Y4F H4 H1 H 0 1 N N N N N N -52.023 36.971 52.858 3.313 1.657 -1.457 H4 Y4F 45 Y4F H5 H2 H 0 1 N N N N N N -49.815 37.859 51.953 3.702 -2.014 -0.602 H5 Y4F 46 Y4F H10 H3 H 0 1 N N N N N N -47.965 40.824 54.296 -0.531 0.360 -0.442 H10 Y4F 47 Y4F H11 H4 H 0 1 N N N N N N -46.707 39.725 54.957 0.486 0.769 -1.843 H11 Y4F 48 Y4F H1 H5 H 0 1 N N N N N N -50.496 42.317 56.058 8.146 -1.792 1.215 H1 Y4F 49 Y4F H6 H6 H 0 1 N N N N N N -49.539 40.838 52.519 2.800 0.005 1.411 H6 Y4F 50 Y4F H13 H7 H 0 1 N N N N N N -45.177 40.050 51.313 -2.303 -0.508 -0.141 H13 Y4F 51 Y4F H14 H8 H 0 1 N N N N N N -45.629 37.689 51.225 -3.107 -2.708 -0.544 H14 Y4F 52 Y4F H16 H9 H 0 1 N N N N N N -43.661 37.119 49.393 -5.220 -2.701 1.210 H16 Y4F 53 Y4F H17 H10 H 0 1 N N N N N N -45.985 37.556 48.716 -3.355 -2.274 3.026 H17 Y4F 54 Y4F H18 H11 H 0 1 N N N N N N -44.824 38.461 47.687 -3.190 -3.677 1.947 H18 Y4F 55 Y4F H8 H12 H 0 1 N N N N N N -47.370 40.710 51.491 0.547 -0.291 1.070 H8 Y4F 56 Y4F H20 H13 H 0 1 N N N N N N -42.210 39.364 51.472 -5.072 0.670 0.051 H20 Y4F 57 Y4F H21 H14 H 0 1 N N N N N N -44.828 41.686 49.740 -2.784 0.267 3.036 H21 Y4F 58 Y4F H9 H15 H 0 1 N N N N N N -46.604 38.493 52.881 0.697 -2.072 -1.270 H9 Y4F 59 Y4F H12 H16 H 0 1 N N N N N N -38.894 42.596 52.355 -3.462 4.974 -1.411 H12 Y4F 60 Y4F H2 H17 H 0 1 N N N N N N -54.336 40.732 57.166 7.862 3.111 -0.718 H2 Y4F 61 Y4F H3 H18 H 0 1 N N N N N N -54.878 40.009 55.806 9.258 2.440 -0.070 H3 Y4F 62 Y4F H23 H19 H 0 1 N N N N N N -40.791 46.141 50.805 -0.929 4.726 3.213 H23 Y4F 63 Y4F H22 H20 H 0 1 N N N N N N -41.704 45.619 49.557 -0.954 6.089 2.231 H22 Y4F 64 Y4F H7 H21 H 0 1 N N N N N N -51.053 40.117 50.935 4.022 -2.004 1.942 H7 Y4F 65 Y4F H15 H22 H 0 1 N N N N N N -43.969 37.002 52.735 -5.376 -3.055 -1.198 H15 Y4F 66 Y4F H19 H23 H 0 1 N N N N N N -48.525 41.231 48.563 -1.720 -4.919 1.438 H19 Y4F 67 Y4F H24 H24 H 0 1 N N N N N N -43.666 41.158 55.616 -1.947 -0.374 -4.882 H24 Y4F 68 # 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 Y4F O29 P27 DOUB N N 1 Y4F C25 O26 SING N N 2 Y4F C25 C24 SING N N 3 Y4F O26 P27 SING N N 4 Y4F P27 O30 SING N N 5 Y4F P27 O28 SING N N 6 Y4F O31 C24 SING N N 7 Y4F O31 C32 SING N N 8 Y4F C24 C22 SING N N 9 Y4F N35 C34 DOUB Y N 10 Y4F N35 C37 SING Y N 11 Y4F C34 N33 SING Y N 12 Y4F N64 C38 SING N N 13 Y4F O28 "C3'" SING N N 14 Y4F C37 C38 DOUB Y N 15 Y4F C37 C36 SING Y N 16 Y4F N33 C32 SING N N 17 Y4F N33 C36 SING Y N 18 Y4F "O2'" "C2'" SING N N 19 Y4F C38 N39 SING Y N 20 Y4F C32 C21 SING N N 21 Y4F C36 N42 DOUB Y N 22 Y4F C22 C21 SING N N 23 Y4F C22 O23 SING N N 24 Y4F N39 C40 DOUB Y N 25 Y4F C21 O20 SING N N 26 Y4F N42 C40 SING Y N 27 Y4F "C3'" "C2'" SING N N 28 Y4F "C3'" "C4'" SING N N 29 Y4F "C2'" "C1'" SING N N 30 Y4F "C1'" N9 SING N N 31 Y4F "C1'" "O4'" SING N N 32 Y4F "C4'" "O4'" SING N N 33 Y4F "C4'" C16 SING N N 34 Y4F O20 P18 SING N N 35 Y4F O19 P18 DOUB N N 36 Y4F C8 N9 SING Y N 37 Y4F C8 N7 DOUB Y N 38 Y4F N9 C4 SING Y N 39 Y4F O17 P18 SING N N 40 Y4F O17 C16 SING N N 41 Y4F P18 O44 SING N N 42 Y4F N7 C5 SING Y N 43 Y4F C4 N3 DOUB Y N 44 Y4F C4 C5 SING Y N 45 Y4F N3 C2 SING Y N 46 Y4F C5 C6 DOUB Y N 47 Y4F C2 N1 DOUB Y N 48 Y4F C6 N1 SING Y N 49 Y4F C6 N01 SING N N 50 Y4F C8 H4 SING N N 51 Y4F "C1'" H5 SING N N 52 Y4F C16 H10 SING N N 53 Y4F C16 H11 SING N N 54 Y4F C2 H1 SING N N 55 Y4F "C2'" H6 SING N N 56 Y4F C21 H13 SING N N 57 Y4F C22 H14 SING N N 58 Y4F C24 H16 SING N N 59 Y4F C25 H17 SING N N 60 Y4F C25 H18 SING N N 61 Y4F "C3'" H8 SING N N 62 Y4F C32 H20 SING N N 63 Y4F C34 H21 SING N N 64 Y4F "C4'" H9 SING N N 65 Y4F C40 H12 SING N N 66 Y4F N01 H2 SING N N 67 Y4F N01 H3 SING N N 68 Y4F N64 H23 SING N N 69 Y4F N64 H22 SING N N 70 Y4F "O2'" H7 SING N N 71 Y4F O23 H15 SING N N 72 Y4F O30 H19 SING N N 73 Y4F O44 H24 SING N N 74 # 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 Y4F SMILES ACDLabs 12.01 "Nc1ncnc2c1ncn2C1OC2COP(=O)(O)OC3C(OC(COP(=O)(O)OC2C1O)C3O)n1cnc2c(N)ncnc21" Y4F InChI InChI 1.06 "InChI=1S/C20H24N10O12P2/c21-15-9-17(25-3-23-15)29(5-27-9)19-12(32)13-8(40-19)2-38-44(35,36)42-14-11(31)7(1-37-43(33,34)41-13)39-20(14)30-6-28-10-16(22)24-4-26-18(10)30/h3-8,11-14,19-20,31-32H,1-2H2,(H,33,34)(H,35,36)(H2,21,23,25)(H2,22,24,26)/t7-,8-,11-,12-,13-,14-,19-,20-/m1/s1" Y4F InChIKey InChI 1.06 UZFVIESUDFOPOB-XPWFQUROSA-N Y4F SMILES_CANONICAL CACTVS 3.385 "Nc1ncnc2n(cnc12)[C@@H]3O[C@@H]4CO[P](O)(=O)O[C@@H]5[C@H](O)[C@@H](CO[P](O)(=O)O[C@H]4[C@H]3O)O[C@H]5n6cnc7c(N)ncnc67" Y4F SMILES CACTVS 3.385 "Nc1ncnc2n(cnc12)[CH]3O[CH]4CO[P](O)(=O)O[CH]5[CH](O)[CH](CO[P](O)(=O)O[CH]4[CH]3O)O[CH]5n6cnc7c(N)ncnc67" Y4F SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@H]4[C@H](O3)COP(=O)(O[C@@H]5[C@@H]([C@@H](COP(=O)(O4)O)O[C@H]5n6cnc7c6ncnc7N)O)O)O)N" Y4F SMILES "OpenEye OEToolkits" 2.0.7 "c1nc(c2c(n1)n(cn2)C3C(C4C(O3)COP(=O)(OC5C(C(COP(=O)(O4)O)OC5n6cnc7c6ncnc7N)O)O)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 Y4F "SYSTEMATIC NAME" ACDLabs 12.01 "(2S,5R,7R,8R,10R,12aR,14R,15R,15aS,16R)-7,14-bis(6-amino-9H-purin-9-yl)-2,10,15,16-tetrahydroxyoctahydro-2H,10H,12H-5,8-methano-2lambda~5~,10lambda~5~-furo[3,2-l][1,3,6,9,11,2,10]pentaoxadiphosphacyclotetradecine-2,10-dione" Y4F "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 "(1~{R},6~{R},8~{R},9~{R},10~{S},15~{R},17~{R},18~{R})-8,17-bis(6-aminopurin-9-yl)-3,12-bis(oxidanyl)-3,12-bis(oxidanylidene)-2,4,7,11,13,16-hexaoxa-3$l^{5},12$l^{5}-diphosphatricyclo[13.2.1.0^{6,10}]octadecane-9,18-diol" # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site Y4F "Create component" 2023-01-04 RCSB Y4F "Initial release" 2024-02-07 RCSB #