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 
# 
