data_ZF9 # _chem_comp.id ZF9 _chem_comp.name ;adenosine 5'-hexaphosphate ; _chem_comp.type "RNA linking" _chem_comp.pdbx_type ATOMN _chem_comp.formula "C10 H19 N5 O22 P6" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2023-03-09 _chem_comp.pdbx_modified_date 2024-03-08 _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 747.121 _chem_comp.one_letter_code ? _chem_comp.three_letter_code ZF9 _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 8GGG _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 ZF9 C10 C1 C 0 1 N N N N N N -47.635 -15.767 13.637 -4.528 -2.679 0.227 C10 ZF9 1 ZF9 O17 O1 O 0 1 N N N N N N -46.848 -16.950 7.982 4.178 -3.392 -1.049 O17 ZF9 2 ZF9 C01 C2 C 0 1 N N S N N N -48.302 -18.023 14.205 -6.663 -1.849 1.288 C01 ZF9 3 ZF9 C02 C3 C 0 1 N N R N N N -47.560 -18.193 15.463 -7.356 -0.473 1.168 C02 ZF9 4 ZF9 C03 C4 C 0 1 N N R N N N -46.107 -18.166 15.094 -6.201 0.501 0.845 C03 ZF9 5 ZF9 C04 C5 C 0 1 Y N N N N N -45.715 -16.135 16.363 -6.498 1.488 -1.458 C04 ZF9 6 ZF9 C05 C6 C 0 1 Y N N N N N -44.292 -16.891 17.847 -7.522 3.348 -1.015 C05 ZF9 7 ZF9 C06 C7 C 0 1 Y N N N N N -44.630 -17.974 16.994 -7.290 2.695 0.208 C06 ZF9 8 ZF9 C07 C8 C 0 1 Y N N N N N -43.304 -19.335 18.121 -8.306 4.438 1.309 C07 ZF9 9 ZF9 C08 C9 C 0 1 Y N N N N N -43.421 -17.174 18.846 -8.177 4.590 -0.990 C08 ZF9 10 ZF9 C09 C10 C 0 1 N N R N N N -47.385 -17.220 13.345 -5.172 -1.543 1.025 C09 ZF9 11 ZF9 N01 N1 N 0 1 Y N N N N N -45.471 -17.417 16.132 -6.647 1.525 -0.104 N01 ZF9 12 ZF9 N02 N2 N 0 1 Y N N N N N -45.008 -15.690 17.421 -7.010 2.560 -1.990 N02 ZF9 13 ZF9 N03 N3 N 0 1 Y N N N N N -44.156 -19.212 17.084 -7.695 3.272 1.335 N03 ZF9 14 ZF9 N04 N4 N 0 1 Y N N N N N -42.927 -18.386 18.993 -8.545 5.089 0.186 N04 ZF9 15 ZF9 N05 N5 N 0 1 N N N N N N -43.020 -16.125 19.762 -8.433 5.279 -2.163 N05 ZF9 16 ZF9 O01 O2 O 0 1 N N N N N N -48.576 -19.309 13.638 -6.843 -2.386 2.600 O01 ZF9 17 ZF9 O02 O3 O 0 1 N N N N N N -46.031 -17.587 13.750 -5.176 -0.324 0.250 O02 ZF9 18 ZF9 O03 O4 O 0 1 N N N N N N -47.921 -19.422 16.113 -7.981 -0.117 2.402 O03 ZF9 19 ZF9 O04 O5 O 0 1 N N N N N N -47.359 -14.978 12.514 -3.141 -2.397 0.031 O04 ZF9 20 ZF9 O05 O6 O 0 1 N N N N N N -47.956 -13.037 10.727 -0.646 -2.816 -0.683 O05 ZF9 21 ZF9 O06 O7 O 0 1 N N N N N N -48.279 -15.488 9.544 1.933 -2.582 -0.227 O06 ZF9 22 ZF9 O07 O8 O 0 1 N N N N N N -46.435 -17.168 10.503 4.170 -1.441 0.553 O07 ZF9 23 ZF9 O08 O9 O 0 1 N N N N N N -44.130 -16.883 9.169 5.707 0.683 0.745 O08 ZF9 24 ZF9 O09 O10 O 0 1 N N N N N N -42.647 -14.634 8.464 6.100 3.259 0.397 O09 ZF9 25 ZF9 O10 O11 O 0 1 N N N N N N -43.783 -12.351 7.870 7.952 4.931 0.012 O10 ZF9 26 ZF9 O11 O12 O 0 1 N N N N N N -42.763 -12.415 9.875 6.223 4.682 -1.810 O11 ZF9 27 ZF9 O12 O13 O 0 1 N N N N N N -41.457 -12.243 7.909 5.646 5.848 0.475 O12 ZF9 28 ZF9 O13 O14 O 0 1 N N N N N N -43.748 -14.946 10.770 7.910 1.808 1.635 O13 ZF9 29 ZF9 O14 O15 O 0 1 N N N N N N -41.969 -16.325 10.353 7.476 1.541 -0.837 O14 ZF9 30 ZF9 O15 O16 O 0 1 N N N N N N -45.166 -19.208 9.647 6.410 -1.330 -0.605 O15 ZF9 31 ZF9 O16 O17 O 0 1 N N N N N N -44.247 -18.158 11.443 6.419 -1.564 1.909 O16 ZF9 32 ZF9 O18 O18 O 0 1 N N N N N N -48.424 -18.058 9.155 3.586 -3.876 1.356 O18 ZF9 33 ZF9 O19 O19 O 0 1 N N N N N N -47.843 -13.409 8.168 0.846 -4.844 -0.499 O19 ZF9 34 ZF9 O20 O20 O 0 1 N N N N N N -46.076 -14.154 9.358 1.083 -3.420 -2.569 O20 ZF9 35 ZF9 O21 O21 O 0 1 N N N N N N -47.716 -12.518 13.243 -2.605 -3.461 -2.312 O21 ZF9 36 ZF9 O22 O22 O 0 1 N N N N N N -49.563 -13.665 12.672 -2.206 -4.733 -0.169 O22 ZF9 37 ZF9 P01 P1 P 0 1 N N N N N N -48.155 -13.541 12.296 -2.151 -3.381 -0.770 P01 ZF9 38 ZF9 P02 P2 P 0 1 N N N N N N -47.529 -14.019 9.454 0.805 -3.446 -0.984 P02 ZF9 39 ZF9 P03 P3 P 0 1 N N N N N N -47.511 -16.920 9.284 3.482 -2.835 0.132 P03 ZF9 40 ZF9 P04 P4 P 0 1 N N N N N N -44.976 -17.866 10.204 5.692 -0.922 0.623 P04 ZF9 41 ZF9 P05 P5 P 0 1 N N N N N N -43.108 -15.685 9.680 6.813 1.817 0.456 P05 ZF9 42 ZF9 P06 P6 P 0 1 N N N N N N -42.620 -12.957 8.521 6.512 4.685 -0.226 P06 ZF9 43 ZF9 H1 H1 H 0 1 N N N N N N -46.988 -15.450 14.468 -4.635 -3.615 0.776 H1 ZF9 44 ZF9 H2 H2 H 0 1 N N N N N N -48.689 -15.633 13.921 -5.021 -2.768 -0.741 H2 ZF9 45 ZF9 H3 H3 H 0 1 N N N N N N -49.234 -17.467 14.384 -7.050 -2.538 0.538 H3 ZF9 46 ZF9 H4 H4 H 0 1 N N N N N N -47.774 -17.344 16.128 -8.086 -0.483 0.359 H4 ZF9 47 ZF9 H5 H5 H 0 1 N N N N N N -45.719 -19.195 15.076 -5.831 0.967 1.759 H5 ZF9 48 ZF9 H6 H6 H 0 1 N N N N N N -46.391 -15.527 15.780 -6.023 0.689 -2.008 H6 ZF9 49 ZF9 H7 H7 H 0 1 N N N N N N -42.873 -20.314 18.268 -8.623 4.880 2.243 H7 ZF9 50 ZF9 H8 H8 H 0 1 N N N N N N -47.557 -17.437 12.280 -4.642 -1.393 1.965 H8 ZF9 51 ZF9 H9 H9 H 0 1 N N N N N N -42.374 -16.494 20.430 -8.159 4.905 -3.015 H9 ZF9 52 ZF9 H10 H10 H 0 1 N N N N N N -42.583 -15.385 19.250 -8.886 6.137 -2.133 H10 ZF9 53 ZF9 H11 H11 H 0 1 N N N N N N -49.161 -19.790 14.211 -7.767 -2.542 2.839 H11 ZF9 54 ZF9 H12 H12 H 0 1 N N N N N N -47.430 -19.509 16.921 -8.674 -0.731 2.683 H12 ZF9 55 ZF9 H13 H13 H 0 1 N N N N N N -43.533 -11.860 9.915 5.297 4.527 -2.040 H13 ZF9 56 ZF9 H14 H14 H 0 1 N N N N N N -41.772 -11.605 7.279 5.842 6.736 0.148 H14 ZF9 57 ZF9 H15 H15 H 0 1 N N N N N N -43.263 -15.085 11.575 7.545 1.982 2.513 H15 ZF9 58 ZF9 H16 H16 H 0 1 N N N N N N -44.116 -19.096 11.520 6.001 -1.338 2.751 H16 ZF9 59 ZF9 H17 H17 H 0 1 N N N N N N -48.315 -18.457 8.300 3.151 -3.576 2.166 H17 ZF9 60 ZF9 H18 H18 H 0 1 N N N N N N -45.781 -13.818 8.520 1.071 -2.534 -2.956 H18 ZF9 61 ZF9 H19 H19 H 0 1 N N N N N N -48.448 -12.257 13.790 -2.593 -2.610 -2.770 H19 ZF9 62 # 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 ZF9 O10 P06 DOUB N N 1 ZF9 O12 P06 SING N N 2 ZF9 O17 P03 DOUB N N 3 ZF9 O19 P02 DOUB N N 4 ZF9 O09 P06 SING N N 5 ZF9 O09 P05 SING N N 6 ZF9 P06 O11 SING N N 7 ZF9 O18 P03 SING N N 8 ZF9 O08 P05 SING N N 9 ZF9 O08 P04 SING N N 10 ZF9 P03 O06 SING N N 11 ZF9 P03 O07 SING N N 12 ZF9 O20 P02 SING N N 13 ZF9 P02 O06 SING N N 14 ZF9 P02 O05 SING N N 15 ZF9 O15 P04 DOUB N N 16 ZF9 P05 O14 DOUB N N 17 ZF9 P05 O13 SING N N 18 ZF9 P04 O07 SING N N 19 ZF9 P04 O16 SING N N 20 ZF9 O05 P01 SING N N 21 ZF9 P01 O04 SING N N 22 ZF9 P01 O22 DOUB N N 23 ZF9 P01 O21 SING N N 24 ZF9 O04 C10 SING N N 25 ZF9 C09 C10 SING N N 26 ZF9 C09 O02 SING N N 27 ZF9 C09 C01 SING N N 28 ZF9 O01 C01 SING N N 29 ZF9 O02 C03 SING N N 30 ZF9 C01 C02 SING N N 31 ZF9 C03 C02 SING N N 32 ZF9 C03 N01 SING N N 33 ZF9 C02 O03 SING N N 34 ZF9 N01 C04 SING Y N 35 ZF9 N01 C06 SING Y N 36 ZF9 C04 N02 DOUB Y N 37 ZF9 C06 N03 DOUB Y N 38 ZF9 C06 C05 SING Y N 39 ZF9 N03 C07 SING Y N 40 ZF9 N02 C05 SING Y N 41 ZF9 C05 C08 DOUB Y N 42 ZF9 C07 N04 DOUB Y N 43 ZF9 C08 N04 SING Y N 44 ZF9 C08 N05 SING N N 45 ZF9 C10 H1 SING N N 46 ZF9 C10 H2 SING N N 47 ZF9 C01 H3 SING N N 48 ZF9 C02 H4 SING N N 49 ZF9 C03 H5 SING N N 50 ZF9 C04 H6 SING N N 51 ZF9 C07 H7 SING N N 52 ZF9 C09 H8 SING N N 53 ZF9 N05 H9 SING N N 54 ZF9 N05 H10 SING N N 55 ZF9 O01 H11 SING N N 56 ZF9 O03 H12 SING N N 57 ZF9 O11 H13 SING N N 58 ZF9 O12 H14 SING N N 59 ZF9 O13 H15 SING N N 60 ZF9 O16 H16 SING N N 61 ZF9 O18 H17 SING N N 62 ZF9 O20 H18 SING N N 63 ZF9 O21 H19 SING N N 64 # 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 ZF9 SMILES ACDLabs 12.01 "O=P(O)(O)OP(=O)(O)OP(=O)(O)OP(=O)(O)OP(=O)(O)OP(=O)(O)OCC1OC(n2cnc3c(N)ncnc32)C(O)C1O" ZF9 InChI InChI 1.06 "InChI=1S/C10H19N5O22P6/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(32-10)1-31-39(21,22)34-41(25,26)36-43(29,30)37-42(27,28)35-40(23,24)33-38(18,19)20/h2-4,6-7,10,16-17H,1H2,(H,21,22)(H,23,24)(H,25,26)(H,27,28)(H,29,30)(H2,11,12,13)(H2,18,19,20)/t4-,6-,7-,10-/m1/s1" ZF9 InChIKey InChI 1.06 MCJDQUICRUJHMC-KQYNXXCUSA-N ZF9 SMILES_CANONICAL CACTVS 3.385 "Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P](O)(=O)O[P](O)(=O)O[P](O)(=O)O[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O" ZF9 SMILES CACTVS 3.385 "Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(=O)O[P](O)(=O)O[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]3O" ZF9 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)OP(=O)(O)OP(=O)(O)OP(=O)(O)OP(=O)(O)O)O)O)N" ZF9 SMILES "OpenEye OEToolkits" 2.0.7 "c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OP(=O)(O)OP(=O)(O)OP(=O)(O)OP(=O)(O)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 ZF9 "SYSTEMATIC NAME" ACDLabs 12.01 "5'-O-[(R)-hydroxy{[(R)-hydroxy{[(S)-hydroxy{[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]oxy}phosphoryl]oxy}phosphoryl]oxy}phosphoryl]oxy}phosphoryl]adenosine" ZF9 "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 "[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [oxidanyl-[oxidanyl-[oxidanyl(phosphonooxy)phosphoryl]oxy-phosphoryl]oxy-phosphoryl] 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 ZF9 "Create component" 2023-03-09 RCSB ZF9 "Initial release" 2024-03-13 RCSB #