data_KD9 # _chem_comp.id KD9 _chem_comp.name ;3'-O-(4-benzoylbenzoyl)adenosine 5'-(tetrahydrogen triphosphate) ; _chem_comp.type non-polymer _chem_comp.pdbx_type HETAIN _chem_comp.formula "C24 H24 N5 O15 P3" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2023-08-10 _chem_comp.pdbx_modified_date 2024-08-09 _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 715.393 _chem_comp.one_letter_code ? _chem_comp.three_letter_code KD9 _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 8TRJ _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 KD9 C10 C1 C 0 1 Y N N N N N 169.053 208.867 244.731 5.629 2.015 0.155 C10 KD9 1 KD9 C13 C2 C 0 1 Y N N N N N 169.934 206.397 243.860 5.463 0.974 -2.421 C13 KD9 2 KD9 C15 C3 C 0 1 N N N N N N 172.269 207.267 243.469 3.259 -0.058 -1.890 C15 KD9 3 KD9 C21 C4 C 0 1 N N R N N N 174.058 203.947 241.542 0.588 -2.766 0.168 C21 KD9 4 KD9 C22 C5 C 0 1 N N R N N N 174.431 204.961 242.755 1.378 -2.575 -1.152 C22 KD9 5 KD9 C28 C6 C 0 1 Y N N N N N 174.941 199.295 240.657 0.714 -7.525 1.325 C28 KD9 6 KD9 C01 C7 C 0 1 Y N N N N N 164.742 211.723 244.333 7.900 5.042 3.372 C01 KD9 7 KD9 C02 C8 C 0 1 Y N N N N N 164.811 210.756 243.344 6.709 4.913 2.680 C02 KD9 8 KD9 C03 C9 C 0 1 Y N N N N N 165.449 209.552 243.595 6.681 4.265 1.463 C03 KD9 9 KD9 C04 C10 C 0 1 Y N N N N N 166.016 209.313 244.837 7.859 3.737 0.930 C04 KD9 10 KD9 C05 C11 C 0 1 Y N N N N N 165.949 210.280 245.825 9.058 3.870 1.634 C05 KD9 11 KD9 C06 C12 C 0 1 Y N N N N N 165.310 211.484 245.574 9.071 4.521 2.850 C06 KD9 12 KD9 C07 C13 C 0 1 N N N N N N 166.722 207.983 245.115 7.837 3.041 -0.373 C07 KD9 13 KD9 C09 C14 C 0 1 Y N N N N N 168.175 207.798 244.685 6.655 2.243 -0.765 C09 KD9 14 KD9 C11 C15 C 0 1 Y N N N N N 170.371 208.699 244.340 4.531 1.266 -0.208 C11 KD9 15 KD9 C12 C16 C 0 1 Y N N N N N 170.813 207.461 243.904 4.440 0.741 -1.499 C12 KD9 16 KD9 C14 C17 C 0 1 Y N N N N N 168.615 206.563 244.251 6.564 1.717 -2.056 C14 KD9 17 KD9 C18 C18 C 0 1 N N S N N N 173.987 206.102 242.379 1.143 -1.075 -1.455 C18 KD9 18 KD9 C19 C19 C 0 1 N N R N N N 174.208 206.094 240.840 -0.122 -0.720 -0.650 C19 KD9 19 KD9 C25 C20 C 0 1 Y N N N N N 176.084 202.607 241.067 -1.004 -4.715 -0.023 C25 KD9 20 KD9 C27 C21 C 0 1 Y N N N N N 175.261 200.644 240.841 0.168 -6.330 0.826 C27 KD9 21 KD9 C30 C22 C 0 1 Y N N N N N 172.738 199.772 241.016 2.652 -6.383 1.843 C30 KD9 22 KD9 C32 C23 C 0 1 Y N N N N N 174.236 201.514 241.114 0.958 -5.168 0.876 C32 KD9 23 KD9 C34 C24 C 0 1 N N N N N N 175.534 206.774 240.528 -1.207 -0.193 -1.592 C34 KD9 24 KD9 N24 N1 N 0 1 Y N N N N N 174.786 202.728 241.248 0.192 -4.167 0.334 N24 KD9 25 KD9 N26 N2 N 0 1 Y N N N N N 176.395 201.354 240.817 -1.016 -5.984 0.267 N26 KD9 26 KD9 N29 N3 N 0 1 Y N N N N N 173.687 198.895 240.750 1.948 -7.501 1.817 N29 KD9 27 KD9 N31 N4 N 0 1 Y N N N N N 172.983 201.052 241.196 2.182 -5.241 1.388 N31 KD9 28 KD9 N33 N5 N 0 1 N N N N N N 175.997 198.355 240.373 -0.018 -8.699 1.307 N33 KD9 29 KD9 O08 O1 O 0 1 N N N N N N 166.142 207.100 245.650 8.790 3.123 -1.122 O08 KD9 30 KD9 O16 O2 O 0 1 N N N N N N 173.104 208.020 243.830 3.178 -0.511 -3.014 O16 KD9 31 KD9 O17 O3 O 0 1 N N N N N N 172.616 206.198 242.637 2.273 -0.282 -1.001 O17 KD9 32 KD9 O20 O4 O 0 1 N N N N N N 174.256 204.618 240.440 -0.572 -1.925 -0.008 O20 KD9 33 KD9 O23 O5 O 0 1 N N N N N N 173.806 204.539 243.925 2.767 -2.845 -0.959 O23 KD9 34 KD9 O35 O6 O 0 1 N N N N N N 176.534 205.807 240.428 -2.332 0.242 -0.827 O35 KD9 35 KD9 O37 O7 O 0 1 N N N N N N 178.322 207.624 240.738 -4.389 -0.275 -2.381 O37 KD9 36 KD9 O38 O8 O 0 1 N N N N N N 179.045 205.314 240.312 -3.297 2.000 -2.359 O38 KD9 37 KD9 O39 O9 O 0 1 N N N N N N 178.082 205.890 242.623 -4.663 1.356 -0.337 O39 KD9 38 KD9 O41 O10 O 0 1 N N N N N N 177.083 208.134 243.414 -6.855 1.944 -1.440 O41 KD9 39 KD9 O42 O11 O 0 1 N N N N N N 179.436 207.649 243.932 -5.509 3.842 -0.461 O42 KD9 40 KD9 O43 O12 O 0 1 N N N N N N 177.611 206.391 245.215 -6.749 2.106 1.077 O43 KD9 41 KD9 O45 O13 O 0 1 N N N N N N 178.347 203.983 244.636 -9.208 1.937 0.534 O45 KD9 42 KD9 O46 O14 O 0 1 N N N N N N 175.981 204.395 245.158 -8.534 1.631 2.947 O46 KD9 43 KD9 O47 O15 O 0 1 N N N N N N 177.669 204.498 246.932 -8.441 3.989 1.788 O47 KD9 44 KD9 P36 P1 P 0 1 N N N N N N 178.025 206.175 241.008 -3.662 0.856 -1.495 P36 KD9 45 KD9 P40 P2 P 0 1 N N N N N N 178.063 207.055 243.782 -5.964 2.304 -0.315 P40 KD9 46 KD9 P44 P3 P 0 1 N N N N N N 177.397 204.784 245.482 -8.254 2.405 1.564 P44 KD9 47 KD9 H101 H1 H 0 0 N N N N N N 168.710 209.833 245.072 5.699 2.421 1.153 H101 KD9 48 KD9 H131 H2 H 0 0 N N N N N N 170.276 205.431 243.519 5.390 0.571 -3.420 H131 KD9 49 KD9 H1 H3 H 0 1 N N N N N N 172.993 203.698 241.659 1.179 -2.432 1.021 H1 KD9 50 KD9 H2 H4 H 0 1 N N N N N N 175.525 204.951 242.873 0.968 -3.201 -1.944 H2 KD9 51 KD9 H011 H5 H 0 0 N N N N N N 164.246 212.662 244.137 7.917 5.554 4.323 H011 KD9 52 KD9 H021 H6 H 0 0 N N N N N N 164.367 210.940 242.377 5.799 5.321 3.094 H021 KD9 53 KD9 H031 H7 H 0 0 N N N N N N 165.505 208.799 242.822 5.750 4.165 0.925 H031 KD9 54 KD9 H051 H8 H 0 0 N N N N N N 166.395 210.096 246.791 9.973 3.464 1.227 H051 KD9 55 KD9 H061 H9 H 0 0 N N N N N N 165.255 212.237 246.347 9.998 4.629 3.393 H061 KD9 56 KD9 H111 H10 H 0 0 N N N N N N 171.055 209.534 244.375 3.740 1.086 0.505 H111 KD9 57 KD9 H141 H11 H 0 0 N N N N N N 167.932 205.727 244.216 7.355 1.896 -2.769 H141 KD9 58 KD9 H3 H12 H 0 1 N N N N N N 174.536 206.949 242.816 0.976 -0.923 -2.521 H3 KD9 59 KD9 H4 H13 H 0 1 N N N N N N 173.378 206.607 240.332 0.115 0.034 0.100 H4 KD9 60 KD9 H251 H14 H 0 0 N N N N N N 176.793 203.421 241.117 -1.821 -4.176 -0.479 H251 KD9 61 KD9 H301 H15 H 0 0 N N N N N N 171.718 199.425 241.089 3.651 -6.408 2.252 H301 KD9 62 KD9 H341 H16 H 0 0 N N N N N N 175.784 207.480 241.334 -0.813 0.645 -2.168 H341 KD9 63 KD9 H342 H17 H 0 0 N N N N N N 175.453 207.319 239.576 -1.515 -0.988 -2.272 H342 KD9 64 KD9 H332 H18 H 0 0 N N N N N N 175.610 197.438 240.274 0.369 -9.517 1.656 H332 KD9 65 KD9 H331 H19 H 0 0 N N N N N N 176.456 198.616 239.524 -0.918 -8.704 0.945 H331 KD9 66 KD9 H231 H20 H 0 0 N N N N N N 174.025 205.133 244.633 2.956 -3.751 -0.679 H231 KD9 67 KD9 H5 H21 H 0 1 N N N N N N 179.091 207.692 240.185 -4.657 -1.056 -1.878 H5 KD9 68 KD9 H6 H22 H 0 1 N N N N N N 179.398 208.583 243.763 -4.922 4.147 0.244 H6 KD9 69 KD9 H7 H23 H 0 1 N N N N N N 175.982 203.724 244.486 -9.424 1.766 3.300 H7 KD9 70 KD9 H8 H24 H 0 1 N N N N N N 178.381 203.874 247.004 -7.846 4.365 2.451 H8 KD9 71 # 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 KD9 O38 P36 DOUB N N 1 KD9 N33 C28 SING N N 2 KD9 O35 C34 SING N N 3 KD9 O35 P36 SING N N 4 KD9 O20 C19 SING N N 5 KD9 O20 C21 SING N N 6 KD9 C34 C19 SING N N 7 KD9 C28 N29 DOUB Y N 8 KD9 C28 C27 SING Y N 9 KD9 O37 P36 SING N N 10 KD9 N29 C30 SING Y N 11 KD9 N26 C27 SING Y N 12 KD9 N26 C25 DOUB Y N 13 KD9 C19 C18 SING N N 14 KD9 C27 C32 DOUB Y N 15 KD9 P36 O39 SING N N 16 KD9 C30 N31 DOUB Y N 17 KD9 C25 N24 SING Y N 18 KD9 C32 N31 SING Y N 19 KD9 C32 N24 SING Y N 20 KD9 N24 C21 SING N N 21 KD9 C21 C22 SING N N 22 KD9 C18 O17 SING N N 23 KD9 C18 C22 SING N N 24 KD9 O39 P40 SING N N 25 KD9 O17 C15 SING N N 26 KD9 C22 O23 SING N N 27 KD9 C02 C03 DOUB Y N 28 KD9 C02 C01 SING Y N 29 KD9 O41 P40 DOUB N N 30 KD9 C15 O16 DOUB N N 31 KD9 C15 C12 SING N N 32 KD9 C03 C04 SING Y N 33 KD9 P40 O42 SING N N 34 KD9 P40 O43 SING N N 35 KD9 C13 C12 DOUB Y N 36 KD9 C13 C14 SING Y N 37 KD9 C12 C11 SING Y N 38 KD9 C14 C09 DOUB Y N 39 KD9 C01 C06 DOUB Y N 40 KD9 C11 C10 DOUB Y N 41 KD9 O45 P44 DOUB N N 42 KD9 C09 C10 SING Y N 43 KD9 C09 C07 SING N N 44 KD9 C04 C07 SING N N 45 KD9 C04 C05 DOUB Y N 46 KD9 C07 O08 DOUB N N 47 KD9 O46 P44 SING N N 48 KD9 O43 P44 SING N N 49 KD9 P44 O47 SING N N 50 KD9 C06 C05 SING Y N 51 KD9 C10 H101 SING N N 52 KD9 C13 H131 SING N N 53 KD9 C21 H1 SING N N 54 KD9 C22 H2 SING N N 55 KD9 C01 H011 SING N N 56 KD9 C02 H021 SING N N 57 KD9 C03 H031 SING N N 58 KD9 C05 H051 SING N N 59 KD9 C06 H061 SING N N 60 KD9 C11 H111 SING N N 61 KD9 C14 H141 SING N N 62 KD9 C18 H3 SING N N 63 KD9 C19 H4 SING N N 64 KD9 C25 H251 SING N N 65 KD9 C30 H301 SING N N 66 KD9 C34 H341 SING N N 67 KD9 C34 H342 SING N N 68 KD9 N33 H332 SING N N 69 KD9 N33 H331 SING N N 70 KD9 O23 H231 SING N N 71 KD9 O37 H5 SING N N 72 KD9 O42 H6 SING N N 73 KD9 O46 H7 SING N N 74 KD9 O47 H8 SING N N 75 # 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 KD9 SMILES ACDLabs 12.01 "O=C(c1ccccc1)c1ccc(cc1)C(=O)OC1C(COP(=O)(O)OP(=O)(O)OP(=O)(O)O)OC(n2cnc3c(N)ncnc32)C1O" KD9 InChI InChI 1.06 "InChI=1S/C24H24N5O15P3/c25-21-17-22(27-11-26-21)29(12-28-17)23-19(31)20(16(41-23)10-40-46(36,37)44-47(38,39)43-45(33,34)35)42-24(32)15-8-6-14(7-9-15)18(30)13-4-2-1-3-5-13/h1-9,11-12,16,19-20,23,31H,10H2,(H,36,37)(H,38,39)(H2,25,26,27)(H2,33,34,35)/t16-,19-,20-,23-/m1/s1" KD9 InChIKey InChI 1.06 AWJJLYZBWRIBCZ-UGTJMOTHSA-N KD9 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)[C@@H](OC(=O)c4ccc(cc4)C(=O)c5ccccc5)[C@H]3O" KD9 SMILES CACTVS 3.385 "Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)[CH](OC(=O)c4ccc(cc4)C(=O)c5ccccc5)[CH]3O" KD9 SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "c1ccc(cc1)C(=O)c2ccc(cc2)C(=O)O[C@@H]3[C@H](O[C@H]([C@@H]3O)n4cnc5c4ncnc5N)COP(=O)(O)OP(=O)(O)OP(=O)(O)O" KD9 SMILES "OpenEye OEToolkits" 2.0.7 "c1ccc(cc1)C(=O)c2ccc(cc2)C(=O)OC3C(OC(C3O)n4cnc5c4ncnc5N)COP(=O)(O)OP(=O)(O)OP(=O)(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 KD9 "SYSTEMATIC NAME" ACDLabs 12.01 ;3'-O-(4-benzoylbenzoyl)adenosine 5'-(tetrahydrogen triphosphate) ; KD9 "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 "[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-4-oxidanyl-2-[[oxidanyl-[oxidanyl(phosphonooxy)phosphoryl]oxy-phosphoryl]oxymethyl]oxolan-3-yl] 4-(phenylcarbonyl)benzoate" # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site KD9 "Create component" 2023-08-10 RCSB KD9 "Initial release" 2024-08-14 RCSB #