data_D4F # _chem_comp.id D4F _chem_comp.name "[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] (4S)-2-(6-oxidanyl-1,3-benzothiazol-2-yl)-4,5-dihydro-1,3-thiazole-4-carboxylate" _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C21 H20 N7 O9 P S2" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms "Luciferyl adenylate" _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2019-06-25 _chem_comp.pdbx_modified_date 2021-03-01 _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 609.529 _chem_comp.one_letter_code ? _chem_comp.three_letter_code D4F _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 6K4D _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site PDBJ # # 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 D4F C13 C1 C 0 1 Y N N -22.827 -30.269 28.625 9.501 -2.864 1.652 C13 D4F 1 D4F C24 C2 C 0 1 N N R -22.911 -33.315 16.442 -4.208 1.902 0.449 C24 D4F 2 D4F C26 C3 C 0 1 N N R -24.107 -35.248 16.851 -6.531 1.436 1.014 C26 D4F 3 D4F C1 C4 C 0 1 N N N -22.261 -28.130 20.149 3.186 1.628 -2.353 C01 D4F 4 D4F C2 C5 C 0 1 N N S -21.308 -29.343 20.312 2.829 0.435 -1.452 C02 D4F 5 D4F C4 C6 C 0 1 N N N -22.448 -29.550 22.284 5.173 0.312 -1.168 C04 D4F 6 D4F C6 C7 C 0 1 Y N N -22.576 -29.726 23.865 6.456 -0.214 -0.657 C06 D4F 7 D4F C8 C8 C 0 1 Y N N -22.739 -29.834 26.196 7.804 -1.584 0.518 C08 D4F 8 D4F C9 C9 C 0 1 Y N N -22.506 -31.215 26.034 8.807 -0.774 -0.033 C09 D4F 9 D4F C11 C10 C 0 1 Y N N -22.398 -32.152 27.129 10.148 -1.018 0.257 C11 D4F 10 D4F C12 C11 C 0 1 Y N N -22.609 -31.675 28.432 10.494 -2.059 1.096 C12 D4F 11 D4F C14 C12 C 0 1 Y N N -22.890 -29.373 27.553 8.190 -2.642 1.374 C14 D4F 12 D4F C16 C13 C 0 1 N N N -21.128 -30.027 18.917 1.936 0.910 -0.335 C16 D4F 13 D4F C23 C14 C 0 1 N N N -22.749 -31.758 16.534 -2.864 1.954 1.178 C23 D4F 14 D4F C25 C15 C 0 1 N N S -24.377 -33.712 16.581 -5.348 2.355 1.389 C25 D4F 15 D4F C27 C16 C 0 1 N N R -22.777 -35.234 17.714 -5.967 0.536 -0.108 C27 D4F 16 D4F C30 C17 C 0 1 Y N N -22.968 -34.171 20.143 -5.893 -1.871 0.648 C30 D4F 17 D4F C32 C18 C 0 1 Y N N -23.613 -35.950 21.279 -7.772 -2.634 -0.119 C32 D4F 18 D4F C33 C19 C 0 1 Y N N -23.480 -36.357 19.926 -7.690 -1.280 -0.485 C33 D4F 19 D4F C35 C20 C 0 1 Y N N -24.111 -38.491 20.458 -9.740 -1.451 -1.509 C35 D4F 20 D4F C37 C21 C 0 1 Y N N -24.011 -36.936 22.263 -8.912 -3.358 -0.507 C37 D4F 21 D4F N3 N1 N 0 1 N N N -22.025 -30.298 21.304 4.015 -0.168 -0.887 N03 D4F 22 D4F N7 N2 N 0 1 Y N N -22.724 -28.985 24.965 6.575 -1.222 0.138 N07 D4F 23 D4F N29 N3 N 0 1 Y N N -23.090 -35.224 19.194 -6.496 -0.825 0.015 N29 D4F 24 D4F N31 N4 N 0 1 Y N N -23.251 -34.591 21.381 -6.641 -2.932 0.565 N31 D4F 25 D4F N34 N5 N 0 1 Y N N -23.748 -37.634 19.489 -8.688 -0.735 -1.173 N34 D4F 26 D4F N36 N6 N 0 1 Y N N -24.275 -38.213 21.802 -9.860 -2.727 -1.193 N36 D4F 27 D4F N38 N7 N 0 1 N N N -24.166 -36.597 23.604 -9.044 -4.697 -0.184 N38 D4F 28 D4F O15 O1 O 0 1 N N N -22.580 -32.470 29.548 11.802 -2.298 1.380 O15 D4F 29 D4F O17 O2 O 0 1 N N N -20.832 -31.209 19.003 2.400 1.123 0.761 O17 D4F 30 D4F O18 O3 O 0 1 N N N -21.244 -29.421 18.059 0.626 1.098 -0.556 O18 D4F 31 D4F O20 O4 O 0 1 N N N -19.415 -29.916 16.135 0.214 3.084 1.117 O20 D4F 32 D4F O21 O5 O 0 1 N N N -21.756 -29.041 15.666 -0.085 0.682 1.830 O21 D4F 33 D4F O22 O6 O 0 1 N N N -21.408 -31.554 16.361 -1.812 1.645 0.262 O22 D4F 34 D4F O28 O7 O 0 1 N N N -22.172 -34.015 17.466 -4.538 0.540 0.100 O28 D4F 35 D4F O39 O8 O 0 1 N N N -23.823 -35.903 15.683 -7.634 2.206 0.531 O39 D4F 36 D4F O40 O9 O 0 1 N N N -25.014 -33.343 15.419 -5.681 3.724 1.148 O40 D4F 37 D4F P19 P1 P 0 1 N N N -20.843 -29.902 16.387 -0.260 1.607 0.688 P19 D4F 38 D4F S5 S1 S 0 1 N N N -22.665 -27.906 21.916 5.005 1.693 -2.259 S05 D4F 39 D4F S10 S2 S 0 1 Y N N -22.381 -31.458 24.244 8.039 0.446 -1.045 S10 D4F 40 D4F H1 H1 H 0 1 N N N -22.946 -29.891 29.630 9.778 -3.677 2.307 H1 D4F 41 D4F H2 H2 H 0 1 N N N -22.557 -33.634 15.451 -4.180 2.528 -0.442 H2 D4F 42 D4F H3 H3 H 0 1 N N N -24.935 -35.692 17.424 -6.834 0.834 1.871 H3 D4F 43 D4F H4 H4 H 0 1 N N N -21.753 -27.253 19.721 2.860 1.447 -3.377 H4 D4F 44 D4F H5 H5 H 0 1 N N N -23.147 -28.372 19.544 2.748 2.547 -1.966 H5 D4F 45 D4F H6 H6 H 0 1 N N N -20.335 -29.023 20.714 2.295 -0.310 -2.041 H6 D4F 46 D4F H8 H8 H 0 1 N N N -22.162 -33.190 26.950 10.916 -0.391 -0.170 H8 D4F 47 D4F H9 H9 H 0 1 N N N -23.054 -28.323 27.744 7.435 -3.279 1.811 H9 D4F 48 D4F H10 H10 H 0 1 N N N -23.077 -31.388 17.517 -2.710 2.954 1.584 H10 D4F 49 D4F H11 H11 H 0 1 N N N -23.326 -31.257 15.742 -2.863 1.228 1.991 H11 D4F 50 D4F H12 H12 H 0 1 N N N -24.819 -33.249 17.476 -5.065 2.208 2.431 H12 D4F 51 D4F H13 H13 H 0 1 N N N -22.145 -36.094 17.448 -6.211 0.950 -1.086 H13 D4F 52 D4F H14 H14 H 0 1 N N N -22.683 -33.159 19.895 -4.933 -1.826 1.141 H14 D4F 53 D4F H15 H15 H 0 1 N N N -24.295 -39.510 20.153 -10.535 -0.977 -2.067 H15 D4F 54 D4F H18 H18 H 0 1 N N N -24.479 -37.397 24.116 -8.345 -5.147 0.316 H18 D4F 55 D4F H19 H19 H 0 1 N N N -23.290 -36.287 23.973 -9.836 -5.186 -0.458 H19 D4F 56 D4F H20 H20 H 0 1 N N N -22.748 -31.941 30.319 12.128 -1.824 2.157 H20 D4F 57 D4F H21 H21 H 0 1 N N N -19.208 -29.291 15.450 0.127 3.744 0.415 H21 D4F 58 D4F H22 H22 H 0 1 N N N -23.664 -36.822 15.865 -8.027 2.789 1.194 H22 D4F 59 D4F H23 H23 H 0 1 N N N -25.933 -33.577 15.473 -6.391 4.061 1.711 H23 D4F 60 # # 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 D4F O40 C25 SING N N 1 D4F O21 P19 DOUB N N 2 D4F O39 C26 SING N N 3 D4F O20 P19 SING N N 4 D4F O22 P19 SING N N 5 D4F O22 C23 SING N N 6 D4F P19 O18 SING N N 7 D4F C24 C23 SING N N 8 D4F C24 C25 SING N N 9 D4F C24 O28 SING N N 10 D4F C25 C26 SING N N 11 D4F C26 C27 SING N N 12 D4F O28 C27 SING N N 13 D4F C27 N29 SING N N 14 D4F O18 C16 SING N N 15 D4F C16 O17 DOUB N N 16 D4F C16 C2 SING N N 17 D4F N29 C33 SING Y N 18 D4F N29 C30 SING Y N 19 D4F N34 C33 DOUB Y N 20 D4F N34 C35 SING Y N 21 D4F C33 C32 SING Y N 22 D4F C30 N31 DOUB Y N 23 D4F C1 C2 SING N N 24 D4F C1 S5 SING N N 25 D4F C2 N3 SING N N 26 D4F C35 N36 DOUB Y N 27 D4F C32 N31 SING Y N 28 D4F C32 C37 DOUB Y N 29 D4F N3 C4 DOUB N N 30 D4F N36 C37 SING Y N 31 D4F S5 C4 SING N N 32 D4F C37 N38 SING N N 33 D4F C4 C6 SING N N 34 D4F C6 S10 SING Y N 35 D4F C6 N7 DOUB Y N 36 D4F S10 C9 SING Y N 37 D4F N7 C8 SING Y N 38 D4F C9 C8 DOUB Y N 39 D4F C9 C11 SING Y N 40 D4F C8 C14 SING Y N 41 D4F C11 C12 DOUB Y N 42 D4F C14 C13 DOUB Y N 43 D4F C12 C13 SING Y N 44 D4F C12 O15 SING N N 45 D4F C13 H1 SING N N 46 D4F C24 H2 SING N N 47 D4F C26 H3 SING N N 48 D4F C1 H4 SING N N 49 D4F C1 H5 SING N N 50 D4F C2 H6 SING N N 51 D4F C11 H8 SING N N 52 D4F C14 H9 SING N N 53 D4F C23 H10 SING N N 54 D4F C23 H11 SING N N 55 D4F C25 H12 SING N N 56 D4F C27 H13 SING N N 57 D4F C30 H14 SING N N 58 D4F C35 H15 SING N N 59 D4F N38 H18 SING N N 60 D4F N38 H19 SING N N 61 D4F O15 H20 SING N N 62 D4F O20 H21 SING N N 63 D4F O39 H22 SING N N 64 D4F O40 H23 SING N N 65 # # 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 D4F InChI InChI 1.03 "InChI=1S/C21H20N7O9PS2/c22-16-13-17(24-6-23-16)28(7-25-13)20-15(31)14(30)11(36-20)4-35-38(33,34)37-21(32)10-5-39-18(27-10)19-26-9-2-1-8(29)3-12(9)40-19/h1-3,6-7,10-11,14-15,20,29-31H,4-5H2,(H,33,34)(H2,22,23,24)/t10-,11-,14-,15-,20-/m1/s1" D4F InChIKey InChI 1.03 DVLIEEOCYVGZDS-RIWZETFMSA-N D4F SMILES_CANONICAL CACTVS 3.385 "Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P](O)(=O)OC(=O)[C@H]4CSC(=N4)c5sc6cc(O)ccc6n5)[C@@H](O)[C@H]3O" D4F SMILES CACTVS 3.385 "Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)OC(=O)[CH]4CSC(=N4)c5sc6cc(O)ccc6n5)[CH](O)[CH]3O" D4F SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "c1cc2c(cc1O)sc(n2)C3=N[C@H](CS3)C(=O)OP(=O)(O)OC[C@@H]4[C@H]([C@H]([C@@H](O4)n5cnc6c5ncnc6N)O)O" D4F SMILES "OpenEye OEToolkits" 2.0.7 "c1cc2c(cc1O)sc(n2)C3=NC(CS3)C(=O)OP(=O)(O)OCC4C(C(C(O4)n5cnc6c5ncnc6N)O)O" # _pdbx_chem_comp_identifier.comp_id D4F _pdbx_chem_comp_identifier.type "SYSTEMATIC NAME" _pdbx_chem_comp_identifier.program "OpenEye OEToolkits" _pdbx_chem_comp_identifier.program_version 2.0.7 _pdbx_chem_comp_identifier.identifier "[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] (4~{S})-2-(6-oxidanyl-1,3-benzothiazol-2-yl)-4,5-dihydro-1,3-thiazole-4-carboxylate" # # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site D4F "Create component" 2019-06-25 PDBJ D4F "Initial release" 2020-05-27 RCSB D4F "Modify synonyms" 2021-03-01 PDBE # _pdbx_chem_comp_synonyms.ordinal 1 _pdbx_chem_comp_synonyms.comp_id D4F _pdbx_chem_comp_synonyms.name "Luciferyl adenylate" _pdbx_chem_comp_synonyms.provenance ? _pdbx_chem_comp_synonyms.type ? ##