data_B5Y # _chem_comp.id B5Y _chem_comp.name "9-(5-O-{(S)-hydroxy[(2-hydroxy-5-methylbenzene-1-carbonyl)oxy]phosphoryl}-alpha-L-lyxofuranosyl)-9H-purin-6-amine" _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C18 H20 N5 O9 P" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2017-08-01 _chem_comp.pdbx_modified_date 2018-05-18 _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 481.353 _chem_comp.one_letter_code ? _chem_comp.three_letter_code B5Y _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 5WM5 _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.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 B5Y C13 C1 C 0 1 N N S -13.535 59.194 0.919 1.404 1.718 -0.855 C13 B5Y 1 B5Y C20 C2 C 0 1 Y N N -8.933 57.027 2.510 -4.943 -2.054 -0.217 C20 B5Y 2 B5Y C21 C3 C 0 1 Y N N -7.682 56.822 1.954 -5.749 -3.168 -0.294 C21 B5Y 3 B5Y C22 C4 C 0 1 Y N N -7.368 55.617 1.346 -7.112 -3.062 -0.073 C22 B5Y 4 B5Y C24 C5 C 0 1 Y N N -9.577 54.839 1.847 -6.881 -0.707 0.315 C24 B5Y 5 B5Y C26 C6 C 0 1 N N N -6.644 57.929 2.024 -5.145 -4.510 -0.621 C26 B5Y 6 B5Y C02 C7 C 0 1 Y N N -8.376 63.347 1.100 6.501 -2.773 0.128 C02 B5Y 7 B5Y C03 C8 C 0 1 Y N N -9.331 62.285 1.234 5.304 -2.084 -0.135 C03 B5Y 8 B5Y C05 C9 C 0 1 Y N N -10.423 60.411 1.400 3.352 -1.361 -0.742 C05 B5Y 9 B5Y C07 C10 C 0 1 Y N N -10.662 62.594 1.358 5.164 -0.781 0.372 C07 B5Y 10 B5Y C09 C11 C 0 1 Y N N -10.112 64.861 1.242 7.262 -0.934 1.298 C09 B5Y 11 B5Y C11 C12 C 0 1 N N R -12.776 61.182 1.675 3.324 0.954 0.262 C11 B5Y 12 B5Y C14 C13 C 0 1 N N N -14.651 58.213 1.276 0.072 2.347 -0.440 C14 B5Y 13 B5Y C18 C14 C 0 1 N N N -11.278 56.328 3.097 -4.643 0.386 0.180 C18 B5Y 14 B5Y C19 C15 C 0 1 Y N N -9.902 56.036 2.465 -5.501 -0.810 0.091 C19 B5Y 15 B5Y C23 C16 C 0 1 Y N N -8.328 54.626 1.292 -7.678 -1.838 0.227 C23 B5Y 16 B5Y C30 C17 C 0 1 N N S -13.824 60.241 -0.219 2.487 2.813 -1.024 C30 B5Y 17 B5Y C32 C18 C 0 1 N N R -13.604 61.430 0.287 3.781 1.987 -0.790 C32 B5Y 18 B5Y N01 N1 N 0 1 N N N -6.953 63.084 0.952 6.698 -4.057 -0.349 N01 B5Y 19 B5Y N04 N2 N 0 1 Y N N -9.208 60.934 1.252 4.163 -2.377 -0.804 N04 B5Y 20 B5Y N06 N3 N 0 1 Y N N -11.340 61.402 1.440 3.924 -0.351 -0.027 N06 B5Y 21 B5Y N08 N4 N 0 1 Y N N -11.020 63.906 1.365 6.159 -0.251 1.076 N08 B5Y 22 B5Y N10 N5 N 0 1 Y N N -8.816 64.595 1.105 7.440 -2.161 0.843 N10 B5Y 23 B5Y O12 O1 O 0 1 N N N -13.242 60.056 2.144 1.897 0.860 0.186 O12 B5Y 24 B5Y O15 O2 O 0 1 N N N -14.240 57.742 2.532 -0.925 1.329 -0.338 O15 B5Y 25 B5Y O17 O3 O 0 1 N N N -12.444 55.564 2.797 -3.317 0.281 -0.036 O17 B5Y 26 B5Y O25 O4 O 0 1 N N N -10.513 53.819 1.786 -7.434 0.495 0.615 O25 B5Y 27 B5Y O27 O5 O 0 1 N N N -11.321 57.243 3.854 -5.132 1.465 0.447 O27 B5Y 28 B5Y O28 O6 O 0 1 N N N -15.016 55.402 1.953 -3.013 2.660 -0.825 O28 B5Y 29 B5Y O29 O7 O 0 1 N N N -14.532 55.935 4.304 -2.494 2.171 1.596 O29 B5Y 30 B5Y O31 O8 O 0 1 N N N -15.080 60.065 -0.823 2.343 3.836 -0.036 O31 B5Y 31 B5Y O33 O9 O 0 1 N N N -14.797 62.105 0.607 4.825 2.813 -0.272 O33 B5Y 32 B5Y P16 P1 P 0 1 N N N -14.043 56.130 2.875 -2.450 1.633 0.079 P16 B5Y 33 B5Y H1 H1 H 0 1 N N N -12.630 58.628 0.652 1.283 1.157 -1.782 H1 B5Y 34 B5Y H2 H2 H 0 1 N N N -9.157 57.971 2.985 -3.880 -2.142 -0.391 H2 B5Y 35 B5Y H3 H3 H 0 1 N N N -6.388 55.456 0.921 -7.737 -3.941 -0.135 H3 B5Y 36 B5Y H4 H4 H 0 1 N N N -6.731 58.570 1.135 -4.850 -5.010 0.301 H4 B5Y 37 B5Y H5 H5 H 0 1 N N N -6.812 58.532 2.928 -5.879 -5.121 -1.147 H5 B5Y 38 B5Y H6 H6 H 0 1 N N N -5.638 57.486 2.060 -4.269 -4.370 -1.254 H6 B5Y 39 B5Y H7 H7 H 0 1 N N N -10.642 59.356 1.476 2.370 -1.324 -1.190 H7 B5Y 40 B5Y H8 H8 H 0 1 N N N -10.434 65.892 1.253 8.052 -0.474 1.873 H8 B5Y 41 B5Y H9 H9 H 0 1 N N N -13.105 61.994 2.340 3.620 1.284 1.258 H9 B5Y 42 B5Y H10 H10 H 0 1 N N N -15.624 58.722 1.340 0.189 2.839 0.526 H10 B5Y 43 B5Y H11 H11 H 0 1 N N N -14.712 57.395 0.544 -0.232 3.081 -1.186 H11 B5Y 44 B5Y H12 H12 H 0 1 N N N -8.103 53.683 0.816 -8.741 -1.763 0.398 H12 B5Y 45 B5Y H13 H13 H 0 1 N N N -13.064 60.046 -0.990 2.466 3.235 -2.029 H13 B5Y 46 B5Y H14 H14 H 0 1 N N N -12.975 62.049 -0.369 4.098 1.494 -1.709 H14 B5Y 47 B5Y H15 H15 H 0 1 N N N -6.460 63.950 0.867 7.529 -4.521 -0.164 H15 B5Y 48 B5Y H16 H16 H 0 1 N N N -6.620 62.589 1.755 6.005 -4.492 -0.869 H16 B5Y 49 B5Y H17 H17 H 0 1 N N N -11.318 54.102 2.203 -7.722 0.999 -0.158 H17 B5Y 50 B5Y H18 H18 H 0 1 N N N -15.324 55.410 4.299 -2.139 1.548 2.245 H18 B5Y 51 B5Y H19 H19 H 0 1 N N N -15.149 59.179 -1.159 3.060 4.485 -0.034 H19 B5Y 52 B5Y H20 H20 H 0 1 N N N -14.591 62.959 0.969 5.086 3.533 -0.862 H20 B5Y 53 # 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 B5Y O31 C30 SING N N 1 B5Y C30 C32 SING N N 2 B5Y C30 C13 SING N N 3 B5Y C32 O33 SING N N 4 B5Y C32 C11 SING N N 5 B5Y C13 C14 SING N N 6 B5Y C13 O12 SING N N 7 B5Y N01 C02 SING N N 8 B5Y C02 N10 DOUB Y N 9 B5Y C02 C03 SING Y N 10 B5Y N10 C09 SING Y N 11 B5Y C03 N04 SING Y N 12 B5Y C03 C07 DOUB Y N 13 B5Y C09 N08 DOUB Y N 14 B5Y N04 C05 DOUB Y N 15 B5Y C14 O15 SING N N 16 B5Y C23 C22 DOUB Y N 17 B5Y C23 C24 SING Y N 18 B5Y C22 C21 SING Y N 19 B5Y C07 N08 SING Y N 20 B5Y C07 N06 SING Y N 21 B5Y C05 N06 SING Y N 22 B5Y N06 C11 SING N N 23 B5Y C11 O12 SING N N 24 B5Y O25 C24 SING N N 25 B5Y C24 C19 DOUB Y N 26 B5Y O28 P16 DOUB N N 27 B5Y C21 C26 SING N N 28 B5Y C21 C20 DOUB Y N 29 B5Y C19 C20 SING Y N 30 B5Y C19 C18 SING N N 31 B5Y O15 P16 SING N N 32 B5Y O17 P16 SING N N 33 B5Y O17 C18 SING N N 34 B5Y P16 O29 SING N N 35 B5Y C18 O27 DOUB N N 36 B5Y C13 H1 SING N N 37 B5Y C20 H2 SING N N 38 B5Y C22 H3 SING N N 39 B5Y C26 H4 SING N N 40 B5Y C26 H5 SING N N 41 B5Y C26 H6 SING N N 42 B5Y C05 H7 SING N N 43 B5Y C09 H8 SING N N 44 B5Y C11 H9 SING N N 45 B5Y C14 H10 SING N N 46 B5Y C14 H11 SING N N 47 B5Y C23 H12 SING N N 48 B5Y C30 H13 SING N N 49 B5Y C32 H14 SING N N 50 B5Y N01 H15 SING N N 51 B5Y N01 H16 SING N N 52 B5Y O25 H17 SING N N 53 B5Y O29 H18 SING N N 54 B5Y O31 H19 SING N N 55 B5Y O33 H20 SING N N 56 # 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 B5Y SMILES ACDLabs 12.01 "C2(COP(OC(=O)c1cc(C)ccc1O)(=O)O)OC(C(C2O)O)n4cnc3c(ncnc34)N" B5Y InChI InChI 1.03 "InChI=1S/C18H20N5O9P/c1-8-2-3-10(24)9(4-8)18(27)32-33(28,29)30-5-11-13(25)14(26)17(31-11)23-7-22-12-15(19)20-6-21-16(12)23/h2-4,6-7,11,13-14,17,24-26H,5H2,1H3,(H,28,29)(H2,19,20,21)/t11-,13+,14+,17+/m0/s1" B5Y InChIKey InChI 1.03 XBOIILKAIKTKFY-ZCTGUTNYSA-N B5Y SMILES_CANONICAL CACTVS 3.385 "Cc1ccc(O)c(c1)C(=O)O[P](O)(=O)OC[C@@H]2O[C@H]([C@H](O)[C@@H]2O)n3cnc4c(N)ncnc34" B5Y SMILES CACTVS 3.385 "Cc1ccc(O)c(c1)C(=O)O[P](O)(=O)OC[CH]2O[CH]([CH](O)[CH]2O)n3cnc4c(N)ncnc34" B5Y SMILES_CANONICAL "OpenEye OEToolkits" 2.0.6 "Cc1ccc(c(c1)C(=O)OP(=O)(O)OC[C@H]2[C@H]([C@H]([C@@H](O2)n3cnc4c3ncnc4N)O)O)O" B5Y SMILES "OpenEye OEToolkits" 2.0.6 "Cc1ccc(c(c1)C(=O)OP(=O)(O)OCC2C(C(C(O2)n3cnc4c3ncnc4N)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 B5Y "SYSTEMATIC NAME" ACDLabs 12.01 "9-(5-O-{(S)-hydroxy[(2-hydroxy-5-methylbenzene-1-carbonyl)oxy]phosphoryl}-alpha-L-lyxofuranosyl)-9H-purin-6-amine" B5Y "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.6 "[[(2~{S},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] 5-methyl-2-oxidanyl-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 B5Y "Create component" 2017-08-01 RCSB B5Y "Initial release" 2018-05-23 RCSB #