data_B5M # _chem_comp.id B5M _chem_comp.name "9-(5-O-{(S)-hydroxy[(2-hydroxy-6-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 B5M _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 5WM4 _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 B5M C13 C1 C 0 1 N N S -13.551 59.740 1.154 1.326 1.723 -0.754 C13 B5M 1 B5M C20 C2 C 0 1 Y N N -8.405 57.161 2.277 -6.127 -1.231 -1.200 C20 B5M 2 B5M C21 C3 C 0 1 Y N N -7.233 56.690 1.646 -6.918 -2.349 -1.349 C21 B5M 3 B5M C22 C4 C 0 1 Y N N -7.221 55.442 1.040 -7.137 -3.199 -0.277 C22 B5M 4 B5M C24 C5 C 0 1 Y N N -9.551 55.132 1.696 -5.762 -1.817 1.119 C24 B5M 5 B5M C26 C6 C 0 1 N N N -8.276 58.584 2.913 -5.898 -0.307 -2.368 C26 B5M 6 B5M C02 C7 C 0 1 Y N N -8.421 63.741 1.214 6.481 -2.762 -0.102 C02 B5M 7 B5M C03 C8 C 0 1 Y N N -9.437 62.742 1.354 5.276 -2.071 -0.313 C03 B5M 8 B5M C05 C9 C 0 1 Y N N -10.638 60.943 1.582 3.313 -1.332 -0.862 C05 B5M 9 B5M C07 C10 C 0 1 Y N N -10.700 63.125 1.419 5.122 -0.808 0.284 C07 B5M 10 B5M C09 C11 C 0 1 Y N N -10.035 65.320 1.208 7.225 -1.000 1.191 C09 B5M 11 B5M C11 C12 C 0 1 N N R -12.939 61.924 1.664 3.260 0.907 0.301 C11 B5M 12 B5M C14 C13 C 0 1 N N N -14.576 58.821 1.849 -0.011 2.305 -0.291 C14 B5M 13 B5M C18 C14 C 0 1 N N N -10.913 56.831 2.983 -4.699 0.246 0.207 C18 B5M 14 B5M C19 C15 C 0 1 Y N N -9.590 56.394 2.319 -5.542 -0.952 0.038 C19 B5M 15 B5M C23 C16 C 0 1 Y N N -8.388 54.658 1.069 -6.566 -2.935 0.952 C23 B5M 16 B5M C30 C17 C 0 1 N N S -14.071 60.643 -0.008 2.395 2.841 -0.850 C30 B5M 17 B5M C32 C18 C 0 1 N N R -14.067 61.893 0.476 3.700 2.016 -0.678 C32 B5M 18 B5M N01 N1 N 0 1 N N N -7.030 63.326 1.144 6.690 -4.009 -0.665 N01 B5M 19 B5M N04 N2 N 0 1 Y N N -9.378 61.388 1.454 4.136 -2.330 -0.998 N04 B5M 20 B5M N06 N3 N 0 1 Y N N -11.461 61.963 1.564 3.875 -0.367 -0.080 N06 B5M 21 B5M N08 N4 N 0 1 Y N N -10.972 64.433 1.345 6.113 -0.317 1.020 N08 B5M 22 B5M N10 N5 N 0 1 Y N N -8.760 64.965 1.140 7.418 -2.188 0.646 N10 B5M 23 B5M O12 O1 O 0 1 N N N -12.952 60.727 2.219 1.834 0.801 0.223 O12 B5M 24 B5M O15 O2 O 0 1 N N N -14.019 57.580 1.709 -0.995 1.269 -0.257 O15 B5M 25 B5M O17 O3 O 0 1 N N N -12.035 56.002 2.809 -3.373 0.174 -0.020 O17 B5M 26 B5M O25 O4 O 0 1 N N N -10.693 54.299 1.705 -5.200 -1.557 2.326 O25 B5M 27 B5M O27 O5 O 0 1 N N N -11.050 57.846 3.631 -5.201 1.298 0.551 O27 B5M 28 B5M O28 O6 O 0 1 N N N -14.571 55.473 2.778 -3.102 2.604 -0.643 O28 B5M 29 B5M O29 O7 O 0 1 N N N -13.885 57.292 4.300 -2.566 1.955 1.736 O29 B5M 30 B5M O31 O8 O 0 1 N N N -15.290 60.220 -0.583 2.243 3.790 0.207 O31 B5M 31 B5M O33 O9 O 0 1 N N N -15.288 62.338 0.926 4.736 2.817 -0.108 O33 B5M 32 B5M P16 P1 P 0 1 N N N -13.658 56.610 2.945 -2.522 1.524 0.186 P16 B5M 33 B5M H1 H1 H 0 1 N N N -12.732 59.117 0.766 1.209 1.226 -1.717 H1 B5M 34 B5M H2 H2 H 0 1 N N N -6.344 57.303 1.635 -7.369 -2.565 -2.307 H2 B5M 35 B5M H3 H3 H 0 1 N N N -6.328 55.078 0.553 -7.759 -4.073 -0.403 H3 B5M 36 B5M H4 H4 H 0 1 N N N -8.554 59.345 2.169 -5.014 -0.629 -2.918 H4 B5M 37 B5M H5 H5 H 0 1 N N N -8.946 58.659 3.783 -6.765 -0.333 -3.028 H5 B5M 38 B5M H6 H6 H 0 1 N N N -7.237 58.749 3.235 -5.749 0.709 -2.004 H6 B5M 39 B5M H7 H7 H 0 1 N N N -10.928 59.908 1.684 2.329 -1.276 -1.304 H7 B5M 40 B5M H8 H8 H 0 1 N N N -10.299 66.366 1.148 8.011 -0.572 1.795 H8 B5M 41 B5M H9 H9 H 0 1 N N N -13.260 62.692 2.383 3.557 1.171 1.316 H9 B5M 42 B5M H10 H10 H 0 1 N N N -14.689 59.086 2.910 0.104 2.730 0.707 H10 B5M 43 B5M H11 H11 H 0 1 N N N -15.556 58.873 1.351 -0.327 3.085 -0.984 H11 B5M 44 B5M H12 H12 H 0 1 N N N -8.389 53.683 0.605 -6.742 -3.602 1.783 H12 B5M 45 B5M H13 H13 H 0 1 N N N -13.304 60.579 -0.794 2.365 3.331 -1.823 H13 B5M 46 B5M H14 H14 H 0 1 N N N -13.702 62.582 -0.299 4.019 1.593 -1.631 H14 B5M 47 B5M H15 H15 H 0 1 N N N -6.447 64.131 1.035 6.001 -4.416 -1.212 H15 B5M 48 B5M H16 H16 H 0 1 N N N -6.783 62.846 1.986 7.527 -4.476 -0.511 H16 B5M 49 B5M H17 H17 H 0 1 N N N -11.403 54.739 2.158 -5.749 -1.013 2.907 H17 B5M 50 B5M H18 H18 H 0 1 N N N -14.577 56.842 4.770 -2.201 1.293 2.339 H18 B5M 51 B5M H19 H19 H 0 1 N N N -15.200 59.328 -0.897 2.952 4.446 0.252 H19 B5M 52 B5M H20 H20 H 0 1 N N N -15.202 63.226 1.251 4.986 3.580 -0.647 H20 B5M 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 B5M O31 C30 SING N N 1 B5M C30 C32 SING N N 2 B5M C30 C13 SING N N 3 B5M C32 O33 SING N N 4 B5M C32 C11 SING N N 5 B5M C22 C23 DOUB Y N 6 B5M C22 C21 SING Y N 7 B5M C23 C24 SING Y N 8 B5M N10 C09 DOUB Y N 9 B5M N10 C02 SING Y N 10 B5M N01 C02 SING N N 11 B5M C13 C14 SING N N 12 B5M C13 O12 SING N N 13 B5M C09 N08 SING Y N 14 B5M C02 C03 DOUB Y N 15 B5M N08 C07 DOUB Y N 16 B5M C03 C07 SING Y N 17 B5M C03 N04 SING Y N 18 B5M C07 N06 SING Y N 19 B5M N04 C05 DOUB Y N 20 B5M N06 C05 SING Y N 21 B5M N06 C11 SING N N 22 B5M C21 C20 DOUB Y N 23 B5M C11 O12 SING N N 24 B5M C24 O25 SING N N 25 B5M C24 C19 DOUB Y N 26 B5M O15 C14 SING N N 27 B5M O15 P16 SING N N 28 B5M C20 C19 SING Y N 29 B5M C20 C26 SING N N 30 B5M C19 C18 SING N N 31 B5M O28 P16 DOUB N N 32 B5M O17 P16 SING N N 33 B5M O17 C18 SING N N 34 B5M P16 O29 SING N N 35 B5M C18 O27 DOUB N N 36 B5M C13 H1 SING N N 37 B5M C21 H2 SING N N 38 B5M C22 H3 SING N N 39 B5M C26 H4 SING N N 40 B5M C26 H5 SING N N 41 B5M C26 H6 SING N N 42 B5M C05 H7 SING N N 43 B5M C09 H8 SING N N 44 B5M C11 H9 SING N N 45 B5M C14 H10 SING N N 46 B5M C14 H11 SING N N 47 B5M C23 H12 SING N N 48 B5M C30 H13 SING N N 49 B5M C32 H14 SING N N 50 B5M N01 H15 SING N N 51 B5M N01 H16 SING N N 52 B5M O25 H17 SING N N 53 B5M O29 H18 SING N N 54 B5M O31 H19 SING N N 55 B5M 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 B5M SMILES ACDLabs 12.01 "C2(COP(OC(=O)c1c(C)cccc1O)(=O)O)OC(C(C2O)O)n4cnc3c(N)ncnc34" B5M InChI InChI 1.03 "InChI=1S/C18H20N5O9P/c1-8-3-2-4-9(24)11(8)18(27)32-33(28,29)30-5-10-13(25)14(26)17(31-10)23-7-22-12-15(19)20-6-21-16(12)23/h2-4,6-7,10,13-14,17,24-26H,5H2,1H3,(H,28,29)(H2,19,20,21)/t10-,13+,14+,17+/m0/s1" B5M InChIKey InChI 1.03 YIFBGYAAIZMTKM-NBCLGQJJSA-N B5M SMILES_CANONICAL CACTVS 3.385 "Cc1cccc(O)c1C(=O)O[P](O)(=O)OC[C@@H]2O[C@H]([C@H](O)[C@@H]2O)n3cnc4c(N)ncnc34" B5M SMILES CACTVS 3.385 "Cc1cccc(O)c1C(=O)O[P](O)(=O)OC[CH]2O[CH]([CH](O)[CH]2O)n3cnc4c(N)ncnc34" B5M SMILES_CANONICAL "OpenEye OEToolkits" 2.0.6 "Cc1cccc(c1C(=O)OP(=O)(O)OC[C@H]2[C@H]([C@H]([C@@H](O2)n3cnc4c3ncnc4N)O)O)O" B5M SMILES "OpenEye OEToolkits" 2.0.6 "Cc1cccc(c1C(=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 B5M "SYSTEMATIC NAME" ACDLabs 12.01 "9-(5-O-{(S)-hydroxy[(2-hydroxy-6-methylbenzene-1-carbonyl)oxy]phosphoryl}-alpha-L-lyxofuranosyl)-9H-purin-6-amine" B5M "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] 2-methyl-6-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 B5M "Create component" 2017-08-01 RCSB B5M "Initial release" 2018-05-23 RCSB #