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 
# 
