data_8EF
# 
_chem_comp.id                                    8EF 
_chem_comp.name                                  "2-[(5S)-3-[(4-azanyl-2-methyl-pyrimidin-5-yl)methyl]-4-methylidene-1,3-thiazolidin-5-yl]ethyl phosphono hydrogen phosphate" 
_chem_comp.type                                  NON-POLYMER 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C12 H20 N4 O7 P2 S" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2017-06-20 
_chem_comp.pdbx_modified_date                    2018-04-20 
_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                        426.322 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     ? 
_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        5XRV 
_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 
8EF "C4'" C1  C 0 1 Y N N -12.878 -32.823 -26.011 4.874  -1.090 -0.839 "C4'" 8EF 1  
8EF "C5'" C2  C 0 1 Y N N -12.984 -32.981 -27.411 4.720  -0.606 0.462  "C5'" 8EF 2  
8EF "C6'" C3  C 0 1 Y N N -11.801 -33.067 -28.113 4.297  -1.482 1.442  "C6'" 8EF 3  
8EF "N1'" N1  N 0 1 Y N N -10.584 -33.007 -27.431 4.052  -2.744 1.119  "N1'" 8EF 4  
8EF "N3'" N2  N 0 1 Y N N -11.685 -32.765 -25.381 4.608  -2.370 -1.084 "N3'" 8EF 5  
8EF O2B   O1  O 0 1 N N N -20.131 -40.433 -25.582 -6.261 -1.470 -1.258 O2B   8EF 6  
8EF PB    P1  P 0 1 N N N -18.969 -41.327 -26.155 -5.787 -0.992 0.205  PB    8EF 7  
8EF O1B   O2  O 0 1 N N N -19.184 -41.248 -27.769 -6.543 0.218  0.597  O1B   8EF 8  
8EF O3B   O3  O 0 1 N N N -18.926 -42.762 -25.800 -6.064 -2.167 1.270  O3B   8EF 9  
8EF O3A   O4  O 0 1 N N N -17.615 -40.449 -26.028 -4.213 -0.655 0.175  O3A   8EF 10 
8EF PA    P2  P 0 1 N N N -16.099 -40.953 -26.266 -3.350 0.612  -0.318 PA    8EF 11 
8EF O2A   O5  O 0 1 N N N -15.015 -40.016 -25.574 -3.292 0.629  -1.927 O2A   8EF 12 
8EF O1A   O6  O 0 1 N N N -15.872 -42.140 -27.118 -3.983 1.859  0.166  O1A   8EF 13 
8EF O7    O7  O 0 1 N N N -15.989 -39.973 -27.563 -1.856 0.505  0.271  O7    8EF 14 
8EF C7    C4  C 0 1 N N N -15.440 -38.696 -27.317 -0.876 1.531  0.099  C7    8EF 15 
8EF C6    C5  C 0 1 N N N -15.969 -37.726 -28.344 0.428  1.110  0.781  C6    8EF 16 
8EF C5    C6  C 0 1 N N S -15.551 -36.426 -27.659 1.477  2.209  0.596  C5    8EF 17 
8EF C4    C7  C 0 1 N N N -14.897 -35.405 -28.401 2.778  1.823  1.271  C4    8EF 18 
8EF CM4   C8  C 0 1 N N N -14.116 -35.620 -29.463 2.872  1.656  2.577  CM4   8EF 19 
8EF S1    S1  S 0 1 N N N -16.812 -35.536 -26.694 1.946  2.365  -1.171 S1    8EF 20 
8EF C2    C9  C 0 1 N N N -16.129 -34.012 -27.147 3.755  2.374  -0.855 C2    8EF 21 
8EF N3    N3  N 0 1 N N N -14.836 -34.274 -27.689 3.852  1.660  0.432  N3    8EF 22 
8EF "C7'" C10 C 0 1 N N N -14.178 -33.071 -28.180 5.010  0.837  0.788  "C7'" 8EF 23 
8EF "C2'" C11 C 0 1 Y N N -10.551 -32.845 -26.092 4.207  -3.171 -0.118 "C2'" 8EF 24 
8EF CM2   C12 C 0 1 N N N -9.329  -32.761 -25.415 3.916  -4.615 -0.437 CM2   8EF 25 
8EF "N4'" N4  N 0 1 N N N -13.983 -32.738 -25.280 5.290  -0.249 -1.858 "N4'" 8EF 26 
8EF H1    H1  H 0 1 N N N -11.815 -33.180 -29.187 4.168  -1.143 2.459  H1    8EF 27 
8EF H2    H2  H 0 1 N N N -20.647 -40.085 -26.300 -5.806 -2.260 -1.580 H2    8EF 28 
8EF H3    H3  H 0 1 N N N -19.032 -43.286 -26.585 -6.994 -2.422 1.341  H3    8EF 29 
8EF H4    H4  H 0 1 N N N -14.144 -40.329 -25.786 -2.888 -0.160 -2.314 H4    8EF 30 
8EF H5    H5  H 0 1 N N N -14.343 -38.746 -27.388 -0.696 1.687  -0.964 H5    8EF 31 
8EF H6    H6  H 0 1 N N N -15.727 -38.359 -26.310 -1.237 2.457  0.546  H6    8EF 32 
8EF H7    H7  H 0 1 N N N -17.060 -37.801 -28.462 0.248  0.955  1.844  H7    8EF 33 
8EF H8    H8  H 0 1 N N N -15.485 -37.853 -29.323 0.789  0.184  0.334  H8    8EF 34 
8EF H9    H9  H 0 1 N N N -14.837 -36.737 -26.882 1.108  3.159  0.982  H9    8EF 35 
8EF H10   H10 H 0 1 N N N -13.945 -36.627 -29.813 3.818  1.381  3.019  H10   8EF 36 
8EF H11   H11 H 0 1 N N N -13.655 -34.786 -29.972 2.002  1.794  3.203  H11   8EF 37 
8EF H12   H12 H 0 1 N N N -16.043 -33.360 -26.265 4.288  1.836  -1.638 H12   8EF 38 
8EF H13   H13 H 0 1 N N N -16.763 -33.525 -27.903 4.128  3.394  -0.765 H13   8EF 39 
8EF H14   H14 H 0 1 N N N -13.945 -33.164 -29.251 5.211  0.935  1.855  H14   8EF 40 
8EF H15   H15 H 0 1 N N N -14.812 -32.187 -28.019 5.880  1.170  0.223  H15   8EF 41 
8EF H16   H16 H 0 1 N N N -8.503  -32.847 -26.136 2.868  -4.720 -0.719 H16   8EF 42 
8EF H17   H17 H 0 1 N N N -9.263  -31.793 -24.896 4.549  -4.939 -1.263 H17   8EF 43 
8EF H18   H18 H 0 1 N N N -9.260  -33.577 -24.680 4.120  -5.228 0.440  H18   8EF 44 
8EF H19   H19 H 0 1 N N N -13.738 -32.638 -24.316 5.250  -0.548 -2.780 H19   8EF 45 
8EF H20   H20 H 0 1 N N N -14.516 -31.944 -25.573 5.622  0.638  -1.650 H20   8EF 46 
# 
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 
8EF CM4   C4    DOUB N N 1  
8EF C4    N3    SING N N 2  
8EF C4    C5    SING N N 3  
8EF C6    C5    SING N N 4  
8EF C6    C7    SING N N 5  
8EF "C7'" N3    SING N N 6  
8EF "C7'" "C5'" SING N N 7  
8EF "C6'" "N1'" DOUB Y N 8  
8EF "C6'" "C5'" SING Y N 9  
8EF O1B   PB    DOUB N N 10 
8EF N3    C2    SING N N 11 
8EF C5    S1    SING N N 12 
8EF O7    C7    SING N N 13 
8EF O7    PA    SING N N 14 
8EF "N1'" "C2'" SING Y N 15 
8EF "C5'" "C4'" DOUB Y N 16 
8EF C2    S1    SING N N 17 
8EF O1A   PA    DOUB N N 18 
8EF PA    O3A   SING N N 19 
8EF PA    O2A   SING N N 20 
8EF PB    O3A   SING N N 21 
8EF PB    O3B   SING N N 22 
8EF PB    O2B   SING N N 23 
8EF "C2'" CM2   SING N N 24 
8EF "C2'" "N3'" DOUB Y N 25 
8EF "C4'" "N3'" SING Y N 26 
8EF "C4'" "N4'" SING N N 27 
8EF "C6'" H1    SING N N 28 
8EF O2B   H2    SING N N 29 
8EF O3B   H3    SING N N 30 
8EF O2A   H4    SING N N 31 
8EF C7    H5    SING N N 32 
8EF C7    H6    SING N N 33 
8EF C6    H7    SING N N 34 
8EF C6    H8    SING N N 35 
8EF C5    H9    SING N N 36 
8EF CM4   H10   SING N N 37 
8EF CM4   H11   SING N N 38 
8EF C2    H12   SING N N 39 
8EF C2    H13   SING N N 40 
8EF "C7'" H14   SING N N 41 
8EF "C7'" H15   SING N N 42 
8EF CM2   H16   SING N N 43 
8EF CM2   H17   SING N N 44 
8EF CM2   H18   SING N N 45 
8EF "N4'" H19   SING N N 46 
8EF "N4'" H20   SING N N 47 
# 
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 
8EF InChI            InChI                1.03  "InChI=1S/C12H20N4O7P2S/c1-8-11(3-4-22-25(20,21)23-24(17,18)19)26-7-16(8)6-10-5-14-9(2)15-12(10)13/h5,11H,1,3-4,6-7H2,2H3,(H,20,21)(H2,13,14,15)(H2,17,18,19)/t11-/m0/s1" 
8EF InChIKey         InChI                1.03  YBJKPSYOFQHZDJ-NSHDSACASA-N                                                                                                                                               
8EF SMILES_CANONICAL CACTVS               3.385 "Cc1ncc(CN2CS[C@@H](CCO[P](O)(=O)O[P](O)(O)=O)C2=C)c(N)n1"                                                                                                                
8EF SMILES           CACTVS               3.385 "Cc1ncc(CN2CS[CH](CCO[P](O)(=O)O[P](O)(O)=O)C2=C)c(N)n1"                                                                                                                  
8EF SMILES_CANONICAL "OpenEye OEToolkits" 2.0.6 "Cc1ncc(c(n1)N)CN2CS[C@H](C2=C)CCOP(=O)(O)OP(=O)(O)O"                                                                                                                     
8EF SMILES           "OpenEye OEToolkits" 2.0.6 "Cc1ncc(c(n1)N)CN2CSC(C2=C)CCOP(=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 
8EF "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.6 "2-[(5~{S})-3-[(4-azanyl-2-methyl-pyrimidin-5-yl)methyl]-4-methylidene-1,3-thiazolidin-5-yl]ethyl phosphono hydrogen phosphate" 
# 
loop_
_pdbx_chem_comp_audit.comp_id 
_pdbx_chem_comp_audit.action_type 
_pdbx_chem_comp_audit.date 
_pdbx_chem_comp_audit.processing_site 
8EF "Create component" 2017-06-20 PDBJ 
8EF "Initial release"  2018-04-25 RCSB 
# 
