data_5EJ
# 
_chem_comp.id                                    5EJ 
_chem_comp.name                                  "1-(2-deoxy-5-O-phosphono-beta-D-erythro-pentofuranosyl)-4-ethoxy-5-methylpyrimidin-2(1H)-one" 
_chem_comp.type                                  "DNA linking" 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C12 H19 N2 O8 P" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2015-09-16 
_chem_comp.pdbx_modified_date                    2016-08-05 
_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                        350.262 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     5EJ 
_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        5DQG 
_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 
5EJ C1    C1  C 0 1 N N N -139.604 0.238  -7.821  5.337  1.980  1.034  C1    5EJ 1  
5EJ C2    C2  C 0 1 N N N -139.124 4.971  -7.134  1.906  -0.023 0.574  C2    5EJ 2  
5EJ P     P1  P 0 1 N N N -132.742 6.179  -10.530 -4.632 1.384  -0.228 P     5EJ 3  
5EJ OP1   O1  O 0 1 N N N -132.193 4.856  -10.129 -4.201 2.316  0.838  OP1   5EJ 4  
5EJ "O5'" O2  O 0 1 N N N -133.565 6.934  -9.380  -3.469 0.303  -0.497 "O5'" 5EJ 5  
5EJ "C5'" C3  C 0 1 N N N -134.709 7.762  -9.650  -2.914 -0.516 0.534  "C5'" 5EJ 6  
5EJ "C4'" C4  C 0 1 N N R -135.639 7.859  -8.449  -1.838 -1.426 -0.062 "C4'" 5EJ 7  
5EJ "C3'" C5  C 0 1 N N S -134.999 7.525  -7.118  -1.311 -2.407 1.008  "C3'" 5EJ 8  
5EJ "O3'" O3  O 0 1 N N N -135.294 8.554  -6.197  -1.947 -3.680 0.877  "O3'" 5EJ 9  
5EJ "C2'" C6  C 0 1 N N N -135.625 6.235  -6.645  0.199  -2.522 0.701  "C2'" 5EJ 10 
5EJ "C1'" C7  C 0 1 N N R -136.994 6.353  -7.266  0.406  -1.597 -0.518 "C1'" 5EJ 11 
5EJ "O4'" O4  O 0 1 N N N -136.718 6.943  -8.549  -0.683 -0.651 -0.452 "O4'" 5EJ 12 
5EJ N1    N1  N 0 1 N N N -137.722 5.079  -7.447  1.693  -0.904 -0.421 N1    5EJ 13 
5EJ C6    C8  C 0 1 N N N -137.072 4.026  -7.961  2.668  -1.154 -1.337 C6    5EJ 14 
5EJ C5    C9  C 0 1 N N N -137.711 2.816  -8.193  3.855  -0.506 -1.235 C5    5EJ 15 
5EJ C7    C10 C 0 1 N N N -136.881 1.674  -8.763  4.953  -0.762 -2.235 C7    5EJ 16 
5EJ C4    C11 C 0 1 N N N -139.171 2.730  -7.845  4.044  0.408  -0.183 C4    5EJ 17 
5EJ N3    N2  N 0 1 N N N -139.798 3.828  -7.342  3.066  0.624  0.683  N3    5EJ 18 
5EJ O2    O5  O 0 1 N N N -139.745 5.927  -6.646  1.021  0.189  1.387  O2    5EJ 19 
5EJ O4    O6  O 0 1 N N N -139.959 1.617  -8.031  5.218  1.067  -0.059 O4    5EJ 20 
5EJ OP2   O7  O 0 1 N N N -131.700 7.045  -11.119 -5.974 0.625  0.233  OP2   5EJ 21 
5EJ C3    C12 C 0 1 N N N -140.343 -0.704 -8.762  6.724  2.625  1.010  C3    5EJ 22 
5EJ H1    H1  H 0 1 N N N -139.849 -0.035 -6.784  4.575  2.754  0.946  H1    5EJ 23 
5EJ H2    H2  H 0 1 N N N -138.522 0.123  -7.985  5.203  1.442  1.973  H2    5EJ 24 
5EJ H4    H4  H 0 1 N N N -134.362 8.772  -9.913  -2.470 0.118  1.301  H4    5EJ 25 
5EJ H5    H5  H 0 1 N N N -135.266 7.334  -10.496 -3.701 -1.125 0.977  H5    5EJ 26 
5EJ H6    H6  H 0 1 N N N -136.030 8.886  -8.398  -2.236 -1.973 -0.916 H6    5EJ 27 
5EJ H7    H7  H 0 1 N N N -133.914 7.394  -7.244  -1.467 -2.002 2.008  H7    5EJ 28 
5EJ H8    H8  H 0 1 N N N -134.896 8.353  -5.358  -1.653 -4.335 1.525  H8    5EJ 29 
5EJ H9    H9  H 0 1 N N N -135.679 6.188  -5.547  0.789  -2.174 1.549  H9    5EJ 30 
5EJ H10   H10 H 0 1 N N N -135.081 5.357  -7.023  0.461  -3.551 0.451  H10   5EJ 31 
5EJ H11   H11 H 0 1 N N N -137.604 7.040  -6.661  0.354  -2.171 -1.443 H11   5EJ 32 
5EJ H12   H12 H 0 1 N N N -136.023 4.121  -8.201  2.499  -1.861 -2.136 H12   5EJ 33 
5EJ H13   H13 H 0 1 N N N -137.518 0.786  -8.892  4.856  -0.066 -3.068 H13   5EJ 34 
5EJ H14   H14 H 0 1 N N N -136.467 1.973  -9.737  5.922  -0.619 -1.754 H14   5EJ 35 
5EJ H15   H15 H 0 1 N N N -136.059 1.438  -8.072  4.878  -1.784 -2.604 H15   5EJ 36 
5EJ H16   H16 H 0 1 N N N -130.870 6.582  -11.127 -6.314 -0.003 -0.419 H16   5EJ 37 
5EJ H17   H17 H 0 1 N N N -140.036 -1.741 -8.560  7.487  1.851  1.099  H17   5EJ 38 
5EJ H18   H18 H 0 1 N N N -141.427 -0.605 -8.603  6.859  3.163  0.072  H18   5EJ 39 
5EJ H19   H19 H 0 1 N N N -140.100 -0.446 -9.804  6.815  3.322  1.844  H19   5EJ 40 
5EJ OP3   OP3 O 0 1 N Y N -133.915 5.953  -11.739 -4.919 2.211  -1.579 OP3   5EJ 41 
5EJ H3    H3  H 0 1 N Y N -133.999 5.026  -11.930 -5.610 2.882  -1.490 H3    5EJ 42 
# 
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 
5EJ OP2   P     SING N N 1  
5EJ P     OP1   DOUB N N 2  
5EJ P     "O5'" SING N N 3  
5EJ "C5'" "O5'" SING N N 4  
5EJ "C5'" "C4'" SING N N 5  
5EJ C7    C5    SING N N 6  
5EJ C3    C1    SING N N 7  
5EJ "O4'" "C4'" SING N N 8  
5EJ "O4'" "C1'" SING N N 9  
5EJ "C4'" "C3'" SING N N 10 
5EJ C5    C6    DOUB N N 11 
5EJ C5    C4    SING N N 12 
5EJ O4    C4    SING N N 13 
5EJ O4    C1    SING N N 14 
5EJ C6    N1    SING N N 15 
5EJ C4    N3    DOUB N N 16 
5EJ N1    "C1'" SING N N 17 
5EJ N1    C2    SING N N 18 
5EJ N3    C2    SING N N 19 
5EJ "C1'" "C2'" SING N N 20 
5EJ C2    O2    DOUB N N 21 
5EJ "C3'" "C2'" SING N N 22 
5EJ "C3'" "O3'" SING N N 23 
5EJ C1    H1    SING N N 24 
5EJ C1    H2    SING N N 25 
5EJ "C5'" H4    SING N N 26 
5EJ "C5'" H5    SING N N 27 
5EJ "C4'" H6    SING N N 28 
5EJ "C3'" H7    SING N N 29 
5EJ "O3'" H8    SING N N 30 
5EJ "C2'" H9    SING N N 31 
5EJ "C2'" H10   SING N N 32 
5EJ "C1'" H11   SING N N 33 
5EJ C6    H12   SING N N 34 
5EJ C7    H13   SING N N 35 
5EJ C7    H14   SING N N 36 
5EJ C7    H15   SING N N 37 
5EJ OP2   H16   SING N N 38 
5EJ C3    H17   SING N N 39 
5EJ C3    H18   SING N N 40 
5EJ C3    H19   SING N N 41 
5EJ P     OP3   SING N N 42 
5EJ OP3   H3    SING N N 43 
# 
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 
5EJ SMILES           ACDLabs              12.01 "C(OC=1C(=CN(C(=O)N=1)C2CC(C(COP(=O)(O)O)O2)O)C)C"                                                                                                 
5EJ InChI            InChI                1.03  "InChI=1S/C12H19N2O8P/c1-3-20-11-7(2)5-14(12(16)13-11)10-4-8(15)9(22-10)6-21-23(17,18)19/h5,8-10,15H,3-4,6H2,1-2H3,(H2,17,18,19)/t8-,9+,10+/m0/s1" 
5EJ InChIKey         InChI                1.03  CNSVITKBNLMDOG-IVZWLZJFSA-N                                                                                                                        
5EJ SMILES_CANONICAL CACTVS               3.385 "CCOC1=NC(=O)N(C=C1C)[C@H]2C[C@H](O)[C@@H](CO[P](O)(O)=O)O2"                                                                                       
5EJ SMILES           CACTVS               3.385 "CCOC1=NC(=O)N(C=C1C)[CH]2C[CH](O)[CH](CO[P](O)(O)=O)O2"                                                                                           
5EJ SMILES_CANONICAL "OpenEye OEToolkits" 1.9.2 "CCOC1=NC(=O)N(C=C1C)[C@H]2C[C@@H]([C@H](O2)COP(=O)(O)O)O"                                                                                         
5EJ SMILES           "OpenEye OEToolkits" 1.9.2 "CCOC1=NC(=O)N(C=C1C)C2CC(C(O2)COP(=O)(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 
5EJ "SYSTEMATIC NAME" ACDLabs              12.01 "1-(2-deoxy-5-O-phosphono-beta-D-erythro-pentofuranosyl)-4-ethoxy-5-methylpyrimidin-2(1H)-one"                        
5EJ "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.9.2 "[(2R,3S,5R)-5-(4-ethoxy-5-methyl-2-oxidanylidene-pyrimidin-1-yl)-3-oxidanyl-oxolan-2-yl]methyl dihydrogen 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 
5EJ "Create component" 2015-09-16 RCSB 
5EJ "Initial release"  2016-08-10 RCSB 
# 
