data_3ME
# 
_chem_comp.id                                    3ME 
_chem_comp.name                                  "PHOSPHORIC ACID MONO-[4-[2-(2-DIMETHYLAMINO-ETHOXY)-ETHOXY]-3-HYDROXY-5- (5-METHYL-2,4-DIOXO-3,4-DIHYDRO-2H-PYRIMIDIN-1-YL)-TETRAHYDRO-FURAN-2-YLMETHYL] ESTER" 
_chem_comp.type                                  "DNA LINKING" 
_chem_comp.pdbx_type                             ATOMN 
_chem_comp.formula                               "C16 H28 N3 O9 P" 
_chem_comp.mon_nstd_parent_comp_id               DU 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2003-03-04 
_chem_comp.pdbx_modified_date                    2009-01-07 
_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                        437.382 
_chem_comp.one_letter_code                       U 
_chem_comp.three_letter_code                     3ME 
_chem_comp.pdbx_model_coordinates_details        ? 
_chem_comp.pdbx_model_coordinates_missing_flag   N 
_chem_comp.pdbx_ideal_coordinates_details        ? 
_chem_comp.pdbx_ideal_coordinates_missing_flag   N 
_chem_comp.pdbx_model_coordinates_db_code        1NZG 
_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 
3ME P      P      P 0 1 N N N -4.941 7.623  11.758 6.174  0.430  0.651  P      3ME 1  
3ME OP1    O1P    O 0 1 N N N -6.287 8.265  11.652 6.928  1.597  -0.162 OP1    3ME 2  
3ME OP2    O2P    O 0 1 N N N -4.853 6.153  11.922 6.995  -0.772 -0.035 OP2    3ME 3  
3ME "O5'"  "O5'"  O 0 1 N N N -4.175 7.969  10.424 4.924  0.341  -0.359 "O5'"  3ME 4  
3ME "C5'"  "C5'"  C 0 1 N N N -4.206 9.281  9.882  3.858  1.084  0.236  "C5'"  3ME 5  
3ME "C4'"  "C4'"  C 0 1 N N R -3.317 9.358  8.681  2.632  1.039  -0.679 "C4'"  3ME 6  
3ME "O4'"  "O4'"  O 0 1 N N N -1.947 9.106  9.055  2.111  -0.300 -0.738 "O4'"  3ME 7  
3ME "C1'"  "C1'"  C 0 1 N N R -1.278 8.444  7.986  0.677  -0.190 -0.862 "C1'"  3ME 8  
3ME N1     N1     N 0 1 N N N -0.848 7.114  8.442  0.025  -1.429 -0.431 N1     3ME 9  
3ME C6     C6     C 0 1 N N N -1.492 6.455  9.473  -0.857 -2.057 -1.268 C6     3ME 10 
3ME C2     C2     C 0 1 N N N 0.229  6.561  7.794  0.303  -1.942 0.781  C2     3ME 11 
3ME O2     O2     O 0 1 N N N 0.784  7.091  6.837  1.090  -1.367 1.509  O2     3ME 12 
3ME N3     N3     N 0 1 N N N 0.627  5.346  8.297  -0.285 -3.077 1.203  N3     3ME 13 
3ME C4     C4     C 0 1 N N N 0.061  4.641  9.344  -1.159 -3.726 0.408  C4     3ME 14 
3ME O4     O4     O 0 1 N N N 0.551  3.578  9.700  -1.688 -4.755 0.788  O4     3ME 15 
3ME C5     C5     C 0 1 N N N -1.093 5.262  9.957  -1.457 -3.200 -0.872 C5     3ME 16 
3ME C5A    C5A    C 0 1 N N N -1.773 4.577  11.105 -2.430 -3.906 -1.780 C5A    3ME 17 
3ME "C2'"  "C2'"  C 0 1 N N R -2.280 8.279  6.849  0.321  0.979  0.091  "C2'"  3ME 18 
3ME "O2'"  "O2'"  O 0 1 N N N -2.286 9.484  6.091  -0.903 1.603  -0.302 "O2'"  3ME 19 
3ME "CB'"  "CB'"  C 0 1 N N N -1.088 9.604  5.329  -1.476 2.171  0.878  "CB'"  3ME 20 
3ME "CC'"  "CC'"  C 0 1 N N N -1.103 10.899 4.533  -2.796 2.858  0.525  "CC'"  3ME 21 
3ME "OD'"  "OD'"  O 0 1 N N N -2.288 10.811 3.779  -3.738 1.880  0.081  "OD'"  3ME 22 
3ME "CE'"  "CE'"  C 0 1 N N N -2.425 11.690 2.662  -4.944 2.581  -0.232 "CE'"  3ME 23 
3ME "CF'"  "CF'"  C 0 1 N N N -3.723 11.360 1.904  -6.000 1.586  -0.717 "CF'"  3ME 24 
3ME "NG'"  "NG'"  N 0 1 N N N -3.897 9.946  1.555  -6.354 0.674  0.379  "NG'"  3ME 25 
3ME "CI'"  "CI'"  C 0 1 N N N -2.968 9.492  0.522  -7.227 1.427  1.289  "CI'"  3ME 26 
3ME "CJ'"  "CJ'"  C 0 1 N N N -5.254 9.568  1.171  -7.176 -0.393 -0.208 "CJ'"  3ME 27 
3ME "C3'"  "C3'"  C 0 1 N N R -3.585 8.312  7.617  1.519  1.939  -0.109 "C3'"  3ME 28 
3ME "O3'"  "O3'"  O 0 1 N N N -4.668 8.592  6.780  1.183  2.972  -1.036 "O3'"  3ME 29 
3ME HO1    HO1    H 0 1 N N N -6.343 9.207  11.546 7.743  1.793  0.321  HO1    3ME 30 
3ME HO2    HO2    H 0 1 N N N -3.997 5.745  11.989 7.818  -0.869 0.464  HO2    3ME 31 
3ME "H5'1" "1H5'" H 0 0 N N N -5.245 9.615  9.655  4.170  2.119  0.374  "H5'1" 3ME 32 
3ME "H5'2" "2H5'" H 0 0 N N N -3.948 10.054 10.643 3.606  0.647  1.202  "H5'2" 3ME 33 
3ME "H4'"  "H4'"  H 0 1 N N N -3.516 10.379 8.279  2.904  1.375  -1.680 "H4'"  3ME 34 
3ME "H1'"  "H1'"  H 0 1 N N N -0.389 9.027  7.650  0.398  0.053  -1.887 "H1'"  3ME 35 
3ME HC6    HC6    H 0 1 N N N -2.381 6.910  9.939  -1.072 -1.641 -2.242 HC6    3ME 36 
3ME HN3    HN3    H 0 1 N N N 1.433  4.919  7.841  -0.076 -3.431 2.082  HN3    3ME 37 
3ME H5A1   1H5A   H 0 0 N N N -1.442 3.590  11.505 -1.893 -4.622 -2.402 H5A1   3ME 38 
3ME H5A2   2H5A   H 0 0 N N N -1.790 5.294  11.958 -3.172 -4.432 -1.179 H5A2   3ME 39 
3ME H5A3   3H5A   H 0 0 N N N -2.854 4.487  10.846 -2.930 -3.175 -2.416 H5A3   3ME 40 
3ME "H2'"  "H2'"  H 0 1 N N N -2.091 7.394  6.196  0.265  0.636  1.124  "H2'"  3ME 41 
3ME "HB'1" "1HB'" H 0 0 N N N -0.177 9.516  5.966  -0.787 2.902  1.301  "HB'1" 3ME 42 
3ME "HB'2" "2HB'" H 0 0 N N N -0.917 8.715  4.677  -1.660 1.382  1.608  "HB'2" 3ME 43 
3ME "HC'1" "1HC'" H 0 0 N N N -1.018 11.822 5.152  -2.626 3.586  -0.269 "HC'1" 3ME 44 
3ME "HC'2" "2HC'" H 0 0 N N N -0.183 11.078 3.928  -3.188 3.367  1.406  "HC'2" 3ME 45 
3ME "HE'1" "1HE'" H 0 0 N N N -2.373 12.762 2.961  -4.746 3.312  -1.016 "HE'1" 3ME 46 
3ME "HE'2" "2HE'" H 0 0 N N N -1.531 11.667 1.996  -5.308 3.093  0.658  "HE'2" 3ME 47 
3ME "HF'1" "1HF'" H 0 0 N N N -4.606 11.725 2.477  -5.602 1.012  -1.554 "HF'1" 3ME 48 
3ME "HF'2" "2HF'" H 0 0 N N N -3.806 11.994 0.990  -6.889 2.128  -1.040 "HF'2" 3ME 49 
3ME "HI'1" "1HI'" H 0 0 N N N -3.100 8.417  0.256  -6.660 2.234  1.752  "HI'1" 3ME 50 
3ME "HI'2" "2HI'" H 0 0 N N N -3.036 10.136 -0.385 -8.063 1.845  0.728  "HI'2" 3ME 51 
3ME "HI'3" "3HI'" H 0 0 N N N -1.913 9.701  0.816  -7.607 0.760  2.063  "HI'3" 3ME 52 
3ME "HJ'1" "1HJ'" H 0 0 N N N -5.386 8.493  0.905  -8.070 0.042  -0.655 "HJ'1" 3ME 53 
3ME "HJ'2" "2HJ'" H 0 0 N N N -5.975 9.858  1.969  -6.602 -0.913 -0.976 "HJ'2" 3ME 54 
3ME "HJ'3" "3HJ'" H 0 0 N N N -5.613 10.217 0.338  -7.465 -1.099 0.570  "HJ'3" 3ME 55 
3ME "H3'"  "H3'"  H 0 1 N N N -3.880 7.337  8.070  1.827  2.368  0.845  "H3'"  3ME 56 
3ME "HO3'" "HO3'" H 0 0 N Y N -4.836 7.937  6.113  1.964  3.537  -1.121 "HO3'" 3ME 57 
# 
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 
3ME P     OP1    SING N N 1  
3ME P     OP2    SING N N 2  
3ME P     "O5'"  SING N N 3  
3ME OP1   HO1    SING N N 4  
3ME OP2   HO2    SING N N 5  
3ME "O5'" "C5'"  SING N N 6  
3ME "C5'" "C4'"  SING N N 7  
3ME "C5'" "H5'1" SING N N 8  
3ME "C5'" "H5'2" SING N N 9  
3ME "C4'" "O4'"  SING N N 10 
3ME "C4'" "C3'"  SING N N 11 
3ME "C4'" "H4'"  SING N N 12 
3ME "O4'" "C1'"  SING N N 13 
3ME "C1'" N1     SING N N 14 
3ME "C1'" "C2'"  SING N N 15 
3ME "C1'" "H1'"  SING N N 16 
3ME N1    C6     SING N N 17 
3ME N1    C2     SING N N 18 
3ME C6    C5     DOUB N N 19 
3ME C6    HC6    SING N N 20 
3ME C2    O2     DOUB N N 21 
3ME C2    N3     SING N N 22 
3ME N3    C4     SING N N 23 
3ME N3    HN3    SING N N 24 
3ME C4    O4     DOUB N N 25 
3ME C4    C5     SING N N 26 
3ME C5    C5A    SING N N 27 
3ME C5A   H5A1   SING N N 28 
3ME C5A   H5A2   SING N N 29 
3ME C5A   H5A3   SING N N 30 
3ME "C2'" "O2'"  SING N N 31 
3ME "C2'" "C3'"  SING N N 32 
3ME "C2'" "H2'"  SING N N 33 
3ME "O2'" "CB'"  SING N N 34 
3ME "CB'" "CC'"  SING N N 35 
3ME "CB'" "HB'1" SING N N 36 
3ME "CB'" "HB'2" SING N N 37 
3ME "CC'" "OD'"  SING N N 38 
3ME "CC'" "HC'1" SING N N 39 
3ME "CC'" "HC'2" SING N N 40 
3ME "OD'" "CE'"  SING N N 41 
3ME "CE'" "CF'"  SING N N 42 
3ME "CE'" "HE'1" SING N N 43 
3ME "CE'" "HE'2" SING N N 44 
3ME "CF'" "NG'"  SING N N 45 
3ME "CF'" "HF'1" SING N N 46 
3ME "CF'" "HF'2" SING N N 47 
3ME "NG'" "CI'"  SING N N 48 
3ME "NG'" "CJ'"  SING N N 49 
3ME "CI'" "HI'1" SING N N 50 
3ME "CI'" "HI'2" SING N N 51 
3ME "CI'" "HI'3" SING N N 52 
3ME "CJ'" "HJ'1" SING N N 53 
3ME "CJ'" "HJ'2" SING N N 54 
3ME "CJ'" "HJ'3" SING N N 55 
3ME "C3'" "O3'"  SING N N 56 
3ME "C3'" "H3'"  SING N N 57 
3ME "O3'" "HO3'" SING N N 58 
# 
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 
3ME SMILES           ACDLabs              10.04 "O=C1NC(=O)N(C=C1C)C2OC(C(O)C2OCCOCCN(C)C)COP(O)O"                                                                                                                                        
3ME InChI            InChI                1.02b "InChI=1/C16H28N3O9P/c1-10-8-19(16(22)17-14(10)21)15-13(26-7-6-25-5-4-18(2)3)12(20)11(28-15)9-27-29(23)24/h8,11-13,15,20,23-24H,4-7,9H2,1-3H3,(H,17,21,22)/t11-,12-,13-,15-/m1/s1/f/h17H" 
3ME InChIKey         InChI                1.02b JWZCBFHCKRALNP-ZOIGVATLDV                                                                                                                                                                 
3ME SMILES_CANONICAL CACTVS               3.341 "CN(C)CCOCCO[C@@H]1[C@H](O)[C@@H](COP(O)O)O[C@H]1N2C=C(C)C(=O)NC2=O"                                                                                                                      
3ME SMILES           CACTVS               3.341 "CN(C)CCOCCO[CH]1[CH](O)[CH](COP(O)O)O[CH]1N2C=C(C)C(=O)NC2=O"                                                                                                                            
3ME SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "CC1=CN(C(=O)NC1=O)[C@H]2[C@@H]([C@@H]([C@H](O2)COP(O)O)O)OCCOCCN(C)C"                                                                                                                    
3ME SMILES           "OpenEye OEToolkits" 1.5.0 "CC1=CN(C(=O)NC1=O)C2C(C(C(O2)COP(O)O)O)OCCOCCN(C)C"                                                                                                                                      
# 
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 
3ME "SYSTEMATIC NAME" ACDLabs              10.04 "5'-O-(dihydroxyphosphanyl)-2'-O-{2-[2-(dimethylamino)ethoxy]ethyl}-5-methyluridine"                                                        
3ME "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "[(2R,3R,4R,5R)-4-[2-(2-dimethylaminoethoxy)ethoxy]-3-hydroxy-5-(5-methyl-2,4-dioxo-pyrimidin-1-yl)oxolan-2-yl]methyl dihydrogen phosphite" 
# 
