data_3ME
# 
_chem_comp.id                                    3ME 
_chem_comp.name                                  
;2'-O-{2-[2-(dimethylamino)ethoxy]ethyl}-5-methyluridine 5'-(dihydrogen phosphate)
;
_chem_comp.type                                  "RNA LINKING" 
_chem_comp.pdbx_type                             ATOMN 
_chem_comp.formula                               "C16 H28 N3 O10 P" 
_chem_comp.mon_nstd_parent_comp_id               U 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2003-03-04 
_chem_comp.pdbx_modified_date                    2011-10-27 
_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                        453.381 
_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   Y 
_chem_comp.pdbx_ideal_coordinates_details        Corina 
_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 6.123  -0.190 -0.062 P      3ME 1  
3ME OP1    O1P    O 0 1 N N N -6.287 8.265  11.652 6.730  -1.501 -0.383 OP1    3ME 2  
3ME OP2    O2P    O 0 1 N N N -4.853 6.153  11.922 6.034  0.702  -1.400 OP2    3ME 3  
3ME "O5'"  "O5'"  O 0 1 N N N -4.175 7.969  10.424 4.645  -0.414 0.534  "O5'"  3ME 4  
3ME "C5'"  "C5'"  C 0 1 N N N -4.206 9.281  9.882  3.632  -1.152 -0.154 "C5'"  3ME 5  
3ME "C4'"  "C4'"  C 0 1 N N R -3.317 9.358  8.681  2.355  -1.171 0.688  "C4'"  3ME 6  
3ME "O4'"  "O4'"  O 0 1 N N N -1.947 9.106  9.055  1.811  0.156  0.781  "O4'"  3ME 7  
3ME "C1'"  "C1'"  C 0 1 N N R -1.278 8.444  7.986  0.374  0.023  0.813  "C1'"  3ME 8  
3ME N1     N1     N 0 1 N N N -0.848 7.114  8.442  -0.270 1.273  0.402  N1     3ME 9  
3ME C6     C6     C 0 1 N N N -1.492 6.455  9.473  -1.209 1.849  1.212  C6     3ME 10 
3ME C2     C2     C 0 1 N N N 0.229  6.561  7.794  0.073  1.846  -0.766 C2     3ME 11 
3ME O2     O2     O 0 1 N N N 0.784  7.091  6.837  0.914  1.319  -1.468 O2     3ME 12 
3ME N3     N3     N 0 1 N N N 0.627  5.346  8.297  -0.503 2.994  -1.168 N3     3ME 13 
3ME C4     C4     C 0 1 N N N 0.061  4.641  9.344  -1.437 3.591  -0.400 C4     3ME 14 
3ME O4     O4     O 0 1 N N N 0.551  3.578  9.700  -1.959 4.630  -0.763 O4     3ME 15 
3ME C5     C5     C 0 1 N N N -1.093 5.262  9.957  -1.803 3.001  0.834  C5     3ME 16 
3ME C5A    C5A    C 0 1 N N N -1.773 4.577  11.105 -2.840 3.651  1.713  C5A    3ME 17 
3ME "C2'"  "C2'"  C 0 1 N N R -2.280 8.279  6.849  0.093  -1.100 -0.218 "C2'"  3ME 18 
3ME "O2'"  "O2'"  O 0 1 N N N -2.286 9.484  6.091  -1.143 -1.758 0.069  "O2'"  3ME 19 
3ME "CB'"  "CB'"  C 0 1 N N N -1.088 9.604  5.329  -1.807 -2.276 -1.086 "CB'"  3ME 20 
3ME "CC'"  "CC'"  C 0 1 N N N -1.103 10.899 4.533  -3.111 -2.955 -0.662 "CC'"  3ME 21 
3ME "OD'"  "OD'"  O 0 1 N N N -2.288 10.811 3.779  -4.002 -1.978 -0.120 "OD'"  3ME 22 
3ME "CE'"  "CE'"  C 0 1 N N N -2.425 11.690 2.662  -5.257 -2.511 0.309  "CE'"  3ME 23 
3ME "CF'"  "CF'"  C 0 1 N N N -3.723 11.360 1.904  -6.126 -1.382 0.868  "CF'"  3ME 24 
3ME "NG'"  "NG'"  N 0 1 N N N -3.897 9.946  1.555  -6.452 -0.436 -0.207 "NG'"  3ME 25 
3ME "CI'"  "CI'"  C 0 1 N N N -2.968 9.492  0.522  -7.308 -1.067 -1.221 "CI'"  3ME 26 
3ME "CJ'"  "CJ'"  C 0 1 N N N -5.254 9.568  1.171  -7.080 0.778  0.331  "CJ'"  3ME 27 
3ME "C3'"  "C3'"  C 0 1 N N R -3.585 8.312  7.617  1.292  -2.054 0.007  "C3'"  3ME 28 
3ME "O3'"  "O3'"  O 0 1 N N N -4.668 8.592  6.780  0.917  -3.136 0.863  "O3'"  3ME 29 
3ME HO2    HO2    H 0 1 N N N -5.728 5.783  11.940 5.646  1.577  -1.264 HO2    3ME 30 
3ME "H5'1" "H5'1" H 0 0 N N N -5.237 9.529  9.588  3.428  -0.681 -1.115 "H5'1" 3ME 31 
3ME "H5'2" "H5'2" H 0 0 N N N -3.856 9.996  10.641 3.976  -2.174 -0.316 "H5'2" 3ME 32 
3ME "H4'"  "H4'"  H 0 1 N N N -3.514 10.365 8.285  2.573  -1.553 1.685  "H4'"  3ME 33 
3ME "H1'"  "H1'"  H 0 1 N N N -0.401 9.020  7.655  0.038  -0.273 1.807  "H1'"  3ME 34 
3ME HC6    HC6    H 0 1 N N N -2.361 6.921  9.914  -1.476 1.385  2.150  HC6    3ME 35 
3ME HN3    HN3    H 0 1 N N N 1.418  4.922  7.855  -0.245 3.394  -2.013 HN3    3ME 36 
3ME H5A1   H5A1   H 0 0 N N N -1.268 3.623  11.314 -2.353 4.343  2.400  H5A1   3ME 37 
3ME H5A2   H5A2   H 0 0 N N N -1.725 5.220  11.996 -3.553 4.195  1.093  H5A2   3ME 38 
3ME H5A3   H5A3   H 0 0 N N N -2.825 4.386  10.847 -3.366 2.884  2.282  H5A3   3ME 39 
3ME "H2'"  "H2'"  H 0 1 N N N -2.094 7.407  6.205  0.095  -0.705 -1.234 "H2'"  3ME 40 
3ME "HB'1" "HB'1" H 0 0 N N N -0.224 9.606  6.009  -2.029 -1.461 -1.774 "HB'1" 3ME 41 
3ME "HB'2" "HB'2" H 0 0 N N N -1.012 8.753  4.636  -1.163 -3.004 -1.579 "HB'2" 3ME 42 
3ME "HC'1" "HC'1" H 0 0 N N N -1.111 11.778 5.194  -3.573 -3.427 -1.529 "HC'1" 3ME 43 
3ME "HC'2" "HC'2" H 0 0 N N N -0.219 10.983 3.884  -2.898 -3.712 0.094  "HC'2" 3ME 44 
3ME "HE'1" "HE'1" H 0 0 N N N -2.463 12.730 3.017  -5.764 -2.973 -0.538 "HE'1" 3ME 45 
3ME "HE'2" "HE'2" H 0 0 N N N -1.565 11.563 1.988  -5.089 -3.258 1.084  "HE'2" 3ME 46 
3ME "HF'1" "HF'1" H 0 0 N N N -4.567 11.651 2.546  -7.046 -1.800 1.276  "HF'1" 3ME 47 
3ME "HF'2" "HF'2" H 0 0 N N N -3.718 11.936 0.967  -5.582 -0.862 1.657  "HF'2" 3ME 48 
3ME "HI'1" "HI'1" H 0 0 N N N -3.149 8.429  0.307  -8.236 -1.401 -0.756 "HI'1" 3ME 49 
3ME "HI'2" "HI'2" H 0 0 N N N -3.121 10.082 -0.393 -7.534 -0.345 -2.006 "HI'2" 3ME 50 
3ME "HI'3" "HI'3" H 0 0 N N N -1.935 9.623  0.875  -6.790 -1.922 -1.653 "HI'3" 3ME 51 
3ME "HJ'1" "HJ'1" H 0 0 N N N -5.282 8.495  0.929  -6.396 1.263  1.027  "HJ'1" 3ME 52 
3ME "HJ'2" "HJ'2" H 0 0 N N N -5.942 9.774  2.005  -7.311 1.461  -0.486 "HJ'2" 3ME 53 
3ME "HJ'3" "HJ'3" H 0 0 N N N -5.561 10.150 0.290  -7.999 0.510  0.852  "HJ'3" 3ME 54 
3ME "H3'"  "H3'"  H 0 1 N N N -3.876 7.350  8.065  1.663  -2.432 -0.946 "H3'"  3ME 55 
3ME "HO3'" "HO3'" H 0 0 N Y N -4.768 7.892  6.145  1.644  -3.733 1.084  "HO3'" 3ME 56 
3ME OXT    OXT    O 0 1 N Y N ?      ?      ?      7.032  0.569  1.029  OXT    3ME 57 
3ME HXT    H1     H 0 1 N Y N ?      ?      ?      7.939  0.738  0.737  H1     3ME 58 
# 
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    DOUB N N 1  
3ME P     OP2    SING N N 2  
3ME P     "O5'"  SING N N 3  
3ME OP2   HO2    SING N N 4  
3ME "O5'" "C5'"  SING N N 5  
3ME "C5'" "C4'"  SING N N 6  
3ME "C5'" "H5'1" SING N N 7  
3ME "C5'" "H5'2" SING N N 8  
3ME "C4'" "O4'"  SING N N 9  
3ME "C4'" "C3'"  SING N N 10 
3ME "C4'" "H4'"  SING N N 11 
3ME "O4'" "C1'"  SING N N 12 
3ME "C1'" N1     SING N N 13 
3ME "C1'" "C2'"  SING N N 14 
3ME "C1'" "H1'"  SING N N 15 
3ME N1    C6     SING N N 16 
3ME N1    C2     SING N N 17 
3ME C6    C5     DOUB N N 18 
3ME C6    HC6    SING N N 19 
3ME C2    O2     DOUB N N 20 
3ME C2    N3     SING N N 21 
3ME N3    C4     SING N N 22 
3ME N3    HN3    SING N N 23 
3ME C4    O4     DOUB N N 24 
3ME C4    C5     SING N N 25 
3ME C5    C5A    SING N N 26 
3ME C5A   H5A1   SING N N 27 
3ME C5A   H5A2   SING N N 28 
3ME C5A   H5A3   SING N N 29 
3ME "C2'" "O2'"  SING N N 30 
3ME "C2'" "C3'"  SING N N 31 
3ME "C2'" "H2'"  SING N N 32 
3ME "O2'" "CB'"  SING N N 33 
3ME "CB'" "CC'"  SING N N 34 
3ME "CB'" "HB'1" SING N N 35 
3ME "CB'" "HB'2" SING N N 36 
3ME "CC'" "OD'"  SING N N 37 
3ME "CC'" "HC'1" SING N N 38 
3ME "CC'" "HC'2" SING N N 39 
3ME "OD'" "CE'"  SING N N 40 
3ME "CE'" "CF'"  SING N N 41 
3ME "CE'" "HE'1" SING N N 42 
3ME "CE'" "HE'2" SING N N 43 
3ME "CF'" "NG'"  SING N N 44 
3ME "CF'" "HF'1" SING N N 45 
3ME "CF'" "HF'2" SING N N 46 
3ME "NG'" "CI'"  SING N N 47 
3ME "NG'" "CJ'"  SING N N 48 
3ME "CI'" "HI'1" SING N N 49 
3ME "CI'" "HI'2" SING N N 50 
3ME "CI'" "HI'3" SING N N 51 
3ME "CJ'" "HJ'1" SING N N 52 
3ME "CJ'" "HJ'2" SING N N 53 
3ME "CJ'" "HJ'3" SING N N 54 
3ME "C3'" "O3'"  SING N N 55 
3ME "C3'" "H3'"  SING N N 56 
3ME "O3'" "HO3'" SING N N 57 
3ME P     OXT    SING N N 58 
3ME OXT   HXT    SING N N 59 
# 
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              12.01 "O=P(O)(O)OCC2OC(N1C(=O)NC(=O)C(=C1)C)C(OCCOCCN(C)C)C2O"                                                                                                                                       
3ME InChI            InChI                1.03  "InChI=1S/C16H28N3O10P/c1-10-8-19(16(22)17-14(10)21)15-13(27-7-6-26-5-4-18(2)3)12(20)11(29-15)9-28-30(23,24)25/h8,11-13,15,20H,4-7,9H2,1-3H3,(H,17,21,22)(H2,23,24,25)/t11-,12-,13-,15-/m1/s1" 
3ME InChIKey         InChI                1.03  ZEPAZACIEWQAFL-RGCMKSIDSA-N                                                                                                                                                                    
3ME SMILES_CANONICAL CACTVS               3.370 "CN(C)CCOCCO[C@@H]1[C@H](O)[C@@H](CO[P](O)(O)=O)O[C@H]1N2C=C(C)C(=O)NC2=O"                                                                                                                     
3ME SMILES           CACTVS               3.370 "CN(C)CCOCCO[CH]1[CH](O)[CH](CO[P](O)(O)=O)O[CH]1N2C=C(C)C(=O)NC2=O"                                                                                                                           
3ME SMILES_CANONICAL "OpenEye OEToolkits" 1.7.2 "CC1=CN(C(=O)NC1=O)[C@H]2[C@@H]([C@@H]([C@H](O2)COP(=O)(O)O)O)OCCOCCN(C)C"                                                                                                                     
3ME SMILES           "OpenEye OEToolkits" 1.7.2 "CC1=CN(C(=O)NC1=O)C2C(C(C(O2)COP(=O)(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              12.01 
;2'-O-{2-[2-(dimethylamino)ethoxy]ethyl}-5-methyluridine 5'-(dihydrogen phosphate)
;
3ME "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.7.2 "[(2R,3R,4R,5R)-4-[2-(2-dimethylaminoethyloxy)ethoxy]-5-[5-methyl-2,4-bis(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 
3ME "Create component"    2003-03-04 RCSB 
3ME "Modify linking type" 2011-06-04 RCSB 
3ME "Modify descriptor"   2011-06-04 RCSB 
3ME "Other modification"  2011-10-27 RCSB 
# 
