data_MCY
# 
_chem_comp.id                                    MCY 
_chem_comp.name                                  "5-METHYL-2'-DEOXYCYTIDINE" 
_chem_comp.type                                  "DNA LINKING" 
_chem_comp.pdbx_type                             ATOMN 
_chem_comp.formula                               "C10 H15 N3 O4" 
_chem_comp.mon_nstd_parent_comp_id               DC 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2000-06-01 
_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                        241.244 
_chem_comp.one_letter_code                       C 
_chem_comp.three_letter_code                     MCY 
_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        1BAE 
_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 
MCY N1     N1   N 0 1 N N N -1.370 -2.857 2.172  -0.251 -0.396 0.778  N1     MCY 1  
MCY C2     C2   C 0 1 N N N -1.405 -2.042 1.062  0.163  0.872  0.950  C2     MCY 2  
MCY N3     N3   N 0 1 N N N -1.369 -0.699 1.266  0.446  1.345  2.162  N3     MCY 3  
MCY C4     C4   C 0 1 N N N -1.305 -0.178 2.504  0.321  0.575  3.236  C4     MCY 4  
MCY C5     C5   C 0 1 N N N -1.275 -0.990 3.583  -0.104 -0.760 3.090  C5     MCY 5  
MCY C6     C6   C 0 1 N N N -1.310 -2.321 3.417  -0.388 -1.226 1.850  C6     MCY 6  
MCY O2     O2   O 0 1 N N N -1.470 -2.524 -0.068 0.280  1.601  -0.020 O2     MCY 7  
MCY N4     N4   N 0 1 N N N -1.260 1.146  2.657  0.617  1.075  4.483  N4     MCY 8  
MCY "C1'"  C1*  C 0 1 N N R -1.357 -4.320 1.958  -0.555 -0.887 -0.567 "C1'"  MCY 9  
MCY "C2'"  C2*  C 0 1 N N N 0.040  -4.872 2.183  -1.679 -0.039 -1.192 "C2'"  MCY 10 
MCY "C3'"  C3*  C 0 1 N N S -0.044 -5.804 3.364  -1.049 0.531  -2.486 "C3'"  MCY 11 
MCY "C4'"  C4*  C 0 1 N N R -1.528 -5.972 3.655  0.121  -0.452 -2.738 "C4'"  MCY 12 
MCY "O4'"  O4*  O 0 1 N N N -2.251 -4.994 2.872  0.601  -0.756 -1.409 "O4'"  MCY 13 
MCY "O3'"  O3*  O 0 1 N N N 0.577  -7.062 3.074  -1.984 0.500  -3.566 "O3'"  MCY 14 
MCY "C5'"  C5*  C 0 1 N N N -1.812 -5.792 5.143  1.216  0.216  -3.571 "C5'"  MCY 15 
MCY "O5'"  O5*  O 0 1 N N N -1.538 -4.456 5.575  2.282  -0.710 -3.789 "O5'"  MCY 16 
MCY C5A    C5A  C 0 1 N N N -1.199 -0.398 4.989  -0.247 -1.653 4.295  C5A    MCY 17 
MCY H6     H6   H 0 1 N N N -1.294 -2.976 4.287  -0.720 -2.244 1.713  H6     MCY 18 
MCY HN41   1HN4 H 0 0 N N N -1.204 1.548  3.582  0.917  1.992  4.579  HN41   MCY 19 
MCY HN42   2HN4 H 0 0 N N N -1.284 1.746  1.845  0.525  0.510  5.266  HN42   MCY 20 
MCY "H1'"  H1*  H 0 1 N N N -1.666 -4.533 0.936  -0.862 -1.932 -0.519 "H1'"  MCY 21 
MCY "H2'"  1H2* H 0 1 N N N 0.733  -4.059 2.398  -2.540 -0.663 -1.431 "H2'"  MCY 22 
MCY "H2''" 2H2* H 0 0 N N N 0.370  -5.420 1.301  -1.967 0.768  -0.519 "H2''" MCY 23 
MCY "H3'"  H3*  H 0 1 N N N 0.443  -5.337 4.225  -0.678 1.543  -2.324 "H3'"  MCY 24 
MCY "H4'"  H4*  H 0 1 N N N -1.842 -6.974 3.348  -0.236 -1.356 -3.231 "H4'"  MCY 25 
MCY "HO3'" *HO3 H 0 0 N Y N 0.524  -7.649 3.818  -2.729 1.059  -3.307 "HO3'" MCY 26 
MCY "H5'"  1H5* H 0 1 N N N -2.861 -6.018 5.335  0.804  0.527  -4.531 "H5'"  MCY 27 
MCY "H5''" 2H5* H 0 0 N N N -1.190 -6.484 5.712  1.597  1.088  -3.039 "H5''" MCY 28 
MCY "HO5'" *HO5 H 0 0 N Y N -2.063 -4.296 6.362  2.949  -0.250 -4.316 "HO5'" MCY 29 
MCY H5A1   1H5A H 0 0 N N N -1.769 0.531  5.024  0.025  -1.099 5.192  H5A1   MCY 30 
MCY H5A2   2H5A H 0 0 N N N -0.158 -0.195 5.242  -1.281 -1.990 4.376  H5A2   MCY 31 
MCY H5A3   3H5A H 0 0 N N N -1.616 -1.105 5.705  0.408  -2.517 4.187  H5A3   MCY 32 
# 
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 
MCY N1    C2     SING N N 1  
MCY N1    C6     SING N N 2  
MCY N1    "C1'"  SING N N 3  
MCY C2    N3     SING N N 4  
MCY C2    O2     DOUB N N 5  
MCY N3    C4     DOUB N N 6  
MCY C4    C5     SING N N 7  
MCY C4    N4     SING N N 8  
MCY C5    C6     DOUB N N 9  
MCY C5    C5A    SING N N 10 
MCY C6    H6     SING N N 11 
MCY N4    HN41   SING N N 12 
MCY N4    HN42   SING N N 13 
MCY "C1'" "C2'"  SING N N 14 
MCY "C1'" "O4'"  SING N N 15 
MCY "C1'" "H1'"  SING N N 16 
MCY "C2'" "C3'"  SING N N 17 
MCY "C2'" "H2'"  SING N N 18 
MCY "C2'" "H2''" SING N N 19 
MCY "C3'" "C4'"  SING N N 20 
MCY "C3'" "O3'"  SING N N 21 
MCY "C3'" "H3'"  SING N N 22 
MCY "C4'" "O4'"  SING N N 23 
MCY "C4'" "C5'"  SING N N 24 
MCY "C4'" "H4'"  SING N N 25 
MCY "O3'" "HO3'" SING N N 26 
MCY "C5'" "O5'"  SING N N 27 
MCY "C5'" "H5'"  SING N N 28 
MCY "C5'" "H5''" SING N N 29 
MCY "O5'" "HO5'" SING N N 30 
MCY C5A   H5A1   SING N N 31 
MCY C5A   H5A2   SING N N 32 
MCY C5A   H5A3   SING N N 33 
# 
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 
MCY SMILES           ACDLabs              10.04 "O=C1N=C(N)C(=CN1C2OC(C(O)C2)CO)C"                                                                                                
MCY InChI            InChI                1.02b "InChI=1/C10H15N3O4/c1-5-3-13(10(16)12-9(5)11)8-2-6(15)7(4-14)17-8/h3,6-8,14-15H,2,4H2,1H3,(H2,11,12,16)/t6-,7+,8+/m0/s1/f/h11H2" 
MCY InChIKey         InChI                1.02b LUCHPKXVUGJYGU-WLKPGDTIDK                                                                                                         
MCY SMILES_CANONICAL CACTVS               3.341 "CC1=CN([C@H]2C[C@H](O)[C@@H](CO)O2)C(=O)N=C1N"                                                                                   
MCY SMILES           CACTVS               3.341 "CC1=CN([CH]2C[CH](O)[CH](CO)O2)C(=O)N=C1N"                                                                                       
MCY SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "CC1=CN(C(=O)N=C1N)[C@H]2C[C@@H]([C@H](O2)CO)O"                                                                                   
MCY SMILES           "OpenEye OEToolkits" 1.5.0 "CC1=CN(C(=O)N=C1N)C2CC(C(O2)CO)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 
MCY "SYSTEMATIC NAME" ACDLabs              10.04 "2'-deoxy-5-methylcytidine"                                                              
MCY "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "4-amino-1-[(2R,4S,5R)-4-hydroxy-5-(hydroxymethyl)oxolan-2-yl]-5-methyl-pyrimidin-2-one" 
# 
