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 2011-06-04 _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 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" MCY InChI InChI 1.03 "InChI=1S/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" MCY InChIKey InChI 1.03 LUCHPKXVUGJYGU-XLPZGREQSA-N # 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" # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site MCY "Create component" 2000-06-01 RCSB MCY "Modify descriptor" 2011-06-04 RCSB #