data_3DT # _chem_comp.id 3DT _chem_comp.name 3-methylthymidine _chem_comp.type non-polymer _chem_comp.pdbx_type HETAIN _chem_comp.formula "C11 H16 N2 O5" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2010-02-16 _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 256.255 _chem_comp.one_letter_code ? _chem_comp.three_letter_code 3DT _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 3LFM _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site PDBJ # 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 3DT N1 N1 N 0 1 N N N 29.108 -6.783 -28.872 -0.544 -0.369 -0.004 N1 3DT 1 3DT C2 C2 C 0 1 N N N 28.562 -7.304 -27.696 -1.601 -1.155 0.271 C2 3DT 2 3DT O2 O2 O 0 1 N N N 29.168 -8.166 -27.060 -1.423 -2.329 0.533 O2 3DT 3 3DT N3 N3 N 0 1 N N N 27.299 -6.870 -27.269 -2.852 -0.660 0.261 N3 3DT 4 3DT C4 C4 C 0 1 N N N 26.591 -5.928 -28.024 -3.066 0.640 -0.027 C4 3DT 5 3DT O4 O4 O 0 1 N N N 25.481 -5.553 -27.648 -4.198 1.089 -0.036 O4 3DT 6 3DT C5 C5 C 0 1 N N N 27.139 -5.417 -29.197 -1.963 1.478 -0.318 C5 3DT 7 3DT C6 C6 C 0 1 N N N 28.394 -5.841 -29.620 -0.718 0.955 -0.301 C6 3DT 8 3DT C7 C7 C 0 1 N N N 26.367 -4.394 -30.030 -2.175 2.934 -0.643 C7 3DT 9 3DT CN CN C 0 1 N N N 26.719 -7.394 -26.012 -3.987 -1.536 0.563 CN 3DT 10 3DT "C1'" "C1'" C 0 1 N N R 30.449 -7.219 -29.331 0.807 -0.936 0.021 "C1'" 3DT 11 3DT "C2'" "C2'" C 0 1 N N N 30.388 -8.224 -30.476 1.418 -0.896 -1.394 "C2'" 3DT 12 3DT "C3'" "C3'" C 0 1 N N S 31.877 -8.208 -30.811 2.706 -0.054 -1.227 "C3'" 3DT 13 3DT "O3'" "O3'" O 0 1 N N N 32.604 -8.894 -29.787 3.783 -0.617 -1.980 "O3'" 3DT 14 3DT "C4'" "C4'" C 0 1 N N R 32.170 -6.708 -30.789 2.975 -0.170 0.294 "C4'" 3DT 15 3DT "O4'" "O4'" O 0 1 N N N 31.208 -6.131 -29.884 1.653 -0.146 0.873 "O4'" 3DT 16 3DT "C5'" "C5'" C 0 1 N N N 31.936 -6.097 -32.174 3.801 1.020 0.787 "C5'" 3DT 17 3DT "O5'" "O5'" O 0 1 N N N 30.630 -6.432 -32.645 4.133 0.832 2.164 "O5'" 3DT 18 3DT H6 H6 H 0 1 N N N 28.819 -5.442 -30.529 0.135 1.579 -0.520 H6 3DT 19 3DT H7 H7 H 0 1 N N N 26.962 -4.114 -30.912 -3.240 3.163 -0.607 H7 3DT 20 3DT H7A H7A H 0 1 N N N 25.412 -4.833 -30.356 -1.646 3.550 0.084 H7A 3DT 21 3DT H7B H7B H 0 1 N N N 26.171 -3.499 -29.421 -1.792 3.143 -1.643 H7B 3DT 22 3DT HN HN H 0 1 N N N 25.731 -6.940 -25.846 -4.183 -1.519 1.635 HN 3DT 23 3DT HNA HNA H 0 1 N N N 26.613 -8.486 -26.085 -4.869 -1.187 0.026 HNA 3DT 24 3DT HNB HNB H 0 1 N N N 27.383 -7.145 -25.171 -3.752 -2.554 0.253 HNB 3DT 25 3DT "H1'" "H1'" H 0 1 N N N 30.905 -7.648 -28.426 0.771 -1.964 0.381 "H1'" 3DT 26 3DT "H2'" "H2'" H 0 1 N N N 30.008 -9.213 -30.182 1.661 -1.904 -1.732 "H2'" 3DT 27 3DT "H2'A" "H2'A" H 0 0 N N N 29.740 -7.913 -31.309 0.733 -0.413 -2.091 "H2'A" 3DT 28 3DT "H3'" "H3'" H 0 1 N N N 32.152 -8.698 -31.757 2.533 0.983 -1.515 "H3'" 3DT 29 3DT "HO3'" "HO3'" H 0 0 N N N 33.531 -8.884 -29.995 3.622 -0.650 -2.933 "HO3'" 3DT 30 3DT "H4'" "H4'" H 0 1 N N N 33.212 -6.520 -30.490 3.478 -1.109 0.525 "H4'" 3DT 31 3DT "H5'" "H5'" H 0 1 N N N 32.028 -5.003 -32.108 4.716 1.096 0.200 "H5'" 3DT 32 3DT "H5'A" "H5'A" H 0 0 N N N 32.686 -6.490 -32.875 3.220 1.936 0.675 "H5'A" 3DT 33 3DT "HO5'" "HO5'" H 0 0 N N N 30.495 -6.049 -33.504 4.657 1.550 2.544 "HO5'" 3DT 34 # 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 3DT N1 C2 SING N N 1 3DT N1 C6 SING N N 2 3DT N1 "C1'" SING N N 3 3DT C2 O2 DOUB N N 4 3DT C2 N3 SING N N 5 3DT N3 C4 SING N N 6 3DT N3 CN SING N N 7 3DT C4 O4 DOUB N N 8 3DT C4 C5 SING N N 9 3DT C5 C6 DOUB N N 10 3DT C5 C7 SING N N 11 3DT "C1'" "C2'" SING N N 12 3DT "C1'" "O4'" SING N N 13 3DT "C2'" "C3'" SING N N 14 3DT "C3'" "O3'" SING N N 15 3DT "C3'" "C4'" SING N N 16 3DT "C4'" "O4'" SING N N 17 3DT "C4'" "C5'" SING N N 18 3DT "C5'" "O5'" SING N N 19 3DT C6 H6 SING N N 20 3DT C7 H7 SING N N 21 3DT C7 H7A SING N N 22 3DT C7 H7B SING N N 23 3DT CN HN SING N N 24 3DT CN HNA SING N N 25 3DT CN HNB SING N N 26 3DT "C1'" "H1'" SING N N 27 3DT "C2'" "H2'" SING N N 28 3DT "C2'" "H2'A" SING N N 29 3DT "C3'" "H3'" SING N N 30 3DT "O3'" "HO3'" SING N N 31 3DT "C4'" "H4'" SING N N 32 3DT "C5'" "H5'" SING N N 33 3DT "C5'" "H5'A" SING N N 34 3DT "O5'" "HO5'" SING N N 35 # 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 3DT SMILES_CANONICAL CACTVS 3.352 "CN1C(=O)N(C=C(C)C1=O)[C@H]2C[C@H](O)[C@@H](CO)O2" 3DT SMILES CACTVS 3.352 "CN1C(=O)N(C=C(C)C1=O)[CH]2C[CH](O)[CH](CO)O2" 3DT SMILES_CANONICAL "OpenEye OEToolkits" 1.7.0 "CC1=CN(C(=O)N(C1=O)C)[C@H]2C[C@@H]([C@H](O2)CO)O" 3DT SMILES "OpenEye OEToolkits" 1.7.0 "CC1=CN(C(=O)N(C1=O)C)C2CC(C(O2)CO)O" 3DT InChI InChI 1.03 "InChI=1S/C11H16N2O5/c1-6-4-13(11(17)12(2)10(6)16)9-3-7(15)8(5-14)18-9/h4,7-9,14-15H,3,5H2,1-2H3/t7-,8+,9+/m0/s1" 3DT InChIKey InChI 1.03 JCVDICFLPGDHAT-DJLDLDEBSA-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 3DT "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.6.1 "1-[(2R,4S,5R)-4-hydroxy-5-(hydroxymethyl)oxolan-2-yl]-3,5-dimethyl-pyrimidine-2,4-dione" # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site 3DT "Create component" 2010-02-16 PDBJ 3DT "Modify descriptor" 2011-06-04 RCSB #