data_0DT # _chem_comp.id 0DT _chem_comp.name ;2'-DEOXY-L-RIBO-FURANOSYL THYMIDINE-5'-MONOPHOSPHATE ; _chem_comp.type "L-DNA LINKING" _chem_comp.pdbx_type ATOMN _chem_comp.formula "C10 H15 N2 O8 P" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2009-07-27 _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 DRT _chem_comp.formula_weight 322.208 _chem_comp.one_letter_code T _chem_comp.three_letter_code 0DT _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 1FV8 _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 0DT OP3 O3P O 0 1 N Y N 2.710 -9.041 0.646 4.787 1.712 -1.378 OP3 0DT 1 0DT P P P 0 1 N N N 2.197 -10.472 1.166 4.284 0.902 -0.080 P 0DT 2 0DT OP1 O1P O 0 1 N N N 2.389 -11.451 0.066 5.345 -0.032 0.360 OP1 0DT 3 0DT OP2 O2P O 0 1 N N N 2.811 -10.732 2.493 3.958 1.940 1.107 OP2 0DT 4 0DT "O5'" "O5'" O 0 1 N N N 0.634 -10.247 1.365 2.955 0.071 -0.447 "O5'" 0DT 5 0DT "C5'" "C5'" C 0 1 N N N 0.146 -9.278 2.293 2.325 -0.831 0.464 "C5'" 0DT 6 0DT "C4'" "C4'" C 0 1 N N S -0.057 -9.914 3.649 1.093 -1.449 -0.201 "C4'" 0DT 7 0DT "O4'" "O4'" O 0 1 N N N -0.079 -11.351 3.495 0.087 -0.439 -0.433 "O4'" 0DT 8 0DT "C3'" "C3'" C 0 1 N N R -1.374 -9.581 4.340 0.421 -2.464 0.751 "C3'" 0DT 9 0DT "O3'" "O3'" O 0 1 N N N -1.251 -9.769 5.754 0.818 -3.796 0.424 "O3'" 0DT 10 0DT "C2'" "C2'" C 0 1 N N N -2.322 -10.603 3.741 -1.091 -2.272 0.497 "C2'" 0DT 11 0DT "C1'" "C1'" C 0 1 N N S -1.424 -11.820 3.531 -1.153 -1.164 -0.578 "C1'" 0DT 12 0DT N1 N1 N 0 1 N N N -1.685 -12.550 2.274 -2.294 -0.278 -0.332 N1 0DT 13 0DT C2 C2 C 0 1 N N N -2.249 -13.804 2.352 -3.545 -0.770 -0.389 C2 0DT 14 0DT O2 O2 O 0 1 N N N -2.533 -14.341 3.408 -3.715 -1.946 -0.644 O2 0DT 15 0DT N3 N3 N 0 1 N N N -2.469 -14.408 1.144 -4.610 0.022 -0.167 N3 0DT 16 0DT C4 C4 C 0 1 N N N -2.191 -13.900 -0.106 -4.438 1.329 0.118 C4 0DT 17 0DT O4 O4 O 0 1 N N N -2.459 -14.560 -1.106 -5.402 2.046 0.320 O4 0DT 18 0DT C5 C5 C 0 1 N N N -1.597 -12.582 -0.118 -3.127 1.859 0.181 C5 0DT 19 0DT C5M C5M C 0 1 N N N -1.276 -11.941 -1.431 -2.908 3.316 0.498 C5M 0DT 20 0DT C6 C6 C 0 1 N N N -1.371 -11.979 1.057 -2.076 1.041 -0.040 C6 0DT 21 0DT HOP3 HOP3 H 0 0 N N N 3.025 -9.122 -0.247 5.586 2.236 -1.229 HOP3 0DT 22 0DT HOP2 HOP2 H 0 0 N N N 3.285 -11.555 2.467 3.270 2.584 0.888 HOP2 0DT 23 0DT "H5'" "H5'1" H 0 1 N N N 0.876 -8.460 2.381 3.025 -1.620 0.737 "H5'" 0DT 24 0DT "H5''" "H5'2" H 0 0 N N N -0.814 -8.880 1.931 2.021 -0.289 1.360 "H5''" 0DT 25 0DT "H4'" "H4'" H 0 1 N N N 0.769 -9.520 4.259 1.370 -1.931 -1.138 "H4'" 0DT 26 0DT "H3'" "H3'" H 0 1 N N N -1.704 -8.541 4.198 0.668 -2.236 1.788 "H3'" 0DT 27 0DT "HO3'" H3T H 0 0 N Y N -2.076 -9.559 6.175 0.425 -4.475 0.990 "HO3'" 0DT 28 0DT "H2'" "H2'1" H 0 1 N N N -3.159 -10.827 4.418 -1.535 -3.194 0.121 "H2'" 0DT 29 0DT "H2''" "H2'2" H 0 0 N N N -2.756 -10.249 2.794 -1.594 -1.948 1.408 "H2''" 0DT 30 0DT "H1'" "H1'" H 0 1 N N N -1.623 -12.523 4.353 -1.222 -1.604 -1.573 "H1'" 0DT 31 0DT H3 H3 H 0 1 N N N -2.877 -15.320 1.172 -5.505 -0.349 -0.212 H3 0DT 32 0DT H71 H5M1 H 0 1 N N N -0.833 -10.949 -1.257 -3.871 3.805 0.648 H71 0DT 33 0DT H72 H5M2 H 0 1 N N N -0.561 -12.570 -1.981 -2.310 3.405 1.405 H72 0DT 34 0DT H73 H5M3 H 0 1 N N N -2.198 -11.833 -2.021 -2.384 3.793 -0.331 H73 0DT 35 0DT H6 H6 H 0 1 N N N -0.921 -10.997 1.052 -1.069 1.427 0.008 H6 0DT 36 # 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 0DT OP3 P SING N N 1 0DT OP3 HOP3 SING N N 2 0DT P OP1 DOUB N N 3 0DT P OP2 SING N N 4 0DT P "O5'" SING N N 5 0DT OP2 HOP2 SING N N 6 0DT "O5'" "C5'" SING N N 7 0DT "C5'" "C4'" SING N N 8 0DT "C5'" "H5'" SING N N 9 0DT "C5'" "H5''" SING N N 10 0DT "C4'" "O4'" SING N N 11 0DT "C4'" "C3'" SING N N 12 0DT "C4'" "H4'" SING N N 13 0DT "O4'" "C1'" SING N N 14 0DT "C3'" "O3'" SING N N 15 0DT "C3'" "C2'" SING N N 16 0DT "C3'" "H3'" SING N N 17 0DT "O3'" "HO3'" SING N N 18 0DT "C2'" "C1'" SING N N 19 0DT "C2'" "H2'" SING N N 20 0DT "C2'" "H2''" SING N N 21 0DT "C1'" N1 SING N N 22 0DT "C1'" "H1'" SING N N 23 0DT N1 C2 SING N N 24 0DT N1 C6 SING N N 25 0DT C2 O2 DOUB N N 26 0DT C2 N3 SING N N 27 0DT N3 C4 SING N N 28 0DT N3 H3 SING N N 29 0DT C4 O4 DOUB N N 30 0DT C4 C5 SING N N 31 0DT C5 C5M SING N N 32 0DT C5 C6 DOUB N N 33 0DT C5M H71 SING N N 34 0DT C5M H72 SING N N 35 0DT C5M H73 SING N N 36 0DT C6 H6 SING N N 37 # 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 0DT SMILES ACDLabs 12.01 "O=P(O)(O)OCC2OC(N1C(=O)NC(=O)C(=C1)C)CC2O" 0DT SMILES_CANONICAL CACTVS 3.370 "CC1=CN([C@@H]2C[C@@H](O)[C@H](CO[P](O)(O)=O)O2)C(=O)NC1=O" 0DT SMILES CACTVS 3.370 "CC1=CN([CH]2C[CH](O)[CH](CO[P](O)(O)=O)O2)C(=O)NC1=O" 0DT SMILES_CANONICAL "OpenEye OEToolkits" 1.7.0 "CC1=CN(C(=O)NC1=O)[C@@H]2C[C@H]([C@@H](O2)COP(=O)(O)O)O" 0DT SMILES "OpenEye OEToolkits" 1.7.0 "CC1=CN(C(=O)NC1=O)C2CC(C(O2)COP(=O)(O)O)O" 0DT InChI InChI 1.03 "InChI=1S/C10H15N2O8P/c1-5-3-12(10(15)11-9(5)14)8-2-6(13)7(20-8)4-19-21(16,17)18/h3,6-8,13H,2,4H2,1H3,(H,11,14,15)(H2,16,17,18)/t6-,7+,8+/m1/s1" 0DT InChIKey InChI 1.03 GYOZYWVXFNDGLU-CSMHCCOUSA-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 0DT "SYSTEMATIC NAME" ACDLabs 12.01 "1-(2-deoxy-5-O-phosphono-beta-L-erythro-pentofuranosyl)-5-methylpyrimidine-2,4(1H,3H)-dione" 0DT "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.7.0 "[(2S,3R,5S)-3-hydroxy-5-(5-methyl-2,4-dioxo-pyrimidin-1-yl)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 0DT "Create component" 2009-07-27 RCSB 0DT "Modify descriptor" 2011-06-04 RCSB #