data_SMT # _chem_comp.id SMT _chem_comp.name "2'-[(METHYLTHIO)ETHYLOXY]-THYMIDINE-5'-MONOPHOSPHATE" _chem_comp.type "RNA LINKING" _chem_comp.pdbx_type ATOMN _chem_comp.formula "C13 H21 N2 O9 P S" _chem_comp.mon_nstd_parent_comp_id DT _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2002-09-10 _chem_comp.pdbx_modified_date 2018-03-14 _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 412.353 _chem_comp.one_letter_code T _chem_comp.three_letter_code SMT _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 1MLX _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 SMT P P P 0 1 N N N 10.751 4.213 5.406 -5.261 0.738 -0.269 P SMT 1 SMT OP1 O1P O 0 1 N N N 11.971 4.728 4.682 -5.124 0.303 -1.677 OP1 SMT 2 SMT OP2 O2P O 0 1 N N N 10.916 3.445 6.670 -5.796 2.256 -0.226 OP2 SMT 3 SMT OP3 O3P O 0 1 N Y N ? ? ? -6.307 -0.221 0.490 OP3 SMT 4 SMT "O5'" "O5'" O 0 1 N N N 9.743 5.400 5.717 -3.828 0.654 0.460 "O5'" SMT 5 SMT "C5'" "C5'" C 0 1 N N N 9.440 6.334 4.704 -2.661 1.311 -0.038 "C5'" SMT 6 SMT "C4'" "C4'" C 0 1 N N R 8.344 7.233 5.184 -1.479 1.024 0.890 "C4'" SMT 7 SMT "O4'" "O4'" O 0 1 N N N 7.136 6.429 5.377 -1.141 -0.372 0.834 "O4'" SMT 8 SMT "C3'" "C3'" C 0 1 N N R 8.503 7.870 6.523 -0.241 1.814 0.421 "C3'" SMT 9 SMT "O3'" "O3'" O 0 1 N N N 9.445 8.960 6.469 0.201 2.705 1.447 "O3'" SMT 10 SMT "C2'" "C2'" C 0 1 N N R 7.087 8.301 6.812 0.825 0.724 0.153 "C2'" SMT 11 SMT "O2'" "O2'" O 0 1 N N N 6.828 9.421 6.046 2.110 1.141 0.621 "O2'" SMT 12 SMT "C1'" "C1'" C 0 1 N N R 6.364 7.051 6.458 0.292 -0.466 0.990 "C1'" SMT 13 SMT N1 N1 N 0 1 N N N 6.251 6.036 7.511 0.787 -1.737 0.455 N1 SMT 14 SMT C2 C2 C 0 1 N N N 5.185 6.193 8.395 0.483 -2.092 -0.806 C2 SMT 15 SMT O2 O2 O 0 1 N N N 4.390 7.127 8.249 -0.200 -1.354 -1.489 O2 SMT 16 SMT N3 N3 N 0 1 N N N 5.092 5.273 9.351 0.925 -3.254 -1.323 N3 SMT 17 SMT C4 C4 C 0 1 N N N 6.000 4.226 9.620 1.684 -4.084 -0.579 C4 SMT 18 SMT O4 O4 O 0 1 N N N 5.744 3.447 10.583 2.085 -5.135 -1.046 O4 SMT 19 SMT C5 C5 C 0 1 N N N 7.097 4.084 8.664 2.011 -3.722 0.750 C5 SMT 20 SMT C5A C5A C 0 1 N N N 8.129 3.062 8.827 2.858 -4.631 1.602 C5A SMT 21 SMT C6 C6 C 0 1 N N N 7.115 5.047 7.708 1.559 -2.548 1.241 C6 SMT 22 SMT "CA'" "CA'" C 0 1 N N N 5.405 9.996 6.308 2.896 1.815 -0.364 "CA'" SMT 23 SMT CB CB C 0 1 N N N ? ? ? 4.242 2.214 0.244 CB SMT 24 SMT SC SC S 0 1 N N N ? ? ? 5.241 3.069 -1.005 SC SMT 25 SMT CD CD C 0 1 N N N ? ? ? 6.771 3.455 -0.111 CD SMT 26 SMT H2P H2P H 0 1 N N N 11.840 3.370 6.877 -5.909 2.608 0.667 H2P SMT 27 SMT H3P H3P H 0 1 N N N ? ? ? -7.194 -0.220 0.104 H3P SMT 28 SMT "H5'" "H5'" H 0 1 N N N 10.334 6.932 4.474 -2.435 0.941 -1.039 "H5'" SMT 29 SMT "H5'2" "H5'2" H 0 0 N N N 9.112 5.803 3.798 -2.838 2.385 -0.079 "H5'2" SMT 30 SMT "H4'" "H4'" H 0 1 N N N 8.156 8.011 4.430 -1.734 1.303 1.912 "H4'" SMT 31 SMT "H3'" "H3'" H 0 1 N N N 8.820 7.119 7.261 -0.464 2.365 -0.492 "H3'" SMT 32 SMT HO3 HO3 H 0 1 N Y N 9.529 9.349 7.332 -0.452 3.373 1.696 HO3 SMT 33 SMT "H2'" "H2'" H 0 1 N N N 6.974 8.510 7.886 0.863 0.469 -0.906 "H2'" SMT 34 SMT "H1'" "H1'" H 0 1 N N N 5.360 7.308 6.089 0.571 -0.354 2.038 "H1'" SMT 35 SMT H3 H3 H 0 1 N N N 4.290 5.329 9.945 0.696 -3.495 -2.235 H3 SMT 36 SMT H5A H5A H 0 1 N N N 8.851 3.134 8.000 3.126 -5.520 1.031 H5A SMT 37 SMT H5A1 H5A1 H 0 0 N N N 8.650 3.217 9.783 3.764 -4.106 1.904 H5A1 SMT 38 SMT H5A2 H5A2 H 0 0 N N N 7.663 2.066 8.821 2.296 -4.925 2.489 H5A2 SMT 39 SMT H6 H6 H 0 1 N N N 7.942 5.003 7.015 1.803 -2.253 2.251 H6 SMT 40 SMT HA1 HA1 H 0 1 N N N 5.135 10.050 7.373 3.063 1.151 -1.212 HA1 SMT 41 SMT HA2 HA2 H 0 1 N N N 5.224 10.972 5.834 2.370 2.709 -0.700 HA2 SMT 42 SMT HB1 HB1 H 0 1 N N N ? ? ? 4.076 2.877 1.093 HB1 SMT 43 SMT HB2 HB2 H 0 1 N N N ? ? ? 4.768 1.320 0.580 HB2 SMT 44 SMT HD1 HD1 H 0 1 N N N ? ? ? 6.541 4.088 0.747 HD1 SMT 45 SMT HD2 HD2 H 0 1 N N N ? ? ? 7.234 2.530 0.234 HD2 SMT 46 SMT HD3 HD3 H 0 1 N N N ? ? ? 7.458 3.979 -0.775 HD3 SMT 47 # 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 SMT P OP1 DOUB N N 1 SMT P OP2 SING N N 2 SMT P OP3 SING N N 3 SMT P "O5'" SING N N 4 SMT OP2 H2P SING N N 5 SMT OP3 H3P SING N N 6 SMT "O5'" "C5'" SING N N 7 SMT "C5'" "C4'" SING N N 8 SMT "C5'" "H5'" SING N N 9 SMT "C5'" "H5'2" SING N N 10 SMT "C4'" "O4'" SING N N 11 SMT "C4'" "C3'" SING N N 12 SMT "C4'" "H4'" SING N N 13 SMT "O4'" "C1'" SING N N 14 SMT "C3'" "O3'" SING N N 15 SMT "C3'" "C2'" SING N N 16 SMT "C3'" "H3'" SING N N 17 SMT "O3'" HO3 SING N N 18 SMT "C2'" "O2'" SING N N 19 SMT "C2'" "C1'" SING N N 20 SMT "C2'" "H2'" SING N N 21 SMT "O2'" "CA'" SING N N 22 SMT "C1'" N1 SING N N 23 SMT "C1'" "H1'" SING N N 24 SMT N1 C2 SING N N 25 SMT N1 C6 SING N N 26 SMT C2 O2 DOUB N N 27 SMT C2 N3 SING N N 28 SMT N3 C4 SING N N 29 SMT N3 H3 SING N N 30 SMT C4 O4 DOUB N N 31 SMT C4 C5 SING N N 32 SMT C5 C5A SING N N 33 SMT C5 C6 DOUB N N 34 SMT C5A H5A SING N N 35 SMT C5A H5A1 SING N N 36 SMT C5A H5A2 SING N N 37 SMT C6 H6 SING N N 38 SMT "CA'" CB SING N N 39 SMT "CA'" HA1 SING N N 40 SMT "CA'" HA2 SING N N 41 SMT CB SC SING N N 42 SMT CB HB1 SING N N 43 SMT CB HB2 SING N N 44 SMT SC CD SING N N 45 SMT CD HD1 SING N N 46 SMT CD HD2 SING N N 47 SMT CD HD3 SING N N 48 # 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 SMT SMILES ACDLabs 12.01 "P(=O)(O)(O)OCC1OC(C(C1O)OCCSC)N2C(=O)NC(=O)C(C)=C2" SMT InChI InChI 1.03 "InChI=1S/C13H21N2O9PS/c1-7-5-15(13(18)14-11(7)17)12-10(22-3-4-26-2)9(16)8(24-12)6-23-25(19,20)21/h5,8-10,12,16H,3-4,6H2,1-2H3,(H,14,17,18)(H2,19,20,21)/t8-,9-,10-,12-/m1/s1" SMT InChIKey InChI 1.03 JQQIRBYIPIMLTK-DNRKLUKYSA-N SMT SMILES_CANONICAL CACTVS 3.385 "CSCCO[C@@H]1[C@H](O)[C@@H](CO[P](O)(O)=O)O[C@H]1N2C=C(C)C(=O)NC2=O" SMT SMILES CACTVS 3.385 "CSCCO[CH]1[CH](O)[CH](CO[P](O)(O)=O)O[CH]1N2C=C(C)C(=O)NC2=O" SMT SMILES_CANONICAL "OpenEye OEToolkits" 1.7.6 "CC1=CN(C(=O)NC1=O)[C@H]2[C@@H]([C@@H]([C@H](O2)COP(=O)(O)O)O)OCCSC" SMT SMILES "OpenEye OEToolkits" 1.7.6 "CC1=CN(C(=O)NC1=O)C2C(C(C(O2)COP(=O)(O)O)O)OCCSC" # 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 SMT "SYSTEMATIC NAME" ACDLabs 12.01 ;5-methyl-2'-O-[2-(methylsulfanyl)ethyl]uridine 5'-(dihydrogen phosphate) ; SMT "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.7.6 "[(2R,3R,4R,5R)-5-[5-methyl-2,4-bis(oxidanylidene)pyrimidin-1-yl]-4-(2-methylsulfanylethoxy)-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 SMT "Create component" 2002-09-10 RCSB SMT "Modify descriptor" 2011-06-04 RCSB SMT "Modify parent residue" 2018-03-14 RCSB #