data_T38 # _chem_comp.id T38 _chem_comp.name ;2'-O-ETHOXYMETHYLENE THYMIDINE 5'-MONOPHOSPHATE ; _chem_comp.type "RNA LINKING" _chem_comp.pdbx_type ATOMN _chem_comp.formula "C13 H21 N2 O10 P" _chem_comp.mon_nstd_parent_comp_id DT _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 1998-07-29 _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 396.287 _chem_comp.one_letter_code T _chem_comp.three_letter_code T38 _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 410D _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 T38 P P P 0 1 N N N 10.758 4.422 5.368 -4.571 -1.370 -0.084 P T38 1 T38 O1P O1P O 0 1 N N N 11.966 4.955 4.715 -4.308 -1.823 -1.468 O1P T38 2 T38 O2P O2P O 0 1 N N N 9.983 3.597 4.245 -5.701 -0.223 -0.100 O2P T38 3 T38 O3P O3P O 0 1 N Y N 10.874 3.608 6.597 -5.082 -2.614 0.800 O3P T38 4 T38 "O5'" "O5'" O 0 1 N N N 9.770 5.618 5.679 -3.216 -0.779 0.554 "O5'" T38 5 T38 "C5'" "C5'" C 0 1 N N N 9.469 6.568 4.659 -2.458 0.266 -0.060 "C5'" T38 6 T38 "C4'" "C4'" C 0 1 N N R 8.380 7.490 5.121 -1.237 0.585 0.805 "C4'" T38 7 T38 "O4'" "O4'" O 0 1 N N N 7.125 6.763 5.242 -0.337 -0.536 0.813 "O4'" T38 8 T38 "C3'" "C3'" C 0 1 N N R 8.580 8.048 6.517 -0.471 1.782 0.208 "C3'" T38 9 T38 "O3'" "O3'" O 0 1 N N N 9.499 9.126 6.512 -0.418 2.859 1.146 "O3'" T38 10 T38 "C2'" "C2'" C 0 1 N N R 7.170 8.505 6.858 0.949 1.228 -0.062 "C2'" T38 11 T38 "O2'" "O2'" O 0 1 N N N 6.865 9.702 6.164 1.947 2.187 0.294 "O2'" T38 12 T38 "C1'" "C1'" C 0 1 N N R 6.363 7.324 6.311 1.002 -0.001 0.881 "C1'" T38 13 T38 N1 N1 N 0 1 N N N 6.179 6.288 7.342 1.975 -0.983 0.394 N1 T38 14 T38 C2 C2 C 0 1 N N N 5.117 6.419 8.199 1.811 -1.538 -0.820 C2 T38 15 T38 O2 O2 O 0 1 N N N 4.325 7.331 8.123 0.855 -1.219 -1.501 O2 T38 16 T38 N3 N3 N 0 1 N N N 5.019 5.437 9.145 2.689 -2.443 -1.292 N3 T38 17 T38 C4 C4 C 0 1 N N N 5.860 4.362 9.320 3.753 -2.807 -0.549 C4 T38 18 T38 O4 O4 O 0 1 N N N 5.656 3.576 10.243 4.549 -3.625 -0.976 O4 T38 19 T38 C5 C5 C 0 1 N N N 6.941 4.269 8.360 3.938 -2.231 0.730 C5 T38 20 T38 C5M C5M C 0 1 N N N 7.878 3.112 8.420 5.120 -2.621 1.580 C5M T38 21 T38 C6 C6 C 0 1 N N N 7.047 5.227 7.439 3.045 -1.322 1.177 C6 T38 22 T38 "CA'" "CA'" C 0 1 N N N 5.586 10.284 6.378 2.338 3.045 -0.780 "CA'" T38 23 T38 "CB'" "CB'" C 0 1 N N N 5.052 10.183 4.104 1.261 5.053 -0.035 "CB'" T38 24 T38 "OC'" "OC'" O 0 1 N N N 4.682 9.741 5.424 1.312 4.013 -1.013 "OC'" T38 25 T38 "CD'" "CD'" C 0 1 N N N 4.867 9.180 3.093 0.133 6.026 -0.384 "CD'" T38 26 T38 H2P H2P H 0 1 N N N 10.469 3.638 3.430 -5.924 0.121 0.776 H2P T38 27 T38 H3P H3P H 0 1 N N N 11.790 3.521 6.835 -5.896 -3.021 0.474 H3P T38 28 T38 "H5'1" "H5'1" H 0 0 N N N 10.371 7.155 4.431 -2.129 -0.056 -1.048 "H5'1" T38 29 T38 "H5'2" "H5'2" H 0 0 N N N 9.138 6.038 3.754 -3.078 1.157 -0.155 "H5'2" T38 30 T38 "H4'" "H4'" H 0 1 N N N 8.272 8.320 4.408 -1.553 0.815 1.822 "H4'" T38 31 T38 "H3'" "H3'" H 0 1 N N N 8.895 7.249 7.204 -0.938 2.109 -0.721 "H3'" T38 32 T38 HA HA H 0 1 N N N 9.606 9.456 7.396 -1.285 3.207 1.395 HA T38 33 T38 "H2'" "H2'" H 0 1 N N N 7.038 8.600 7.946 1.057 0.925 -1.103 "H2'" T38 34 T38 "H1'" "H1'" H 0 1 N N N 5.387 7.682 5.952 1.242 0.306 1.899 "H1'" T38 35 T38 H3 H3 H 0 1 N N N 4.250 5.508 9.781 2.555 -2.833 -2.170 H3 T38 36 T38 H5M1 H5M1 H 0 0 N N N 8.629 3.206 7.622 5.722 -3.358 1.048 H5M1 T38 37 T38 H5M2 H5M2 H 0 0 N N N 8.382 3.099 9.398 5.725 -1.739 1.789 H5M2 T38 38 T38 H5M3 H5M3 H 0 0 N N N 7.315 2.177 8.285 4.767 -3.050 2.518 H5M3 T38 39 T38 H6 H6 H 0 1 N N N 7.860 5.166 6.730 3.172 -0.868 2.148 H6 T38 40 T38 "HA'1" "HA'1" H 0 0 N N N 5.237 10.051 7.395 3.265 3.555 -0.518 "HA'1" T38 41 T38 "HA'2" "HA'2" H 0 0 N N N 5.648 11.375 6.252 2.490 2.452 -1.681 "HA'2" T38 42 T38 "HB'1" "HB'1" H 0 0 N N N 4.437 11.057 3.844 1.075 4.619 0.947 "HB'1" T38 43 T38 "HB'2" "HB'2" H 0 0 N N N 6.113 10.472 4.118 2.211 5.587 -0.023 "HB'2" T38 44 T38 "HD'1" "HD'1" H 0 0 N N N 5.168 9.584 2.115 0.318 6.460 -1.367 "HD'1" T38 45 T38 "HD'2" "HD'2" H 0 0 N N N 5.484 8.301 3.332 -0.817 5.491 -0.397 "HD'2" T38 46 T38 "HD'3" "HD'3" H 0 0 N N N 3.808 8.886 3.058 0.093 6.819 0.362 "HD'3" T38 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 T38 P O1P DOUB N N 1 T38 P O2P SING N N 2 T38 P O3P SING N N 3 T38 P "O5'" SING N N 4 T38 O2P H2P SING N N 5 T38 O3P H3P SING N N 6 T38 "O5'" "C5'" SING N N 7 T38 "C5'" "C4'" SING N N 8 T38 "C5'" "H5'1" SING N N 9 T38 "C5'" "H5'2" SING N N 10 T38 "C4'" "O4'" SING N N 11 T38 "C4'" "C3'" SING N N 12 T38 "C4'" "H4'" SING N N 13 T38 "O4'" "C1'" SING N N 14 T38 "C3'" "O3'" SING N N 15 T38 "C3'" "C2'" SING N N 16 T38 "C3'" "H3'" SING N N 17 T38 "O3'" HA SING N N 18 T38 "C2'" "O2'" SING N N 19 T38 "C2'" "C1'" SING N N 20 T38 "C2'" "H2'" SING N N 21 T38 "O2'" "CA'" SING N N 22 T38 "C1'" N1 SING N N 23 T38 "C1'" "H1'" SING N N 24 T38 N1 C2 SING N N 25 T38 N1 C6 SING N N 26 T38 C2 O2 DOUB N N 27 T38 C2 N3 SING N N 28 T38 N3 C4 SING N N 29 T38 N3 H3 SING N N 30 T38 C4 O4 DOUB N N 31 T38 C4 C5 SING N N 32 T38 C5 C5M SING N N 33 T38 C5 C6 DOUB N N 34 T38 C5M H5M1 SING N N 35 T38 C5M H5M2 SING N N 36 T38 C5M H5M3 SING N N 37 T38 C6 H6 SING N N 38 T38 "CA'" "OC'" SING N N 39 T38 "CA'" "HA'1" SING N N 40 T38 "CA'" "HA'2" SING N N 41 T38 "CB'" "OC'" SING N N 42 T38 "CB'" "CD'" SING N N 43 T38 "CB'" "HB'1" SING N N 44 T38 "CB'" "HB'2" SING N N 45 T38 "CD'" "HD'1" SING N N 46 T38 "CD'" "HD'2" SING N N 47 T38 "CD'" "HD'3" 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 T38 SMILES ACDLabs 12.01 "P(=O)(O)(O)OCC1OC(C(C1O)OCOCC)N2C(=O)NC(=O)C(C)=C2" T38 InChI InChI 1.03 "InChI=1S/C13H21N2O10P/c1-3-22-6-23-10-9(16)8(5-24-26(19,20)21)25-12(10)15-4-7(2)11(17)14-13(15)18/h4,8-10,12,16H,3,5-6H2,1-2H3,(H,14,17,18)(H2,19,20,21)/t8-,9-,10-,12-/m1/s1" T38 InChIKey InChI 1.03 ZHEHKUXUPODKJV-DNRKLUKYSA-N T38 SMILES_CANONICAL CACTVS 3.385 "CCOCO[C@@H]1[C@H](O)[C@@H](CO[P](O)(O)=O)O[C@H]1N2C=C(C)C(=O)NC2=O" T38 SMILES CACTVS 3.385 "CCOCO[CH]1[CH](O)[CH](CO[P](O)(O)=O)O[CH]1N2C=C(C)C(=O)NC2=O" T38 SMILES_CANONICAL "OpenEye OEToolkits" 1.7.6 "CCOCO[C@@H]1[C@@H]([C@H](O[C@H]1N2C=C(C(=O)NC2=O)C)COP(=O)(O)O)O" T38 SMILES "OpenEye OEToolkits" 1.7.6 "CCOCOC1C(C(OC1N2C=C(C(=O)NC2=O)C)COP(=O)(O)O)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 T38 "SYSTEMATIC NAME" ACDLabs 12.01 ;2'-O-(ethoxymethyl)-5-methyluridine 5'-(dihydrogen phosphate) ; T38 "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.7.6 "[(2R,3R,4R,5R)-4-(ethoxymethoxy)-5-[5-methyl-2,4-bis(oxidanylidene)pyrimidin-1-yl]-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 T38 "Create component" 1998-07-29 RCSB T38 "Modify descriptor" 2011-06-04 RCSB T38 "Modify parent residue" 2018-03-14 RCSB #