data_T39 # _chem_comp.id T39 _chem_comp.name ;2'-O-METHOXYETHYLENE 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 2013-01-10 _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 T39 _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 411D _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 T39 P P P 0 1 N N N -4.559 6.080 7.621 5.145 0.075 -0.028 P T39 1 T39 OP1 OP1 O 0 1 N N N -5.756 6.865 7.275 5.833 -1.194 -0.354 OP1 T39 2 T39 OP2 OP2 O 0 1 N N N -4.719 4.826 8.388 5.009 0.969 -1.360 OP2 T39 3 T39 "O5'" "O5'" O 0 1 N N N -3.686 5.796 6.315 3.678 -0.245 0.555 "O5'" T39 4 T39 "C5'" "C5'" C 0 1 N N N -3.385 6.839 5.374 2.719 -1.040 -0.145 "C5'" T39 5 T39 "C4'" "C4'" C 0 1 N N R -2.338 6.393 4.391 1.439 -1.144 0.688 "C4'" T39 6 T39 "O4'" "O4'" O 0 1 N N N -1.089 6.154 5.094 0.814 0.147 0.786 "O4'" T39 7 T39 "C3'" "C3'" C 0 1 N N R -2.591 5.077 3.659 0.438 -2.086 -0.008 "C3'" T39 8 T39 "O3'" "O3'" O 0 1 N N N -3.489 5.187 2.560 0.127 -3.197 0.837 "O3'" T39 9 T39 "C2'" "C2'" C 0 1 N N R -1.195 4.716 3.194 -0.816 -1.207 -0.234 "C2'" T39 10 T39 "O2'" "O2'" O 0 1 N N N -0.823 5.499 2.077 -2.011 -1.942 0.039 "O2'" T39 11 T39 "C1'" "C1'" C 0 1 N N R -0.383 5.106 4.435 -0.613 -0.077 0.806 "C1'" T39 12 T39 N1 N1 N 0 1 N N N -0.202 3.962 5.361 -1.330 1.134 0.399 N1 T39 13 T39 C2 C2 C 0 1 N N N 0.885 3.135 5.134 -0.963 1.781 -0.722 C2 T39 14 T39 O2 O2 O 0 1 N N N 1.671 3.278 4.215 -0.039 1.353 -1.385 O2 T39 15 T39 N3 N3 N 0 1 N N N 1.020 2.113 6.022 -1.605 2.895 -1.119 N3 T39 16 T39 C4 C4 C 0 1 N N N 0.200 1.824 7.089 -2.632 3.383 -0.394 C4 T39 17 T39 O4 O4 O 0 1 N N N 0.467 0.862 7.799 -3.214 4.391 -0.753 O4 T39 18 T39 C5 C5 C 0 1 N N N -0.924 2.713 7.270 -3.029 2.712 0.788 C5 T39 19 T39 C7 C7 C 0 1 N N N -1.876 2.466 8.406 -4.173 3.236 1.616 C7 T39 20 T39 C6 C6 C 0 1 N N N -1.069 3.733 6.415 -2.371 1.593 1.160 C6 T39 21 T39 "CA'" "CA'" C 0 1 N N N 0.493 5.193 1.578 -2.561 -2.602 -1.103 "CA'" T39 22 T39 "CD'" "CD'" C 0 1 N N N 0.035 7.582 -0.306 -6.059 -3.017 0.120 "CD'" T39 23 T39 "CB'" "CB'" C 0 1 N N N 1.293 6.397 1.442 -3.830 -3.353 -0.696 "CB'" T39 24 T39 "OC'" "OC'" O 0 1 N N N 0.497 7.548 1.068 -4.827 -2.416 -0.284 "OC'" T39 25 T39 OP3 OP3 O 0 1 N Y N -3.667 7.084 8.485 5.997 0.881 1.075 OP3 T39 26 T39 HOP2 HOP2 H 0 0 N N N -5.640 4.681 8.570 4.566 1.817 -1.221 HOP2 T39 27 T39 "H5'" "H5'" H 0 1 N N N -3.014 7.719 5.919 2.492 -0.575 -1.104 "H5'" T39 28 T39 "H5''" "H5''" H 0 0 N N N -4.301 7.105 4.827 3.126 -2.037 -0.312 "H5''" T39 29 T39 "H4'" "H4'" H 0 1 N N N -2.192 7.186 3.643 1.674 -1.519 1.684 "H4'" T39 30 T39 "H3'" "H3'" H 0 1 N N N -2.944 4.323 4.378 0.838 -2.433 -0.960 "H3'" T39 31 T39 "HO3'" "HO3'" H 0 0 N Y N -4.355 5.414 2.879 0.890 -3.749 1.057 "HO3'" T39 32 T39 H7 H7 H 0 1 N N N -1.112 3.637 2.999 -0.832 -0.805 -1.247 H7 T39 33 T39 "H1'" "H1'" H 0 1 N N N 0.604 5.465 4.108 -0.936 -0.402 1.795 "H1'" T39 34 T39 H3 H3 H 0 1 N N N 1.801 1.504 5.884 -1.328 3.350 -1.930 H3 T39 35 T39 H71 H71 H 0 1 N N N -1.554 1.577 8.968 -4.575 4.137 1.153 H71 T39 36 T39 H72 H72 H 0 1 N N N -1.883 3.339 9.075 -4.955 2.479 1.676 H72 T39 37 T39 H73 H73 H 0 1 N N N -2.888 2.301 8.007 -3.818 3.471 2.619 H73 T39 38 T39 H6 H6 H 0 1 N N N -1.901 4.408 6.554 -2.661 1.066 2.057 H6 T39 39 T39 HCA2 HCA2 H 0 0 N N N 0.401 4.710 0.594 -2.806 -1.863 -1.867 HCA2 T39 40 T39 HCA1 HCA1 H 0 0 N N N 0.992 4.507 2.278 -1.833 -3.308 -1.501 HCA1 T39 41 T39 HCD1 HCD1 H 0 0 N N N -0.555 8.495 -0.473 -6.476 -3.585 -0.712 HCD1 T39 42 T39 HCD2 HCD2 H 0 0 N N N 0.901 7.576 -0.984 -5.879 -3.686 0.961 HCD2 T39 43 T39 HCD3 HCD3 H 0 0 N N N -0.592 6.700 -0.504 -6.763 -2.240 0.417 HCD3 T39 44 T39 HCB1 HCB1 H 0 0 N N N 2.056 6.229 0.668 -4.201 -3.928 -1.545 HCB1 T39 45 T39 HCB2 HCB2 H 0 0 N N N 1.785 6.605 2.404 -3.604 -4.029 0.129 HCB2 T39 46 T39 HOP3 HOP3 H 0 0 N Y N -4.114 7.919 8.562 6.893 1.107 0.791 HOP3 T39 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 T39 "CD'" "OC'" SING N N 1 T39 "OC'" "CB'" SING N N 2 T39 "CB'" "CA'" SING N N 3 T39 "CA'" "O2'" SING N N 4 T39 "O2'" "C2'" SING N N 5 T39 "O3'" "C3'" SING N N 6 T39 "C2'" "C3'" SING N N 7 T39 "C2'" "C1'" SING N N 8 T39 "C3'" "C4'" SING N N 9 T39 O2 C2 DOUB N N 10 T39 "C4'" "O4'" SING N N 11 T39 "C4'" "C5'" SING N N 12 T39 "C1'" "O4'" SING N N 13 T39 "C1'" N1 SING N N 14 T39 C2 N1 SING N N 15 T39 C2 N3 SING N N 16 T39 N1 C6 SING N N 17 T39 "C5'" "O5'" SING N N 18 T39 N3 C4 SING N N 19 T39 "O5'" P SING N N 20 T39 C6 C5 DOUB N N 21 T39 C4 C5 SING N N 22 T39 C4 O4 DOUB N N 23 T39 C5 C7 SING N N 24 T39 OP1 P DOUB N N 25 T39 P OP2 SING N N 26 T39 P OP3 SING N N 27 T39 OP2 HOP2 SING N N 28 T39 "C5'" "H5'" SING N N 29 T39 "C5'" "H5''" SING N N 30 T39 "C4'" "H4'" SING N N 31 T39 "C3'" "H3'" SING N N 32 T39 "O3'" "HO3'" SING N N 33 T39 "C2'" H7 SING N N 34 T39 "C1'" "H1'" SING N N 35 T39 N3 H3 SING N N 36 T39 C7 H71 SING N N 37 T39 C7 H72 SING N N 38 T39 C7 H73 SING N N 39 T39 C6 H6 SING N N 40 T39 "CA'" HCA2 SING N N 41 T39 "CA'" HCA1 SING N N 42 T39 "CD'" HCD1 SING N N 43 T39 "CD'" HCD2 SING N N 44 T39 "CD'" HCD3 SING N N 45 T39 "CB'" HCB1 SING N N 46 T39 "CB'" HCB2 SING N N 47 T39 OP3 HOP3 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 T39 SMILES ACDLabs 12.01 "O=P(O)(O)OCC2OC(N1C(=O)NC(=O)C(=C1)C)C(OCCOC)C2O" T39 InChI InChI 1.03 "InChI=1S/C13H21N2O10P/c1-7-5-15(13(18)14-11(7)17)12-10(23-4-3-22-2)9(16)8(25-12)6-24-26(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" T39 InChIKey InChI 1.03 BLSQXXFKLSKRRX-DNRKLUKYSA-N T39 SMILES_CANONICAL CACTVS 3.370 "COCCO[C@@H]1[C@H](O)[C@@H](CO[P](O)(O)=O)O[C@H]1N2C=C(C)C(=O)NC2=O" T39 SMILES CACTVS 3.370 "COCCO[CH]1[CH](O)[CH](CO[P](O)(O)=O)O[CH]1N2C=C(C)C(=O)NC2=O" T39 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)OCCOC" T39 SMILES "OpenEye OEToolkits" 1.7.6 "CC1=CN(C(=O)NC1=O)C2C(C(C(O2)COP(=O)(O)O)O)OCCOC" # 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 T39 "SYSTEMATIC NAME" ACDLabs 12.01 ;2'-O-(2-methoxyethyl)-5-methyluridine 5'-(dihydrogen phosphate) ; T39 "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.7.6 "[(2R,3R,4R,5R)-4-(2-methoxyethoxy)-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 T39 "Create component" 1998-07-29 RCSB T39 "Modify descriptor" 2011-06-04 RCSB T39 "Modify component atom id" 2013-01-10 RCSB #