data_2OT # _chem_comp.id 2OT _chem_comp.name ;2'-O-[2-(N,N-DIMETHYLAMINOOXY)ETHYL] THYMIDINE-5'-MONOPHOSPHATE ; _chem_comp.type "RNA LINKING" _chem_comp.pdbx_type ATOMN _chem_comp.formula "C14 H24 N3 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 2004-12-21 _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 425.328 _chem_comp.one_letter_code T _chem_comp.three_letter_code 2OT _chem_comp.pdbx_model_coordinates_details ? _chem_comp.pdbx_model_coordinates_missing_flag Y _chem_comp.pdbx_ideal_coordinates_details ? _chem_comp.pdbx_ideal_coordinates_missing_flag N _chem_comp.pdbx_model_coordinates_db_code 1YB9 _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 2OT P P P 0 1 N N N -4.388 6.442 6.972 2.787 0.324 -4.407 P 2OT 1 2OT OP1 O1P O 0 1 N N N -5.566 7.224 6.495 3.659 1.172 -5.286 OP1 2OT 2 2OT OP2 O2P O 0 1 N N N -4.598 5.174 7.651 1.198 0.588 -4.548 OP2 2OT 3 2OT "O5'" O5* O 0 1 N N N -3.394 6.194 5.760 3.063 0.476 -2.819 "O5'" 2OT 4 2OT "C5'" C5* C 0 1 N N N -3.050 7.257 4.865 2.282 -0.292 -1.921 "C5'" 2OT 5 2OT "C4'" C4* C 0 1 N N R -2.007 6.788 3.892 2.725 0.023 -0.498 "C4'" 2OT 6 2OT "O4'" O4* O 0 1 N N N -0.779 6.493 4.610 2.470 1.422 -0.246 "O4'" 2OT 7 2OT "C1'" C1* C 0 1 N N R -0.101 5.410 3.970 1.373 1.543 0.675 "C1'" 2OT 8 2OT N1 N1 N 0 1 N N N 0.045 4.298 4.948 0.452 2.524 0.177 N1 2OT 9 2OT C6 C6 C 0 1 N N N -0.834 4.136 6.000 0.309 2.663 -1.199 C6 2OT 10 2OT C2 C2 C 0 1 N N N 1.097 3.420 4.761 -0.300 3.336 1.055 C2 2OT 11 2OT O2 O2 O 0 1 N N N 1.857 3.502 3.828 -0.225 3.269 2.283 O2 2OT 12 2OT N3 N3 N 0 1 N N N 1.200 2.431 5.702 -1.159 4.248 0.431 N3 2OT 13 2OT C4 C4 C 0 1 N N N 0.365 2.210 6.766 -1.338 4.427 -0.932 C4 2OT 14 2OT O4 O4 O 0 1 N N N 0.581 1.274 7.528 -2.112 5.251 -1.413 O4 2OT 15 2OT C5 C5 C 0 1 N N N -0.736 3.135 6.892 -0.514 3.537 -1.792 C5 2OT 16 2OT C5M C5M C 0 1 N N N -1.713 2.924 8.002 -0.651 3.669 -3.275 C5M 2OT 17 2OT "C2'" C2* C 0 1 N N R -0.938 5.011 2.754 0.748 0.163 0.786 "C2'" 2OT 18 2OT "O2'" O2* O 0 1 N N N -0.434 5.818 1.665 0.137 -0.058 2.041 "O2'" 2OT 19 2OT "CB'" "CB'" C 0 1 N N N 0.850 5.431 1.139 -0.332 -1.396 2.174 "CB'" 2OT 20 2OT "CC'" "CC'" C 0 1 N N N 1.754 6.664 1.060 -0.951 -1.569 3.547 "CC'" 2OT 21 2OT "OD'" "OD'" O 0 1 N N N 2.360 6.880 2.339 0.039 -1.320 4.537 "OD'" 2OT 22 2OT "NE'" "NE'" N 0 1 N N N 3.001 8.048 2.553 -0.585 -1.494 5.845 "NE'" 2OT 23 2OT "CF'" "CF'" C 0 1 N N N 4.116 7.889 3.481 -1.049 -2.878 5.852 "CF'" 2OT 24 2OT "CG'" "CG'" C 0 1 N N N 2.051 9.035 3.047 0.502 -1.303 6.800 "CG'" 2OT 25 2OT "C3'" C3* C 0 1 N N R -2.320 5.481 3.197 1.940 -0.742 0.560 "C3'" 2OT 26 2OT "O3'" O3* O 0 1 N N N -3.277 5.608 2.155 2.742 -0.809 1.739 "O3'" 2OT 27 2OT OP3 O3P O 0 1 N Y N ? ? ? 2.921 -1.270 -4.647 OP3 2OT 28 2OT HOP2 2HOP H 0 0 N N N -3.848 4.676 7.955 0.799 0.616 -5.443 HOP2 2OT 29 2OT "H5'" 1H5* H 0 1 N N N -2.731 8.176 5.410 1.229 -0.035 -2.051 "H5'" 2OT 30 2OT "H5''" 2H5* H 0 0 N N N -3.945 7.676 4.349 2.428 -1.352 -2.133 "H5''" 2OT 31 2OT "H4'" H4* H 0 1 N N N -1.945 7.613 3.145 3.804 -0.139 -0.410 "H4'" 2OT 32 2OT "H1'" H1* H 0 1 N N N 0.923 5.688 3.627 1.754 1.910 1.633 "H1'" 2OT 33 2OT H6 H6 H 0 1 N N N -1.664 4.849 6.136 0.928 1.995 -1.790 H6 2OT 34 2OT HN3 HN3 H 0 1 N N N 1.985 1.788 5.599 -1.709 4.843 1.045 HN3 2OT 35 2OT H71 1H5M H 0 1 N N N -2.727 2.860 7.543 -1.057 2.748 -3.690 H71 2OT 36 2OT H72 2H5M H 0 1 N N N -1.632 2.094 8.742 0.324 3.866 -3.719 H72 2OT 37 2OT H73 3H5M H 0 1 N N N -1.770 3.877 8.579 -1.320 4.497 -3.510 H73 2OT 38 2OT "H2'" H2* H 0 1 N N N -0.928 3.942 2.439 -0.000 0.004 -0.000 "H2'" 2OT 39 2OT "HB'1" "1HB'" H 0 0 N N N 0.765 4.905 0.160 -1.066 -1.580 1.383 "HB'1" 2OT 40 2OT "HB'2" "2HB'" H 0 0 N N N 1.314 4.602 1.723 0.520 -2.071 2.050 "HB'2" 2OT 41 2OT "HC'1" "1HC'" H 0 0 N N N 1.212 7.565 0.689 -1.324 -2.588 3.686 "HC'1" 2OT 42 2OT "HC'2" "2HC'" H 0 0 N N N 2.507 6.587 0.241 -1.768 -0.855 3.691 "HC'2" 2OT 43 2OT "HF'1" "1HF'" H 0 0 N N N 4.820 7.095 3.138 -2.051 -2.941 5.420 "HF'1" 2OT 44 2OT "HF'2" "2HF'" H 0 0 N N N 4.646 8.854 3.658 -1.082 -3.261 6.875 "HF'2" 2OT 45 2OT "HF'3" "3HF'" H 0 0 N N N 3.785 7.425 4.439 -0.373 -3.506 5.264 "HF'3" 2OT 46 2OT "HG'1" "1HG'" H 0 0 N N N 1.506 8.680 3.953 0.329 -0.399 7.390 "HG'1" 2OT 47 2OT "HG'2" "2HG'" H 0 0 N N N 2.581 10.000 3.224 1.455 -1.204 6.274 "HG'2" 2OT 48 2OT "HG'3" "3HG'" H 0 0 N N N 1.173 9.153 2.370 0.563 -2.159 7.478 "HG'3" 2OT 49 2OT "H3'" H3* H 0 1 N N N -2.828 4.734 3.851 1.675 -1.764 0.277 "H3'" 2OT 50 2OT "HO3'" H3T H 0 0 N Y N -3.473 4.787 1.719 3.447 -0.153 1.628 "HO3'" 2OT 51 2OT HOP3 3HOP H 0 0 N N N 0.750 -0.498 0.304 2.886 -1.617 -5.563 HOP3 2OT 52 # 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 2OT P OP1 DOUB N N 1 2OT P OP2 SING N N 2 2OT P "O5'" SING N N 3 2OT P OP3 SING N N 4 2OT OP2 HOP2 SING N N 5 2OT "O5'" "C5'" SING N N 6 2OT "C5'" "C4'" SING N N 7 2OT "C5'" "H5'" SING N N 8 2OT "C5'" "H5''" SING N N 9 2OT "C4'" "O4'" SING N N 10 2OT "C4'" "C3'" SING N N 11 2OT "C4'" "H4'" SING N N 12 2OT "O4'" "C1'" SING N N 13 2OT "C1'" N1 SING N N 14 2OT "C1'" "C2'" SING N N 15 2OT "C1'" "H1'" SING N N 16 2OT N1 C6 SING N N 17 2OT N1 C2 SING N N 18 2OT C6 C5 DOUB N N 19 2OT C6 H6 SING N N 20 2OT C2 O2 DOUB N N 21 2OT C2 N3 SING N N 22 2OT N3 C4 SING N N 23 2OT N3 HN3 SING N N 24 2OT C4 O4 DOUB N N 25 2OT C4 C5 SING N N 26 2OT C5 C5M SING N N 27 2OT C5M H71 SING N N 28 2OT C5M H72 SING N N 29 2OT C5M H73 SING N N 30 2OT "C2'" "O2'" SING N N 31 2OT "C2'" "C3'" SING N N 32 2OT "C2'" "H2'" SING N N 33 2OT "O2'" "CB'" SING N N 34 2OT "CB'" "CC'" SING N N 35 2OT "CB'" "HB'1" SING N N 36 2OT "CB'" "HB'2" SING N N 37 2OT "CC'" "OD'" SING N N 38 2OT "CC'" "HC'1" SING N N 39 2OT "CC'" "HC'2" SING N N 40 2OT "OD'" "NE'" SING N N 41 2OT "NE'" "CF'" SING N N 42 2OT "NE'" "CG'" SING N N 43 2OT "CF'" "HF'1" SING N N 44 2OT "CF'" "HF'2" SING N N 45 2OT "CF'" "HF'3" SING N N 46 2OT "CG'" "HG'1" SING N N 47 2OT "CG'" "HG'2" SING N N 48 2OT "CG'" "HG'3" SING N N 49 2OT "C3'" "O3'" SING N N 50 2OT "C3'" "H3'" SING N N 51 2OT "O3'" "HO3'" SING N N 52 2OT OP3 HOP3 SING N N 53 # 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 2OT SMILES ACDLabs 10.04 "O=C1NC(=O)N(C=C1C)C2OC(C(O)C2OCCON(C)C)COP(=O)(O)O" 2OT SMILES_CANONICAL CACTVS 3.341 "CN(C)OCCO[C@@H]1[C@H](O)[C@@H](CO[P](O)(O)=O)O[C@H]1N2C=C(C)C(=O)NC2=O" 2OT SMILES CACTVS 3.341 "CN(C)OCCO[CH]1[CH](O)[CH](CO[P](O)(O)=O)O[CH]1N2C=C(C)C(=O)NC2=O" 2OT SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "CC1=CN(C(=O)NC1=O)[C@H]2[C@@H]([C@@H]([C@H](O2)COP(=O)(O)O)O)OCCON(C)C" 2OT SMILES "OpenEye OEToolkits" 1.5.0 "CC1=CN(C(=O)NC1=O)C2C(C(C(O2)COP(=O)(O)O)O)OCCON(C)C" 2OT InChI InChI 1.03 "InChI=1S/C14H24N3O10P/c1-8-6-17(14(20)15-12(8)19)13-11(24-4-5-25-16(2)3)10(18)9(27-13)7-26-28(21,22)23/h6,9-11,13,18H,4-5,7H2,1-3H3,(H,15,19,20)(H2,21,22,23)/t9-,10-,11-,13-/m1/s1" 2OT InChIKey InChI 1.03 OPZZJWKFPFNZJV-PRULPYPASA-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 2OT "SYSTEMATIC NAME" ACDLabs 10.04 ;2'-O-{2-[(dimethylamino)oxy]ethyl}-5-methyluridine 5'-(dihydrogen phosphate) ; 2OT "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "[(2R,3R,4R,5R)-4-(2-dimethylaminooxyethoxy)-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 2OT "Create component" 2004-12-21 RCSB 2OT "Modify linking type" 2011-06-04 RCSB 2OT "Modify descriptor" 2011-06-04 RCSB #