data_2GT # _chem_comp.id 2GT _chem_comp.name ;2'-O-PROPARGYL THYMIDINE-5'-MONOPHOSPHATE ; _chem_comp.type "RNA LINKING" _chem_comp.pdbx_type ATOMN _chem_comp.formula "C13 H17 N2 O9 P" _chem_comp.mon_nstd_parent_comp_id DT _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2004-12-17 _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 376.256 _chem_comp.one_letter_code T _chem_comp.three_letter_code 2GT _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 1Y9S _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 2GT P P P 0 1 N N N 10.749 4.067 5.377 2.787 0.324 -4.407 P 2GT 1 2GT OP1 O1P O 0 1 N N N 11.961 4.604 4.673 3.659 1.172 -5.286 OP1 2GT 2 2GT OP2 O2P O 0 1 N N N 10.921 3.350 6.620 1.198 0.588 -4.548 OP2 2GT 3 2GT "O5'" O5* O 0 1 N N N 9.747 5.281 5.596 3.063 0.476 -2.819 "O5'" 2GT 4 2GT "C5'" C5* C 0 1 N N N 9.479 6.145 4.523 2.282 -0.292 -1.921 "C5'" 2GT 5 2GT "C4'" C4* C 0 1 N N R 8.428 7.143 4.925 2.725 0.023 -0.498 "C4'" 2GT 6 2GT "O4'" O4* O 0 1 N N N 7.160 6.460 5.106 2.470 1.422 -0.246 "O4'" 2GT 7 2GT "C1'" C1* C 0 1 N N R 6.438 7.082 6.161 1.373 1.543 0.675 "C1'" 2GT 8 2GT N1 N1 N 0 1 N N N 6.258 6.107 7.266 0.452 2.524 0.177 N1 2GT 9 2GT C6 C6 C 0 1 N N N 7.110 5.029 7.466 0.309 2.663 -1.199 C6 2GT 10 2GT C2 C2 C 0 1 N N N 5.200 6.336 8.099 -0.300 3.336 1.055 C2 2GT 11 2GT O2 O2 O 0 1 N N N 4.485 7.315 7.980 -0.225 3.269 2.283 O2 2GT 12 2GT N3 N3 N 0 1 N N N 5.027 5.398 9.095 -1.159 4.248 0.431 N3 2GT 13 2GT C4 C4 C 0 1 N N N 5.827 4.304 9.354 -1.338 4.427 -0.932 C4 2GT 14 2GT O4 O4 O 0 1 N N N 5.576 3.577 10.291 -2.112 5.251 -1.413 O4 2GT 15 2GT C5 C5 C 0 1 N N N 6.949 4.135 8.461 -0.514 3.537 -1.792 C5 2GT 16 2GT C5M C5M C 0 1 N N N 7.884 2.988 8.690 -0.651 3.669 -3.275 C5M 2GT 17 2GT "C2'" C2* C 0 1 N N R 7.268 8.288 6.624 0.748 0.163 0.786 "C2'" 2GT 18 2GT "O2'" O2* O 0 1 N N N 6.939 9.362 5.745 0.137 -0.058 2.041 "O2'" 2GT 19 2GT "CB'" "CB'" C 0 1 N N N 5.693 9.974 6.052 -0.332 -1.396 2.174 "CB'" 2GT 20 2GT "CC'" "CC'" C 0 1 N N N 5.418 11.002 5.044 -0.958 -1.592 3.481 "CC'" 2GT 21 2GT "CD'" "CD'" C 0 1 N N N 5.193 11.831 4.192 -1.472 -1.755 4.554 "CD'" 2GT 22 2GT "C3'" C3* C 0 1 N N R 8.666 7.817 6.267 1.940 -0.742 0.560 "C3'" 2GT 23 2GT "O3'" O3* O 0 1 N N N 9.613 8.876 6.221 2.742 -0.809 1.739 "O3'" 2GT 24 2GT OP3 O3P O 0 1 N Y N ? ? ? 2.921 -1.270 -4.647 OP3 2GT 25 2GT HOP2 2HOP H 0 0 N N N 10.154 3.010 7.066 0.799 0.616 -5.443 HOP2 2GT 26 2GT "H5'" 1H5* H 0 1 N N N 9.199 5.590 3.597 1.229 -0.035 -2.051 "H5'" 2GT 27 2GT "H5''" 2H5* H 0 0 N N N 10.403 6.639 4.141 2.428 -1.352 -2.133 "H5''" 2GT 28 2GT "H4'" H4* H 0 1 N N N 8.448 7.904 4.110 3.804 -0.139 -0.410 "H4'" 2GT 29 2GT "H1'" H1* H 0 1 N N N 5.428 7.419 5.830 1.754 1.910 1.633 "H1'" 2GT 30 2GT H6 H6 H 0 1 N N N 7.969 4.873 6.792 0.928 1.995 -1.790 H6 2GT 31 2GT HN3 HN3 H 0 1 N N N 4.221 5.527 9.706 -1.709 4.843 1.045 HN3 2GT 32 2GT H71 1H5M H 0 1 N N N 8.912 3.410 8.785 -1.057 2.748 -3.690 H71 2GT 33 2GT H72 2H5M H 0 1 N N N 7.751 2.248 9.514 0.324 3.866 -3.719 H72 2GT 34 2GT H73 3H5M H 0 1 N N N 7.948 2.415 7.735 -1.320 4.497 -3.510 H73 2GT 35 2GT "H2'" H2* H 0 1 N N N 7.130 8.603 7.685 -0.000 0.004 -0.000 "H2'" 2GT 36 2GT "HB'1" "1HB'" H 0 0 N N N 5.658 10.375 7.092 -1.036 -1.599 1.361 "HB'1" 2GT 37 2GT "HB'2" "2HB'" H 0 0 N N N 4.864 9.234 6.145 0.525 -2.065 2.052 "HB'2" 2GT 38 2GT "HD'" "HD'" H 0 1 N N N 4.990 12.578 3.424 -1.928 -1.900 5.505 "HD'" 2GT 39 2GT "H3'" H3* H 0 1 N N N 9.123 7.137 7.023 1.675 -1.764 0.277 "H3'" 2GT 40 2GT "HO3'" H3T H 0 0 N Y N 9.762 9.297 7.060 3.447 -0.153 1.628 "HO3'" 2GT 41 2GT HOP3 3HOP H 0 0 N N N -0.767 -0.340 0.446 2.886 -1.617 -5.563 HOP3 2GT 42 # 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 2GT P OP1 DOUB N N 1 2GT P OP2 SING N N 2 2GT P "O5'" SING N N 3 2GT P OP3 SING N N 4 2GT OP2 HOP2 SING N N 5 2GT "O5'" "C5'" SING N N 6 2GT "C5'" "C4'" SING N N 7 2GT "C5'" "H5'" SING N N 8 2GT "C5'" "H5''" SING N N 9 2GT "C4'" "O4'" SING N N 10 2GT "C4'" "C3'" SING N N 11 2GT "C4'" "H4'" SING N N 12 2GT "O4'" "C1'" SING N N 13 2GT "C1'" N1 SING N N 14 2GT "C1'" "C2'" SING N N 15 2GT "C1'" "H1'" SING N N 16 2GT N1 C6 SING N N 17 2GT N1 C2 SING N N 18 2GT C6 C5 DOUB N N 19 2GT C6 H6 SING N N 20 2GT C2 O2 DOUB N N 21 2GT C2 N3 SING N N 22 2GT N3 C4 SING N N 23 2GT N3 HN3 SING N N 24 2GT C4 O4 DOUB N N 25 2GT C4 C5 SING N N 26 2GT C5 C5M SING N N 27 2GT C5M H71 SING N N 28 2GT C5M H72 SING N N 29 2GT C5M H73 SING N N 30 2GT "C2'" "O2'" SING N N 31 2GT "C2'" "C3'" SING N N 32 2GT "C2'" "H2'" SING N N 33 2GT "O2'" "CB'" SING N N 34 2GT "CB'" "CC'" SING N N 35 2GT "CB'" "HB'1" SING N N 36 2GT "CB'" "HB'2" SING N N 37 2GT "CC'" "CD'" TRIP N N 38 2GT "CD'" "HD'" SING N N 39 2GT "C3'" "O3'" SING N N 40 2GT "C3'" "H3'" SING N N 41 2GT "O3'" "HO3'" SING N N 42 2GT OP3 HOP3 SING N N 43 # 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 2GT SMILES ACDLabs 10.04 "O=C1NC(=O)N(C=C1C)C2OC(C(O)C2OCC#C)COP(=O)(O)O" 2GT SMILES_CANONICAL CACTVS 3.341 "CC1=CN([C@@H]2O[C@H](CO[P](O)(O)=O)[C@@H](O)[C@H]2OCC#C)C(=O)NC1=O" 2GT SMILES CACTVS 3.341 "CC1=CN([CH]2O[CH](CO[P](O)(O)=O)[CH](O)[CH]2OCC#C)C(=O)NC1=O" 2GT 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)OCC#C" 2GT SMILES "OpenEye OEToolkits" 1.5.0 "CC1=CN(C(=O)NC1=O)C2C(C(C(O2)COP(=O)(O)O)O)OCC#C" 2GT InChI InChI 1.03 "InChI=1S/C13H17N2O9P/c1-3-4-22-10-9(16)8(6-23-25(19,20)21)24-12(10)15-5-7(2)11(17)14-13(15)18/h1,5,8-10,12,16H,4,6H2,2H3,(H,14,17,18)(H2,19,20,21)/t8-,9-,10-,12-/m1/s1" 2GT InChIKey InChI 1.03 HARKMJGNXJUASR-DNRKLUKYSA-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 2GT "SYSTEMATIC NAME" ACDLabs 10.04 ;5-methyl-2'-O-prop-2-yn-1-yluridine 5'-(dihydrogen phosphate) ; 2GT "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "[(2R,3R,4R,5R)-3-hydroxy-5-(5-methyl-2,4-dioxo-pyrimidin-1-yl)-4-prop-2-ynoxy-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 2GT "Create component" 2004-12-17 RCSB 2GT "Modify linking type" 2011-06-04 RCSB 2GT "Modify descriptor" 2011-06-04 RCSB #