data_P2T # _chem_comp.id P2T _chem_comp.name ;2'-O-PROPYL THYMIDINE-5-MONOPHOSPHATE ; _chem_comp.type "RNA LINKING" _chem_comp.pdbx_type ATOMN _chem_comp.formula "C13 H21 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 380.288 _chem_comp.one_letter_code T _chem_comp.three_letter_code P2T _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 1Y8V _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 P2T P P P 0 1 N N N 10.769 3.863 5.483 2.787 0.324 -4.407 P P2T 1 P2T OP1 O1P O 0 1 N N N 11.990 4.379 4.759 3.659 1.172 -5.286 OP1 P2T 2 P2T OP2 O2P O 0 1 N N N 10.933 3.118 6.733 1.198 0.588 -4.548 OP2 P2T 3 P2T "O5'" O5* O 0 1 N N N 9.822 5.101 5.715 3.063 0.476 -2.819 "O5'" P2T 4 P2T "C5'" C5* C 0 1 N N N 9.543 5.981 4.642 2.282 -0.292 -1.921 "C5'" P2T 5 P2T "C4'" C4* C 0 1 N N R 8.484 6.954 5.038 2.725 0.023 -0.498 "C4'" P2T 6 P2T "O4'" O4* O 0 1 N N N 7.219 6.267 5.218 2.470 1.422 -0.246 "O4'" P2T 7 P2T "C1'" C1* C 0 1 N N R 6.460 6.928 6.225 1.373 1.543 0.675 "C1'" P2T 8 P2T N1 N1 N 0 1 N N N 6.247 5.993 7.343 0.452 2.524 0.177 N1 P2T 9 P2T C6 C6 C 0 1 N N N 7.101 4.932 7.569 0.309 2.663 -1.199 C6 P2T 10 P2T C2 C2 C 0 1 N N N 5.161 6.224 8.174 -0.300 3.336 1.055 C2 P2T 11 P2T O2 O2 O 0 1 N N N 4.415 7.177 8.032 -0.225 3.269 2.283 O2 P2T 12 P2T N3 N3 N 0 1 N N N 5.004 5.303 9.194 -1.159 4.248 0.431 N3 P2T 13 P2T C4 C4 C 0 1 N N N 5.812 4.227 9.465 -1.338 4.427 -0.932 C4 P2T 14 P2T O4 O4 O 0 1 N N N 5.562 3.499 10.405 -2.112 5.251 -1.413 O4 P2T 15 P2T C5 C5 C 0 1 N N N 6.942 4.050 8.569 -0.514 3.537 -1.792 C5 P2T 16 P2T C5M C5M C 0 1 N N N 7.863 2.897 8.795 -0.651 3.669 -3.275 C5M P2T 17 P2T "C2'" C2* C 0 1 N N R 7.286 8.135 6.675 0.748 0.163 0.786 "C2'" P2T 18 P2T "O2'" O2* O 0 1 N N N 6.971 9.184 5.767 0.137 -0.058 2.041 "O2'" P2T 19 P2T "CB'" "CB'" C 0 1 N N N 5.729 9.824 6.017 -0.332 -1.396 2.174 "CB'" P2T 20 P2T "CC'" "CC'" C 0 1 N N N 5.312 10.588 4.760 -0.992 -1.552 3.535 "CC'" P2T 21 P2T "CD'" "CD'" C 0 1 N N N 5.133 9.679 3.534 -1.506 -2.964 3.754 "CD'" P2T 22 P2T "C3'" C3* C 0 1 N N R 8.691 7.646 6.372 1.940 -0.742 0.560 "C3'" P2T 23 P2T "O3'" O3* O 0 1 N N N 9.639 8.687 6.312 2.742 -0.809 1.739 "O3'" P2T 24 P2T OP3 O3P O 0 1 N Y N ? ? ? 2.921 -1.270 -4.647 OP3 P2T 25 P2T HOP2 2HOP H 0 0 N N N 10.165 2.793 7.188 0.799 0.616 -5.443 HOP2 P2T 26 P2T "H5'" 1H5* H 0 1 N N N 9.276 5.431 3.710 1.229 -0.035 -2.051 "H5'" P2T 27 P2T "H5''" 2H5* H 0 0 N N N 10.462 6.493 4.272 2.428 -1.352 -2.133 "H5''" P2T 28 P2T "H4'" H4* H 0 1 N N N 8.513 7.703 4.213 3.804 -0.139 -0.410 "H4'" P2T 29 P2T "H1'" H1* H 0 1 N N N 5.463 7.261 5.854 1.754 1.910 1.633 "H1'" P2T 30 P2T H6 H6 H 0 1 N N N 7.969 4.779 6.906 0.928 1.995 -1.790 H6 P2T 31 P2T HN3 HN3 H 0 1 N N N 4.205 5.431 9.814 -1.709 4.843 1.045 HN3 P2T 32 P2T H71 1H5M H 0 1 N N N 8.897 3.308 8.875 -1.057 2.748 -3.690 H71 P2T 33 P2T H72 2H5M H 0 1 N N N 7.731 2.165 9.625 0.324 3.866 -3.719 H72 P2T 34 P2T H73 3H5M H 0 1 N N N 7.909 2.317 7.844 -1.320 4.497 -3.510 H73 P2T 35 P2T "H2'" H2* H 0 1 N N N 7.134 8.481 7.724 -0.000 0.004 -0.000 "H2'" P2T 36 P2T "HB'1" "1HB'" H 0 0 N N N 5.758 10.474 6.922 0.521 -2.075 2.072 "HB'1" P2T 37 P2T "HB'2" "2HB'" H 0 0 N N N 4.944 9.112 6.365 -1.045 -1.597 1.368 "HB'2" P2T 38 P2T "HC'1" "1HC'" H 0 0 N N N 6.028 11.414 4.541 -0.277 -1.289 4.323 "HC'1" P2T 39 P2T "HC'2" "2HC'" H 0 0 N N N 4.392 11.189 4.947 -1.818 -0.837 3.627 "HC'2" P2T 40 P2T "HD'1" "1HD'" H 0 0 N N N 4.417 8.853 3.753 -0.688 -3.691 3.703 "HD'1" P2T 41 P2T "HD'2" "2HD'" H 0 0 N N N 4.829 10.236 2.617 -1.975 -3.049 4.739 "HD'2" P2T 42 P2T "HD'3" "3HD'" H 0 0 N N N 6.054 9.078 3.347 -2.251 -3.232 2.999 "HD'3" P2T 43 P2T "H3'" H3* H 0 1 N N N 9.117 6.985 7.162 1.675 -1.764 0.277 "H3'" P2T 44 P2T "HO3'" H3T H 0 0 N Y N 9.769 9.120 7.147 3.447 -0.153 1.628 "HO3'" P2T 45 P2T HOP3 3HOP H 0 0 N N N -0.768 -0.325 0.455 2.886 -1.617 -5.563 HOP3 P2T 46 # 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 P2T P OP1 DOUB N N 1 P2T P OP2 SING N N 2 P2T P "O5'" SING N N 3 P2T P OP3 SING N N 4 P2T OP2 HOP2 SING N N 5 P2T "O5'" "C5'" SING N N 6 P2T "C5'" "C4'" SING N N 7 P2T "C5'" "H5'" SING N N 8 P2T "C5'" "H5''" SING N N 9 P2T "C4'" "O4'" SING N N 10 P2T "C4'" "C3'" SING N N 11 P2T "C4'" "H4'" SING N N 12 P2T "O4'" "C1'" SING N N 13 P2T "C1'" N1 SING N N 14 P2T "C1'" "C2'" SING N N 15 P2T "C1'" "H1'" SING N N 16 P2T N1 C6 SING N N 17 P2T N1 C2 SING N N 18 P2T C6 C5 DOUB N N 19 P2T C6 H6 SING N N 20 P2T C2 O2 DOUB N N 21 P2T C2 N3 SING N N 22 P2T N3 C4 SING N N 23 P2T N3 HN3 SING N N 24 P2T C4 O4 DOUB N N 25 P2T C4 C5 SING N N 26 P2T C5 C5M SING N N 27 P2T C5M H71 SING N N 28 P2T C5M H72 SING N N 29 P2T C5M H73 SING N N 30 P2T "C2'" "O2'" SING N N 31 P2T "C2'" "C3'" SING N N 32 P2T "C2'" "H2'" SING N N 33 P2T "O2'" "CB'" SING N N 34 P2T "CB'" "CC'" SING N N 35 P2T "CB'" "HB'1" SING N N 36 P2T "CB'" "HB'2" SING N N 37 P2T "CC'" "CD'" SING N N 38 P2T "CC'" "HC'1" SING N N 39 P2T "CC'" "HC'2" SING N N 40 P2T "CD'" "HD'1" SING N N 41 P2T "CD'" "HD'2" SING N N 42 P2T "CD'" "HD'3" SING N N 43 P2T "C3'" "O3'" SING N N 44 P2T "C3'" "H3'" SING N N 45 P2T "O3'" "HO3'" SING N N 46 P2T OP3 HOP3 SING N N 47 # 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 P2T SMILES ACDLabs 10.04 "O=C1NC(=O)N(C=C1C)C2OC(C(O)C2OCCC)COP(=O)(O)O" P2T SMILES_CANONICAL CACTVS 3.341 "CCCO[C@@H]1[C@H](O)[C@@H](CO[P](O)(O)=O)O[C@H]1N2C=C(C)C(=O)NC2=O" P2T SMILES CACTVS 3.341 "CCCO[CH]1[CH](O)[CH](CO[P](O)(O)=O)O[CH]1N2C=C(C)C(=O)NC2=O" P2T SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "CCCO[C@@H]1[C@@H]([C@H](O[C@H]1N2C=C(C(=O)NC2=O)C)COP(=O)(O)O)O" P2T SMILES "OpenEye OEToolkits" 1.5.0 "CCCOC1C(C(OC1N2C=C(C(=O)NC2=O)C)COP(=O)(O)O)O" P2T InChI InChI 1.03 "InChI=1S/C13H21N2O9P/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/h5,8-10,12,16H,3-4,6H2,1-2H3,(H,14,17,18)(H2,19,20,21)/t8-,9-,10-,12-/m1/s1" P2T InChIKey InChI 1.03 YCUXLAVNRCJWRL-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 P2T "SYSTEMATIC NAME" ACDLabs 10.04 ;5-methyl-2'-O-propyluridine 5'-(dihydrogen phosphate) ; P2T "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "[(2R,3R,4R,5R)-3-hydroxy-5-(5-methyl-2,4-dioxo-pyrimidin-1-yl)-4-propoxy-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 P2T "Create component" 2004-12-17 RCSB P2T "Modify linking type" 2011-06-04 RCSB P2T "Modify descriptor" 2011-06-04 RCSB #