data_5HT # _chem_comp.id 5HT _chem_comp.name 5-HYDROXY-THYMIDINE _chem_comp.type "DNA LINKING" _chem_comp.pdbx_type ATOMN _chem_comp.formula "C10 H16 N2 O6" _chem_comp.mon_nstd_parent_comp_id DT _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2000-02-24 _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 260.244 _chem_comp.one_letter_code T _chem_comp.three_letter_code 5HT _chem_comp.pdbx_model_coordinates_details ? _chem_comp.pdbx_model_coordinates_missing_flag N _chem_comp.pdbx_ideal_coordinates_details ? _chem_comp.pdbx_ideal_coordinates_missing_flag N _chem_comp.pdbx_model_coordinates_db_code 1EHL _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 5HT "O5'" O5* O 0 1 N N N -2.869 61.350 12.333 2.572 0.452 -3.637 "O5'" 5HT 1 5HT "C5'" C5* C 0 1 N N N -1.704 61.611 11.567 1.181 0.775 -3.598 "C5'" 5HT 2 5HT "C4'" C4* C 0 1 N N R -0.472 61.029 12.220 0.420 -0.332 -2.866 "C4'" 5HT 3 5HT "O4'" O4* O 0 1 N N N -0.842 60.618 13.584 0.809 -0.386 -1.474 "O4'" 5HT 4 5HT "C3'" C3* C 0 1 N N S 0.062 59.755 11.606 -1.093 -0.008 -2.809 "C3'" 5HT 5 5HT "O3'" O3* O 0 1 N N N 0.937 59.962 10.500 -1.758 -0.464 -3.989 "O3'" 5HT 6 5HT "C2'" C2* C 0 1 N N N 0.721 59.033 12.761 -1.551 -0.815 -1.570 "C2'" 5HT 7 5HT "C1'" C1* C 0 1 N N R 0.010 59.552 14.016 -0.255 -1.046 -0.769 "C1'" 5HT 8 5HT N1 N1 N 0 1 N N N -0.761 58.371 14.606 -0.391 -0.478 0.573 N1 5HT 9 5HT C2 C2 C 0 1 N N N -0.369 57.820 15.683 -0.637 0.833 0.715 C2 5HT 10 5HT O2 O2 O 0 1 N N N 0.660 58.154 16.218 -0.845 1.508 -0.273 O2 5HT 11 5HT N3 N3 N 0 1 N N N -1.110 56.782 16.265 -0.658 1.418 1.924 N3 5HT 12 5HT C4 C4 C 0 1 N N N -2.327 56.295 15.741 -0.201 0.774 3.014 C4 5HT 13 5HT O4 O4 O 0 1 N N N -2.781 55.229 16.104 -0.303 1.287 4.109 O4 5HT 14 5HT C5 C5 C 0 1 N N R -3.004 57.170 14.709 0.433 -0.585 2.874 C5 5HT 15 5HT C5M C5M C 0 1 N N N -3.790 58.278 15.416 0.277 -1.360 4.184 C5M 5HT 16 5HT O5 O5 O 0 1 N N N -3.878 56.378 13.954 1.821 -0.435 2.569 O5 5HT 17 5HT C6 C6 C 0 1 N N N -1.917 57.829 13.744 -0.258 -1.350 1.742 C6 5HT 18 5HT "HO5'" H5T H 0 0 N Y N -3.643 61.715 11.922 3.014 1.173 -4.106 "HO5'" 5HT 19 5HT "H5'" 1H5* H 0 1 N N N -1.817 61.253 10.516 0.801 0.864 -4.616 "H5'" 5HT 20 5HT "H5''" 2H5* H 0 0 N N N -1.583 62.701 11.365 1.041 1.720 -3.074 "H5''" 5HT 21 5HT "H4'" H4* H 0 1 N N N 0.300 61.827 12.124 0.589 -1.295 -3.347 "H4'" 5HT 22 5HT "H3'" H3* H 0 1 N N N -0.756 59.154 11.143 -1.258 1.058 -2.660 "H3'" 5HT 23 5HT "HO3'" H3T H 0 0 N Y N 1.272 59.161 10.114 -2.704 -0.318 -3.851 "HO3'" 5HT 24 5HT "H2'" 1H2* H 0 1 N N N 0.709 57.922 12.663 -1.986 -1.767 -1.874 "H2'" 5HT 25 5HT "H2''" 2H2* H 0 0 N N N 1.829 59.148 12.790 -2.265 -0.239 -0.981 "H2''" 5HT 26 5HT "H1'" H1* H 0 1 N N N 0.692 59.945 14.804 -0.047 -2.114 -0.701 "H1'" 5HT 27 5HT H3 H3 H 0 1 N N N -0.743 56.357 17.116 -1.007 2.319 2.013 H3 5HT 28 5HT H71 1H5M H 0 1 N N N -4.288 58.922 14.655 0.768 -0.814 4.989 H71 5HT 29 5HT H72 2H5M H 0 1 N N N -4.511 57.872 16.163 -0.781 -1.474 4.415 H72 5HT 30 5HT H73 3H5M H 0 1 N N N -3.151 58.867 16.114 0.735 -2.344 4.080 H73 5HT 31 5HT HO5 HO5 H 0 1 N N N -4.303 56.927 13.306 2.217 0.051 3.305 HO5 5HT 32 5HT H61 1H6 H 0 1 N N N -2.354 58.607 13.076 0.336 -2.224 1.478 H61 5HT 33 5HT H62 2H6 H 0 1 N N N -1.566 57.126 12.951 -1.247 -1.669 2.071 H62 5HT 34 # 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 5HT "O5'" "C5'" SING N N 1 5HT "O5'" "HO5'" SING N N 2 5HT "C5'" "C4'" SING N N 3 5HT "C5'" "H5'" SING N N 4 5HT "C5'" "H5''" SING N N 5 5HT "C4'" "O4'" SING N N 6 5HT "C4'" "C3'" SING N N 7 5HT "C4'" "H4'" SING N N 8 5HT "O4'" "C1'" SING N N 9 5HT "C3'" "O3'" SING N N 10 5HT "C3'" "C2'" SING N N 11 5HT "C3'" "H3'" SING N N 12 5HT "O3'" "HO3'" SING N N 13 5HT "C2'" "C1'" SING N N 14 5HT "C2'" "H2'" SING N N 15 5HT "C2'" "H2''" SING N N 16 5HT "C1'" N1 SING N N 17 5HT "C1'" "H1'" SING N N 18 5HT N1 C2 SING N N 19 5HT N1 C6 SING N N 20 5HT C2 O2 DOUB N N 21 5HT C2 N3 SING N N 22 5HT N3 C4 SING N N 23 5HT N3 H3 SING N N 24 5HT C4 O4 DOUB N N 25 5HT C4 C5 SING N N 26 5HT C5 C5M SING N N 27 5HT C5 O5 SING N N 28 5HT C5 C6 SING N N 29 5HT C5M H71 SING N N 30 5HT C5M H72 SING N N 31 5HT C5M H73 SING N N 32 5HT O5 HO5 SING N N 33 5HT C6 H61 SING N N 34 5HT C6 H62 SING N N 35 # 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 5HT SMILES ACDLabs 10.04 "O=C1N(CC(O)(C(=O)N1)C)C2OC(C(O)C2)CO" 5HT SMILES_CANONICAL CACTVS 3.341 "C[C@@]1(O)CN([C@H]2C[C@H](O)[C@@H](CO)O2)C(=O)NC1=O" 5HT SMILES CACTVS 3.341 "C[C]1(O)CN([CH]2C[CH](O)[CH](CO)O2)C(=O)NC1=O" 5HT SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "C[C@]1(CN(C(=O)NC1=O)[C@H]2C[C@@H]([C@H](O2)CO)O)O" 5HT SMILES "OpenEye OEToolkits" 1.5.0 "CC1(CN(C(=O)NC1=O)C2CC(C(O2)CO)O)O" 5HT InChI InChI 1.03 "InChI=1S/C10H16N2O6/c1-10(17)4-12(9(16)11-8(10)15)7-2-5(14)6(3-13)18-7/h5-7,13-14,17H,2-4H2,1H3,(H,11,15,16)/t5-,6+,7+,10+/m0/s1" 5HT InChIKey InChI 1.03 MRODUHNLAXSPFV-MPXCPUAZSA-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 5HT "SYSTEMATIC NAME" ACDLabs 10.04 5-hydroxythymidine 5HT "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "(5R)-5-hydroxy-1-[(2R,4S,5R)-4-hydroxy-5-(hydroxymethyl)oxolan-2-yl]-5-methyl-1,3-diazinane-2,4-dione" # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site 5HT "Create component" 2000-02-24 RCSB 5HT "Modify descriptor" 2011-06-04 RCSB #