data_ATD # _chem_comp.id ATD _chem_comp.name "THYMIDINE-3'-PHOSPHATE" _chem_comp.type "DNA LINKING" _chem_comp.pdbx_type HETAIN _chem_comp.formula "C10 H15 N2 O8 P" _chem_comp.mon_nstd_parent_comp_id DT _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 1999-09-29 _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 322.208 _chem_comp.one_letter_code T _chem_comp.three_letter_code ATD _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 1BX5 _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 ATD P P P 0 1 N N N -4.128 6.474 5.377 0.951 -0.076 -3.841 P ATD 1 ATD OP1 O1P O 0 1 N N N -5.451 7.119 5.223 -0.299 -0.588 -4.444 OP1 ATD 2 ATD OP2 O2P O 0 1 N N N -3.469 6.422 6.699 1.690 0.901 -4.886 OP2 ATD 3 ATD OP3 O3P O 0 1 N Y N -3.117 7.102 4.296 1.920 -1.311 -3.485 OP3 ATD 4 ATD "O5'" O5* O 0 1 N N N -8.444 3.779 6.545 -3.794 0.239 -1.511 "O5'" ATD 5 ATD "C5'" C5* C 0 1 N N N -7.678 4.212 5.448 -2.536 -0.278 -1.949 "C5'" ATD 6 ATD "C4'" C4* C 0 1 N N R -6.187 3.975 5.635 -1.408 0.375 -1.147 "C4'" ATD 7 ATD "O4'" O4* O 0 1 N N N -5.783 2.666 5.955 -1.553 0.057 0.242 "O4'" ATD 8 ATD "C3'" C3* C 0 1 N N S -5.399 4.357 4.403 -0.045 -0.177 -1.614 "C3'" ATD 9 ATD "O3'" O3* O 0 1 N N N -4.199 4.972 4.784 0.605 0.738 -2.497 "O3'" ATD 10 ATD "C2'" C2* C 0 1 N N N -5.170 3.029 3.693 0.734 -0.304 -0.277 "C2'" ATD 11 ATD "C1'" C1* C 0 1 N N S -5.233 2.014 4.824 -0.410 -0.685 0.695 "C1'" ATD 12 ATD N1 N1 N 0 1 N N N -3.846 1.540 5.049 -0.063 -0.300 2.065 N1 ATD 13 ATD C2 C2 C 0 1 N N N -3.436 0.330 4.483 0.206 0.987 2.347 C2 ATD 14 ATD O2 O2 O 0 1 N N N -4.154 -0.354 3.763 0.159 1.817 1.460 O2 ATD 15 ATD N3 N3 N 0 1 N N N -2.161 -0.090 4.796 0.528 1.369 3.597 N3 ATD 16 ATD C4 C4 C 0 1 N N N -1.272 0.568 5.625 0.580 0.461 4.593 C4 ATD 17 ATD O4 O4 O 0 1 N N N -0.176 0.060 5.837 0.870 0.805 5.724 O4 ATD 18 ATD C5 C5 C 0 1 N N N -1.758 1.852 6.133 0.302 -0.897 4.309 C5 ATD 19 ATD C5M C5M C 0 1 N N N -0.943 2.715 7.070 0.358 -1.933 5.402 C5M ATD 20 ATD C6 C6 C 0 1 N N N -2.983 2.305 5.785 -0.017 -1.253 3.046 C6 ATD 21 ATD HOP2 2HOP H 0 0 N N N -2.619 6.007 6.797 1.879 0.374 -5.675 HOP2 ATD 22 ATD HOP3 3HOP H 0 0 N N N -2.267 6.687 4.394 2.722 -0.935 -3.095 HOP3 ATD 23 ATD "HO'5" 5HO* H 0 0 N N N -9.375 3.927 6.428 -4.475 -0.197 -2.040 "HO'5" ATD 24 ATD "H5'" 1H5* H 0 1 N N N -7.891 5.264 5.244 -2.402 -0.059 -3.009 "H5'" ATD 25 ATD "H5''" 2H5* H 0 0 N N N -7.964 3.642 4.597 -2.513 -1.356 -1.795 "H5''" ATD 26 ATD "H4'" H4* H 0 1 N N N -5.884 4.580 6.437 -1.435 1.456 -1.285 "H4'" ATD 27 ATD "H3'" H3* H 0 1 N N N -5.933 5.047 3.795 -0.163 -1.152 -2.088 "H3'" ATD 28 ATD "H2'" 1H2* H 0 1 N N N -5.947 2.796 2.979 1.188 0.645 0.004 "H2'" ATD 29 ATD "H2''" 2H2* H 0 0 N N N -4.206 3.031 3.194 1.482 -1.094 -0.331 "H2''" ATD 30 ATD "H1'" H1* H 0 1 N N N -5.897 1.167 4.639 -0.610 -1.755 0.643 "H1'" ATD 31 ATD H3 H3 H 0 1 N N N -1.896 -1.006 4.442 0.719 2.301 3.783 H3 ATD 32 ATD H71 1H5M H 0 1 N N N -0.386 2.088 7.767 0.632 -1.454 6.342 H71 ATD 33 ATD H72 2H5M H 0 1 N N N -0.279 3.337 6.490 -0.618 -2.404 5.506 H72 ATD 34 ATD H73 3H5M H 0 1 N N N -1.592 3.380 7.637 1.101 -2.689 5.150 H73 ATD 35 ATD H6 H6 H 0 1 N N N -3.314 3.282 6.093 -0.235 -2.284 2.811 H6 ATD 36 # 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 ATD P OP1 DOUB N N 1 ATD P OP2 SING N N 2 ATD P OP3 SING N N 3 ATD P "O3'" SING N N 4 ATD OP2 HOP2 SING N N 5 ATD OP3 HOP3 SING N N 6 ATD "O5'" "C5'" SING N N 7 ATD "O5'" "HO'5" SING N N 8 ATD "C5'" "C4'" SING N N 9 ATD "C5'" "H5'" SING N N 10 ATD "C5'" "H5''" SING N N 11 ATD "C4'" "O4'" SING N N 12 ATD "C4'" "C3'" SING N N 13 ATD "C4'" "H4'" SING N N 14 ATD "O4'" "C1'" SING N N 15 ATD "C3'" "O3'" SING N N 16 ATD "C3'" "C2'" SING N N 17 ATD "C3'" "H3'" SING N N 18 ATD "C2'" "C1'" SING N N 19 ATD "C2'" "H2'" SING N N 20 ATD "C2'" "H2''" SING N N 21 ATD "C1'" N1 SING N N 22 ATD "C1'" "H1'" SING N N 23 ATD N1 C2 SING N N 24 ATD N1 C6 SING N N 25 ATD C2 O2 DOUB N N 26 ATD C2 N3 SING N N 27 ATD N3 C4 SING N N 28 ATD N3 H3 SING N N 29 ATD C4 O4 DOUB N N 30 ATD C4 C5 SING N N 31 ATD C5 C5M SING N N 32 ATD C5 C6 DOUB N N 33 ATD C5M H71 SING N N 34 ATD C5M H72 SING N N 35 ATD C5M H73 SING N N 36 ATD C6 H6 SING N N 37 # 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 ATD SMILES ACDLabs 10.04 "O=C1NC(=O)N(C=C1C)C2OC(C(OP(=O)(O)O)C2)CO" ATD SMILES_CANONICAL CACTVS 3.341 "CC1=CN([C@@H]2C[C@H](O[P](O)(O)=O)[C@@H](CO)O2)C(=O)NC1=O" ATD SMILES CACTVS 3.341 "CC1=CN([CH]2C[CH](O[P](O)(O)=O)[CH](CO)O2)C(=O)NC1=O" ATD SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "CC1=CN(C(=O)NC1=O)[C@@H]2C[C@@H]([C@H](O2)CO)OP(=O)(O)O" ATD SMILES "OpenEye OEToolkits" 1.5.0 "CC1=CN(C(=O)NC1=O)C2CC(C(O2)CO)OP(=O)(O)O" ATD InChI InChI 1.03 "InChI=1S/C10H15N2O8P/c1-5-3-12(10(15)11-9(5)14)8-2-6(7(4-13)19-8)20-21(16,17)18/h3,6-8,13H,2,4H2,1H3,(H,11,14,15)(H2,16,17,18)/t6-,7+,8-/m0/s1" ATD InChIKey InChI 1.03 XXYIANZGUOSQHY-RNJXMRFFSA-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 ATD "SYSTEMATIC NAME" ACDLabs 10.04 ;3'-thymidylic acid ; ATD "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "[(2R,3S,5S)-2-(hydroxymethyl)-5-(5-methyl-2,4-dioxo-pyrimidin-1-yl)oxolan-3-yl] 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 ATD "Create component" 1999-09-29 RCSB ATD "Modify descriptor" 2011-06-04 RCSB #