data_TYD # _chem_comp.id TYD _chem_comp.name "THYMIDINE-5'-DIPHOSPHATE" _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C10 H16 N2 O11 P2" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 1999-07-08 _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 402.188 _chem_comp.one_letter_code ? _chem_comp.three_letter_code TYD _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 1NDC _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site EBI # 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 TYD PA PA P 0 1 N N S 16.634 -11.407 -21.793 -0.143 -0.002 -2.900 PA TYD 1 TYD O1A O1A O 0 1 N N N 16.219 -12.867 -21.800 0.633 1.210 -2.558 O1A TYD 2 TYD O2A O2A O 0 1 N N N 16.524 -10.610 -22.998 -1.473 0.421 -3.703 O2A TYD 3 TYD O3A O3A O 0 1 N N N 15.773 -10.641 -20.670 0.752 -0.972 -3.821 O3A TYD 4 TYD PB PB P 0 1 N N N 14.681 -11.094 -19.566 1.126 -0.140 -5.147 PB TYD 5 TYD O1B O1B O 0 1 N N N 15.443 -11.044 -18.307 1.884 1.074 -4.771 O1B TYD 6 TYD O2B O2B O 0 1 N N N 14.287 -12.514 -19.907 2.027 -1.055 -6.119 O2B TYD 7 TYD O3B O3B O 0 1 N N N 13.620 -10.096 -19.691 -0.224 0.285 -5.912 O3B TYD 8 TYD "O5'" O5* O 0 1 N N N 18.138 -11.284 -21.252 -0.555 -0.774 -1.549 "O5'" TYD 9 TYD "C5'" C5* C 0 1 N N N 18.457 -11.907 -19.996 -1.345 0.133 -0.779 "C5'" TYD 10 TYD "C4'" C4* C 0 1 N N R 19.207 -10.960 -19.107 -1.772 -0.541 0.525 "C4'" TYD 11 TYD "O4'" O4* O 0 1 N N N 20.350 -10.541 -19.811 -0.624 -0.809 1.363 "O4'" TYD 12 TYD "C3'" C3* C 0 1 N N S 18.490 -9.655 -18.781 -2.631 0.421 1.383 "C3'" TYD 13 TYD "O3'" O3* O 0 1 N N N 17.656 -10.054 -17.699 -4.008 0.349 1.007 "O3'" TYD 14 TYD "C2'" C2* C 0 1 N N N 19.648 -8.765 -18.408 -2.418 -0.137 2.811 "C2'" TYD 15 TYD "C1'" C1* C 0 1 N N R 20.741 -9.203 -19.415 -1.113 -0.949 2.708 "C1'" TYD 16 TYD N1 N1 N 0 1 Y N N 20.795 -8.342 -20.623 -0.124 -0.425 3.654 N1 TYD 17 TYD C2 C2 C 0 1 Y N N 21.603 -7.208 -20.613 0.276 0.854 3.558 C2 TYD 18 TYD O2 O2 O 0 1 N N N 22.324 -6.949 -19.653 -0.186 1.564 2.685 O2 TYD 19 TYD N3 N3 N 0 1 Y N N 21.573 -6.390 -21.756 1.182 1.362 4.414 N3 TYD 20 TYD C4 C4 C 0 1 Y N N 20.810 -6.645 -22.891 1.701 0.590 5.390 C4 TYD 21 TYD O4 O4 O 0 1 N N N 20.879 -5.881 -23.847 2.522 1.048 6.165 O4 TYD 22 TYD C5 C5 C 0 1 Y N N 19.985 -7.833 -22.803 1.292 -0.760 5.499 C5 TYD 23 TYD C5M C5M C 0 1 N N N 19.146 -8.280 -23.993 1.860 -1.645 6.578 C5M TYD 24 TYD C6 C6 C 0 1 Y N N 19.961 -8.590 -21.694 0.381 -1.243 4.627 C6 TYD 25 TYD HOA2 2HOA H 0 0 N N N 16.783 -9.696 -22.993 -1.949 -0.395 -3.906 HOA2 TYD 26 TYD HOB2 2HOB H 0 0 N N N 13.645 -12.780 -19.258 2.228 -0.520 -6.899 HOB2 TYD 27 TYD HOB3 3HOB H 0 0 N N N 12.978 -10.362 -19.042 -0.687 -0.532 -6.140 HOB3 TYD 28 TYD "H5'1" 1H5* H 0 0 N N N 17.547 -12.311 -19.493 -2.230 0.417 -1.347 "H5'1" TYD 29 TYD "H5'2" 2H5* H 0 0 N N N 19.010 -12.864 -20.139 -0.758 1.023 -0.552 "H5'2" TYD 30 TYD "H4'" H4* H 0 1 N N N 19.376 -11.523 -18.159 -2.317 -1.462 0.319 "H4'" TYD 31 TYD "H3'" H3* H 0 1 N N N 17.864 -9.131 -19.541 -2.262 1.444 1.307 "H3'" TYD 32 TYD "HO3'" *HO3 H 0 0 N N N 17.209 -9.240 -17.495 -4.498 0.898 1.635 "HO3'" TYD 33 TYD "H2'1" 1H2* H 0 0 N N N 19.420 -7.673 -18.407 -3.249 -0.784 3.095 "H2'1" TYD 34 TYD "H2'2" 2H2* H 0 0 N N N 19.950 -8.812 -17.336 -2.306 0.676 3.527 "H2'2" TYD 35 TYD "H1'" H1* H 0 1 N N N 21.750 -9.137 -18.945 -1.311 -1.999 2.923 "H1'" TYD 36 TYD HN3 HN3 H 0 1 N N N 22.148 -5.547 -21.762 1.460 2.287 4.330 HN3 TYD 37 TYD H51 1H5 H 0 1 N N N 18.511 -9.194 -23.925 2.573 -1.078 7.176 H51 TYD 38 TYD H52 2H5 H 0 1 N N N 18.498 -7.427 -24.304 1.053 -2.002 7.218 H52 TYD 39 TYD H53 3H5 H 0 1 N N N 19.819 -8.386 -24.875 2.365 -2.497 6.121 H53 TYD 40 TYD H6 H6 H 0 1 N N N 19.245 -9.428 -21.662 0.054 -2.270 4.697 H6 TYD 41 # 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 TYD PA O1A DOUB N N 1 TYD PA O2A SING N N 2 TYD PA O3A SING N N 3 TYD PA "O5'" SING N N 4 TYD O2A HOA2 SING N N 5 TYD O3A PB SING N N 6 TYD PB O1B DOUB N N 7 TYD PB O2B SING N N 8 TYD PB O3B SING N N 9 TYD O2B HOB2 SING N N 10 TYD O3B HOB3 SING N N 11 TYD "O5'" "C5'" SING N N 12 TYD "C5'" "C4'" SING N N 13 TYD "C5'" "H5'1" SING N N 14 TYD "C5'" "H5'2" SING N N 15 TYD "C4'" "O4'" SING N N 16 TYD "C4'" "C3'" SING N N 17 TYD "C4'" "H4'" SING N N 18 TYD "O4'" "C1'" SING N N 19 TYD "C3'" "O3'" SING N N 20 TYD "C3'" "C2'" SING N N 21 TYD "C3'" "H3'" SING N N 22 TYD "O3'" "HO3'" SING N N 23 TYD "C2'" "C1'" SING N N 24 TYD "C2'" "H2'1" SING N N 25 TYD "C2'" "H2'2" SING N N 26 TYD "C1'" N1 SING N N 27 TYD "C1'" "H1'" SING N N 28 TYD N1 C2 SING Y N 29 TYD N1 C6 SING Y N 30 TYD C2 O2 DOUB N N 31 TYD C2 N3 SING Y N 32 TYD N3 C4 SING Y N 33 TYD N3 HN3 SING N N 34 TYD C4 O4 DOUB N N 35 TYD C4 C5 SING Y N 36 TYD C5 C5M SING N N 37 TYD C5 C6 DOUB Y N 38 TYD C5M H51 SING N N 39 TYD C5M H52 SING N N 40 TYD C5M H53 SING N N 41 TYD C6 H6 SING N N 42 # 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 TYD SMILES ACDLabs 10.04 "O=P(O)(O)OP(=O)(O)OCC2OC(N1C(=O)NC(=O)C(=C1)C)CC2O" TYD SMILES_CANONICAL CACTVS 3.341 "CC1=CN([C@H]2C[C@H](O)[C@@H](CO[P@@](O)(=O)O[P](O)(O)=O)O2)C(=O)NC1=O" TYD SMILES CACTVS 3.341 "CC1=CN([CH]2C[CH](O)[CH](CO[P](O)(=O)O[P](O)(O)=O)O2)C(=O)NC1=O" TYD SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "CC1=CN(C(=O)NC1=O)[C@H]2C[C@@H]([C@H](O2)CO[P@](=O)(O)OP(=O)(O)O)O" TYD SMILES "OpenEye OEToolkits" 1.5.0 "CC1=CN(C(=O)NC1=O)C2CC(C(O2)COP(=O)(O)OP(=O)(O)O)O" TYD InChI InChI 1.03 "InChI=1S/C10H16N2O11P2/c1-5-3-12(10(15)11-9(5)14)8-2-6(13)7(22-8)4-21-25(19,20)23-24(16,17)18/h3,6-8,13H,2,4H2,1H3,(H,19,20)(H,11,14,15)(H2,16,17,18)/t6-,7+,8+/m0/s1" TYD InChIKey InChI 1.03 UJLXYODCHAELLY-XLPZGREQSA-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 TYD "SYSTEMATIC NAME" ACDLabs 10.04 ;thymidine 5'-(trihydrogen diphosphate) ; TYD "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "[(2R,3S,5R)-3-hydroxy-5-(5-methyl-2,4-dioxo-pyrimidin-1-yl)oxolan-2-yl]methyl phosphono hydrogen 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 TYD "Create component" 1999-07-08 EBI TYD "Modify descriptor" 2011-06-04 RCSB #