data_TDY # _chem_comp.id TDY _chem_comp.name ;5-(METHYLAMINO)THYMIDINE 5'-(DIHYDROGEN PHOSPHATE) ; _chem_comp.type "DNA LINKING" _chem_comp.pdbx_type ATOMN _chem_comp.formula "C11 H20 N3 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 2009-08-14 _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 353.266 _chem_comp.one_letter_code T _chem_comp.three_letter_code TDY _chem_comp.pdbx_model_coordinates_details ? _chem_comp.pdbx_model_coordinates_missing_flag N _chem_comp.pdbx_ideal_coordinates_details Corina _chem_comp.pdbx_ideal_coordinates_missing_flag N _chem_comp.pdbx_model_coordinates_db_code 2WQ6 _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 TDY P P P 0 1 N N N -3.343 -25.687 23.393 -4.335 -1.275 -0.045 P TDY 1 TDY OP1 OP1 O 0 1 N N N -2.999 -27.045 23.787 -5.520 -0.444 -0.355 OP1 TDY 2 TDY "O5'" "O5'" O 0 1 N N N -3.482 -25.655 21.840 -3.149 -0.335 0.503 "O5'" TDY 3 TDY "C5'" "C5'" C 0 1 N N N -3.671 -24.395 21.182 -2.653 0.794 -0.219 "C5'" TDY 4 TDY "C4'" "C4'" C 0 1 N N R -3.405 -24.532 19.694 -1.534 1.461 0.582 "C4'" TDY 5 TDY "O4'" "O4'" O 0 1 N N N -4.523 -25.237 19.074 -0.387 0.589 0.677 "O4'" TDY 6 TDY "C3'" "C3'" C 0 1 N N S -3.301 -23.237 18.932 -0.985 2.698 -0.173 "C3'" TDY 7 TDY "O3'" "O3'" O 0 1 N N N -1.983 -22.735 19.041 -1.758 3.862 0.126 "O3'" TDY 8 TDY "C2'" "C2'" C 0 1 N N N -3.665 -23.677 17.518 0.446 2.822 0.405 "C2'" TDY 9 TDY "C1'" "C1'" C 0 1 N N R -4.634 -24.826 17.727 0.750 1.420 0.966 "C1'" TDY 10 TDY N1 N1 N 0 1 N N N -6.096 -24.517 17.468 1.944 0.872 0.319 N1 TDY 11 TDY C2 C2 C 0 1 N N N -6.711 -25.215 16.530 1.925 0.617 -1.000 C2 TDY 12 TDY O2 O2 O 0 1 N N N -6.169 -26.082 15.828 0.952 0.942 -1.652 O2 TDY 13 TDY N3 N3 N 0 1 N N N -8.046 -24.953 16.265 2.955 0.012 -1.615 N3 TDY 14 TDY C4 C4 C 0 1 N N N -8.799 -24.011 16.968 3.937 -0.575 -0.906 C4 TDY 15 TDY O4 O4 O 0 1 N N N -9.968 -23.833 16.664 4.898 -1.045 -1.476 O4 TDY 16 TDY C5 C5 C 0 1 N N R -8.156 -23.374 18.202 3.841 -0.647 0.597 C5 TDY 17 TDY C5M C5M C 0 1 N N N -8.418 -24.203 19.437 5.246 -0.737 1.195 C5M TDY 18 TDY C6 C6 C 0 1 N N N -6.619 -23.260 18.023 3.145 0.616 1.117 C6 TDY 19 TDY N5 N5 N 0 1 N N N -8.583 -22.104 18.337 3.066 -1.835 0.983 N5 TDY 20 TDY OP2 OP2 O 0 1 N N N -4.478 -24.971 24.026 -4.721 -2.362 1.079 OP2 TDY 21 TDY CM5 CM5 C 0 1 N N N -8.870 -21.005 19.163 3.706 -3.063 0.493 CM5 TDY 22 TDY OP3 OP3 O 0 1 N Y N -2.126 -24.745 23.663 -3.847 -2.033 -1.379 OP3 TDY 23 TDY HA HA H 0 1 N N N -4.284 -24.818 24.943 -5.431 -2.964 0.816 HA TDY 24 TDY HP3 HP3 H 0 1 N N N -1.685 -24.554 22.844 -3.072 -2.597 -1.250 HP3 TDY 25 TDY HA1 HA1 H 0 1 N N N -4.707 -24.059 21.335 -2.264 0.466 -1.183 HA1 TDY 26 TDY HB2 HB2 H 0 1 N N N -2.969 -23.661 21.605 -3.462 1.507 -0.377 HB2 TDY 27 TDY HB HB H 0 1 N N N -2.437 -25.051 19.639 -1.887 1.739 1.575 HB TDY 28 TDY HC HC H 0 1 N N N -3.945 -22.419 19.287 -0.957 2.518 -1.247 HC TDY 29 TDY HD HD H 0 1 N N N -4.352 -25.592 16.990 0.903 1.477 2.044 HD TDY 30 TDY "H3'" "H3'" H 0 1 N N N -1.614 -22.622 18.173 -1.454 4.663 -0.322 "H3'" TDY 31 TDY HB1 HB1 H 0 1 N N N -4.132 -22.858 16.952 1.154 3.080 -0.383 HB1 TDY 32 TDY HC2 HC2 H 0 1 N N N -2.784 -23.972 16.930 0.473 3.566 1.201 HC2 TDY 33 TDY H61C H61C H 0 0 N N N -6.149 -23.067 18.999 3.822 1.467 1.037 H61C TDY 34 TDY H62C H62C H 0 0 N N N -6.390 -22.432 17.336 2.863 0.473 2.160 H62C TDY 35 TDY H3 H3 H 0 1 N N N -8.493 -25.466 15.532 2.991 -0.002 -2.584 H3 TDY 36 TDY H5M1 H5M1 H 0 0 N N N -8.482 -25.265 19.159 5.819 0.145 0.910 H5M1 TDY 37 TDY H5M2 H5M2 H 0 0 N N N -7.597 -24.060 20.155 5.176 -0.790 2.282 H5M2 TDY 38 TDY H5M3 H5M3 H 0 0 N N N -9.366 -23.887 19.896 5.744 -1.631 0.820 H5M3 TDY 39 TDY H51N H51N H 0 0 N N N -7.888 -21.666 17.767 2.933 -1.870 1.983 H51N TDY 40 TDY HM51 HM51 H 0 0 N N N -8.945 -21.341 20.208 4.707 -3.145 0.917 HM51 TDY 41 TDY HM52 HM52 H 0 0 N N N -8.066 -20.260 19.074 3.112 -3.926 0.793 HM52 TDY 42 TDY HM53 HM53 H 0 0 N N N -9.824 -20.554 18.854 3.774 -3.028 -0.594 HM53 TDY 43 # 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 TDY P OP1 DOUB N N 1 TDY P "O5'" SING N N 2 TDY P OP2 SING N N 3 TDY P OP3 SING N N 4 TDY "O5'" "C5'" SING N N 5 TDY "C5'" "C4'" SING N N 6 TDY "C4'" "O4'" SING N N 7 TDY "C4'" "C3'" SING N N 8 TDY "O4'" "C1'" SING N N 9 TDY "C3'" "O3'" SING N N 10 TDY "C3'" "C2'" SING N N 11 TDY "C2'" "C1'" SING N N 12 TDY "C1'" N1 SING N N 13 TDY N1 C2 SING N N 14 TDY N1 C6 SING N N 15 TDY C2 O2 DOUB N N 16 TDY C2 N3 SING N N 17 TDY N3 C4 SING N N 18 TDY C4 O4 DOUB N N 19 TDY C4 C5 SING N N 20 TDY C5 C5M SING N N 21 TDY C5 C6 SING N N 22 TDY C5 N5 SING N N 23 TDY OP2 HA SING N N 24 TDY OP3 HP3 SING N N 25 TDY "C5'" HA1 SING N N 26 TDY "C5'" HB2 SING N N 27 TDY "C4'" HB SING N N 28 TDY "C3'" HC SING N N 29 TDY "C1'" HD SING N N 30 TDY "O3'" "H3'" SING N N 31 TDY "C2'" HB1 SING N N 32 TDY "C2'" HC2 SING N N 33 TDY C6 H61C SING N N 34 TDY C6 H62C SING N N 35 TDY N3 H3 SING N N 36 TDY C5M H5M1 SING N N 37 TDY C5M H5M2 SING N N 38 TDY C5M H5M3 SING N N 39 TDY N5 H51N SING N N 40 TDY N5 CM5 SING N N 41 TDY CM5 HM51 SING N N 42 TDY CM5 HM52 SING N N 43 TDY CM5 HM53 SING N N 44 # 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 TDY SMILES ACDLabs 10.04 "O=C1N(CC(C(=O)N1)(NC)C)C2OC(C(O)C2)COP(=O)(O)O" TDY SMILES_CANONICAL CACTVS 3.352 "CN[C@]1(C)CN([C@H]2C[C@H](O)[C@@H](CO[P](O)(O)=O)O2)C(=O)NC1=O" TDY SMILES CACTVS 3.352 "CN[C]1(C)CN([CH]2C[CH](O)[CH](CO[P](O)(O)=O)O2)C(=O)NC1=O" TDY SMILES_CANONICAL "OpenEye OEToolkits" 1.6.1 "C[C@]1(CN(C(=O)NC1=O)[C@H]2C[C@@H]([C@H](O2)COP(=O)(O)O)O)NC" TDY SMILES "OpenEye OEToolkits" 1.6.1 "CC1(CN(C(=O)NC1=O)C2CC(C(O2)COP(=O)(O)O)O)NC" TDY InChI InChI 1.03 "InChI=1S/C11H20N3O8P/c1-11(12-2)5-14(10(17)13-9(11)16)8-3-6(15)7(22-8)4-21-23(18,19)20/h6-8,12,15H,3-5H2,1-2H3,(H,13,16,17)(H2,18,19,20)/t6-,7+,8+,11+/m0/s1" TDY InChIKey InChI 1.03 GANAXGZWNNBICE-PRKAOEEVSA-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 TDY "SYSTEMATIC NAME" ACDLabs 10.04 ;5-(methylamino)thymidine 5'-(dihydrogen phosphate) ; TDY "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.6.1 "[(2R,3S,5R)-3-hydroxy-5-[(5R)-5-methyl-5-methylamino-2,4-dioxo-1,3-diazinan-1-yl]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 TDY "Create component" 2009-08-14 EBI TDY "Modify descriptor" 2011-06-04 RCSB #