data_D4M # _chem_comp.id D4M _chem_comp.name "[(5R)-5-(5-METHYL-2,4-DIOXO-3,4-DIHYDROPYRIMIDIN-1(2H)-YL)-2,5-DIHYDROFURAN-2-YL]METHYL DIHYDROGEN PHOSPHATE" _chem_comp.type "DNA LINKING" _chem_comp.pdbx_type ATOMN _chem_comp.formula "C10 H13 N2 O7 P" _chem_comp.mon_nstd_parent_comp_id DT _chem_comp.pdbx_synonyms ;2',3'-DIDEOXY-2',3-DIDEHYDROTHYMIDINE 5'-MONOPHOSPHATE; 2',3'-DEHYDRO-2',3'-DEOXY-THYMIDINE 5'-MONOPHOSPHATE ; _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2005-05-10 _chem_comp.pdbx_modified_date 2020-05-27 _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 304.193 _chem_comp.one_letter_code T _chem_comp.three_letter_code D4M _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 1Z4Q _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 D4M OP2 O2P O 0 1 N N N 17.153 38.848 28.332 -3.538 -1.876 -0.640 OP2 D4M 1 D4M P P P 0 1 N N N 16.496 40.073 29.009 -4.141 -0.650 0.212 P D4M 2 D4M OP1 O1P O 0 1 N N N 17.643 41.181 29.184 -5.013 0.172 -0.657 OP1 D4M 3 D4M OP3 O3P O 0 1 N Y N 15.868 39.871 30.400 -5.000 -1.224 1.446 OP3 D4M 4 D4M "O5'" O5* O 0 1 N N N 15.370 40.574 27.944 -2.935 0.257 0.774 "O5'" D4M 5 D4M "C5'" C5* C 0 1 N N N 14.189 41.270 28.442 -2.285 0.830 -0.363 "C5'" D4M 6 D4M "C4'" C4* C 0 1 N N S 13.921 42.352 27.407 -1.122 1.709 0.104 "C4'" D4M 7 D4M "O4'" O4* O 0 1 N N N 13.480 41.639 26.176 -0.099 0.897 0.712 "O4'" D4M 8 D4M "C3'" C3* C 0 1 N N N 12.783 43.259 27.861 -0.464 2.379 -1.080 "C3'" D4M 9 D4M "C2'" C2* C 0 1 N N N 11.829 43.224 26.934 0.839 2.302 -0.929 "C2'" D4M 10 D4M "C1'" C1* C 0 1 N N R 12.207 42.268 25.783 1.125 1.574 0.365 "C1'" D4M 11 D4M N1 N1 N 0 1 N N N 11.163 41.234 25.544 2.203 0.601 0.170 N1 D4M 12 D4M C6 C6 C 0 1 N N N 10.703 40.403 26.598 3.384 0.755 0.843 C6 D4M 13 D4M C5 C5 C 0 1 N N N 9.728 39.435 26.360 4.377 -0.142 0.664 C5 D4M 14 D4M C5M C5M C 0 1 N N N 9.305 38.526 27.522 5.686 0.011 1.396 C5M D4M 15 D4M C4 C4 C 0 1 N N N 9.164 39.281 25.070 4.176 -1.225 -0.225 C4 D4M 16 D4M O4 O4 O 0 1 N N N 8.302 38.430 24.755 5.057 -2.046 -0.404 O4 D4M 17 D4M N3 N3 N 0 1 N N N 9.602 40.108 24.066 2.995 -1.343 -0.866 N3 D4M 18 D4M C2 C2 C 0 1 N N N 10.582 41.062 24.249 2.022 -0.435 -0.669 C2 D4M 19 D4M O2 O2 O 0 1 N N N 10.893 41.742 23.269 0.964 -0.553 -1.257 O2 D4M 20 D4M HOP2 2HOP H 0 0 N N N 16.473 38.191 28.228 -2.977 -2.385 -0.038 HOP2 D4M 21 D4M HOP3 3HOP H 0 0 N N N 15.464 40.623 30.816 -5.710 -1.760 1.066 HOP3 D4M 22 D4M "H5'" 1H5* H 0 1 N N N 13.317 40.603 28.640 -2.997 1.437 -0.921 "H5'" D4M 23 D4M "H5''" 2H5* H 0 0 N N N 14.291 41.652 29.484 -1.904 0.034 -1.003 "H5''" D4M 24 D4M "H4'" H4* H 0 1 N N N 14.830 42.976 27.247 -1.478 2.458 0.811 "H4'" D4M 25 D4M "H3'" H3* H 0 1 N N N 12.662 43.876 28.766 -0.977 2.842 -1.910 "H3'" D4M 26 D4M "H2'" H2* H 0 1 N N N 10.930 43.845 27.085 1.579 2.691 -1.613 "H2'" D4M 27 D4M "H1'" H1* H 0 1 N N N 12.299 42.832 24.825 1.396 2.285 1.145 "H1'" D4M 28 D4M H6 H6 H 0 1 N N N 11.109 40.511 27.617 3.521 1.589 1.515 H6 D4M 29 D4M H71 1H5M H 0 1 N N N 8.525 37.751 27.331 5.633 -0.515 2.349 H71 D4M 30 D4M H72 2H5M H 0 1 N N N 10.210 38.032 27.945 6.491 -0.409 0.793 H72 D4M 31 D4M H73 3H5M H 0 1 N N N 8.985 39.160 28.381 5.880 1.069 1.576 H73 D4M 32 D4M H3 H3 H 0 1 N N N 9.180 40.009 23.142 2.849 -2.084 -1.475 H3 D4M 33 # 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 D4M OP2 P SING N N 1 D4M OP2 HOP2 SING N N 2 D4M P OP1 DOUB N N 3 D4M P OP3 SING N N 4 D4M P "O5'" SING N N 5 D4M OP3 HOP3 SING N N 6 D4M "O5'" "C5'" SING N N 7 D4M "C5'" "C4'" SING N N 8 D4M "C5'" "H5'" SING N N 9 D4M "C5'" "H5''" SING N N 10 D4M "C4'" "O4'" SING N N 11 D4M "C4'" "C3'" SING N N 12 D4M "C4'" "H4'" SING N N 13 D4M "O4'" "C1'" SING N N 14 D4M "C3'" "C2'" DOUB N N 15 D4M "C3'" "H3'" SING N N 16 D4M "C2'" "C1'" SING N N 17 D4M "C2'" "H2'" SING N N 18 D4M "C1'" N1 SING N N 19 D4M "C1'" "H1'" SING N N 20 D4M N1 C6 SING N N 21 D4M N1 C2 SING N N 22 D4M C6 C5 DOUB N N 23 D4M C6 H6 SING N N 24 D4M C5 C5M SING N N 25 D4M C5 C4 SING N N 26 D4M C5M H71 SING N N 27 D4M C5M H72 SING N N 28 D4M C5M H73 SING N N 29 D4M C4 O4 DOUB N N 30 D4M C4 N3 SING N N 31 D4M N3 C2 SING N N 32 D4M N3 H3 SING N N 33 D4M C2 O2 DOUB N N 34 # 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 D4M SMILES ACDLabs 10.04 "O=C1NC(=O)N(C=C1C)C2OC(C=C2)COP(=O)(O)O" D4M SMILES_CANONICAL CACTVS 3.341 "CC1=CN([C@@H]2O[C@H](CO[P](O)(O)=O)C=C2)C(=O)NC1=O" D4M SMILES CACTVS 3.341 "CC1=CN([CH]2O[CH](CO[P](O)(O)=O)C=C2)C(=O)NC1=O" D4M SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "CC1=CN(C(=O)NC1=O)[C@H]2C=C[C@H](O2)COP(=O)(O)O" D4M SMILES "OpenEye OEToolkits" 1.5.0 "CC1=CN(C(=O)NC1=O)C2C=CC(O2)COP(=O)(O)O" D4M InChI InChI 1.03 "InChI=1S/C10H13N2O7P/c1-6-4-12(10(14)11-9(6)13)8-3-2-7(19-8)5-18-20(15,16)17/h2-4,7-8H,5H2,1H3,(H,11,13,14)(H2,15,16,17)/t7-,8+/m0/s1" D4M InChIKey InChI 1.03 XLPGURCDSRIXFL-JGVFFNPUSA-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 D4M "SYSTEMATIC NAME" ACDLabs 10.04 "[(2S,5R)-5-(5-methyl-2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-2,5-dihydrofuran-2-yl]methyl dihydrogen phosphate" D4M "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "[(2S,5R)-5-(5-methyl-2,4-dioxo-pyrimidin-1-yl)-2,5-dihydrofuran-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 D4M "Create component" 2005-05-10 RCSB D4M "Modify descriptor" 2011-06-04 RCSB D4M "Modify synonyms" 2020-05-27 PDBE # loop_ _pdbx_chem_comp_synonyms.ordinal _pdbx_chem_comp_synonyms.comp_id _pdbx_chem_comp_synonyms.name _pdbx_chem_comp_synonyms.provenance _pdbx_chem_comp_synonyms.type 1 D4M ;2',3'-DIDEOXY-2',3-DIDEHYDROTHYMIDINE 5'-MONOPHOSPHATE ; ? ? 2 D4M ;2',3'-DEHYDRO-2',3'-DEOXY-THYMIDINE 5'-MONOPHOSPHATE ; ? ? #