data_NMS # _chem_comp.id NMS _chem_comp.name "1-(O2-(2-METHYLAMINO-2-OXO-ETHYL)-O5-HYDROXYPHOSPHINYL-BETA-D-RIBOFURANOSYL)THYMINE" _chem_comp.type "DNA LINKING" _chem_comp.pdbx_type ATOMN _chem_comp.formula "C13 H20 N3 O10 P" _chem_comp.mon_nstd_parent_comp_id DT _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2004-11-24 _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 409.286 _chem_comp.one_letter_code T _chem_comp.three_letter_code NMS _chem_comp.pdbx_model_coordinates_details ? _chem_comp.pdbx_model_coordinates_missing_flag Y _chem_comp.pdbx_ideal_coordinates_details ? _chem_comp.pdbx_ideal_coordinates_missing_flag N _chem_comp.pdbx_model_coordinates_db_code 1XUX _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 NMS P P P 0 1 N N N 24.347 7.107 44.844 2.787 0.324 -4.407 P NMS 1 NMS OP2 O2P O 0 1 N N N 25.634 7.706 45.123 1.198 0.588 -4.548 OP2 NMS 2 NMS OP1 O1P O 0 1 N N N 24.202 5.719 44.444 3.659 1.172 -5.286 OP1 NMS 3 NMS "O5'" O5* O 0 1 N N N 23.371 7.252 46.059 3.063 0.476 -2.819 "O5'" NMS 4 NMS N1 N1 N 0 1 N N N 19.861 6.186 47.423 0.452 2.524 0.177 N1 NMS 5 NMS C6 C6 C 0 1 N N N 20.607 5.637 46.417 0.309 2.663 -1.199 C6 NMS 6 NMS C2 C2 C 0 1 N N N 18.736 5.584 47.899 -0.300 3.336 1.055 C2 NMS 7 NMS O2 O2 O 0 1 N N N 18.044 6.030 48.794 -0.225 3.269 2.283 O2 NMS 8 NMS N3 N3 N 0 1 N N N 18.397 4.404 47.287 -1.159 4.248 0.431 N3 NMS 9 NMS C4 C4 C 0 1 N N N 19.091 3.792 46.274 -1.338 4.427 -0.932 C4 NMS 10 NMS O4 O4 O 0 1 N N N 18.675 2.758 45.834 -2.112 5.251 -1.413 O4 NMS 11 NMS C5 C5 C 0 1 N N N 20.274 4.492 45.826 -0.514 3.537 -1.792 C5 NMS 12 NMS C5M C5M C 0 1 N N N 21.106 3.906 44.720 -0.651 3.669 -3.275 C5M NMS 13 NMS "C2'" C2* C 0 1 N N R 21.019 7.245 49.268 0.748 0.163 0.786 "C2'" NMS 14 NMS "C5'" C5* C 0 1 N N N 23.250 8.536 46.647 2.282 -0.292 -1.921 "C5'" NMS 15 NMS "C4'" C4* C 0 1 N N R 22.301 8.377 47.796 2.725 0.023 -0.498 "C4'" NMS 16 NMS "O4'" O4* O 0 1 N N N 20.973 8.198 47.180 2.470 1.422 -0.246 "O4'" NMS 17 NMS "C1'" C1* C 0 1 N N R 20.181 7.439 48.107 1.373 1.543 0.675 "C1'" NMS 18 NMS "C3'" C3* C 0 1 N N R 22.392 7.188 48.685 1.940 -0.742 0.560 "C3'" NMS 19 NMS "O3'" O3* O 0 1 N N N 23.399 7.338 49.660 2.742 -0.809 1.739 "O3'" NMS 20 NMS "O6'" "O6'" O 0 1 N N N 20.733 8.289 50.152 0.137 -0.058 2.041 "O6'" NMS 21 NMS "C7'" "C7'" C 0 1 N N N 19.378 8.070 50.609 -0.332 -1.396 2.174 "C7'" NMS 22 NMS "C8'" "C8'" C 0 1 N N N 19.383 8.204 52.102 -0.980 -1.603 3.526 "C8'" NMS 23 NMS "O8'" "O8'" O 0 1 N N N 18.409 8.058 52.794 -1.077 -0.708 4.360 "O8'" NMS 24 NMS "N9'" "N9'" N 0 1 N N N 20.631 8.475 52.602 -1.433 -2.904 3.682 "N9'" NMS 25 NMS C10 C10 C 0 1 N N N 20.725 8.653 54.053 -2.091 -3.371 4.881 C10 NMS 26 NMS OP3 O3P O 0 1 N Y N ? ? ? 2.921 -1.270 -4.647 OP3 NMS 27 NMS HOP2 2HOP H 0 0 N N N 25.729 8.614 45.385 0.799 0.616 -5.443 HOP2 NMS 28 NMS H6 H6 H 0 1 N N N 21.522 6.142 46.065 0.928 1.995 -1.790 H6 NMS 29 NMS HN3 HN3 H 0 1 N N N 17.551 3.939 47.616 -1.709 4.843 1.045 HN3 NMS 30 NMS H71 1H5M H 0 1 N N N 22.152 3.807 45.094 -1.057 2.748 -3.690 H71 NMS 31 NMS H72 2H5M H 0 1 N N N 20.827 2.947 44.225 0.324 3.866 -3.719 H72 NMS 32 NMS H73 3H5M H 0 1 N N N 21.216 4.682 43.927 -1.320 4.497 -3.510 H73 NMS 33 NMS "H2'" H2* H 0 1 N N N 20.872 6.325 49.881 -0.000 0.004 -0.000 "H2'" NMS 34 NMS "H5'" 1H5* H 0 1 N N N 22.945 9.329 45.925 1.229 -0.035 -2.051 "H5'" NMS 35 NMS "H5''" 2H5* H 0 0 N N N 24.228 8.986 46.937 2.428 -1.352 -2.133 "H5''" NMS 36 NMS "H4'" H4* H 0 1 N N N 22.525 9.263 48.434 3.804 -0.139 -0.410 "H4'" NMS 37 NMS "H1'" H1* H 0 1 N N N 19.229 7.921 48.430 1.754 1.910 1.633 "H1'" NMS 38 NMS "H3'" H3* H 0 1 N N N 22.664 6.226 48.191 1.675 -1.764 0.277 "H3'" NMS 39 NMS "HO3'" H3T H 0 0 N Y N 24.273 7.302 49.289 3.447 -0.153 1.628 "HO3'" NMS 40 NMS "H7'1" "1H7'" H 0 0 N N N 18.952 7.101 50.260 0.521 -2.074 2.075 "H7'1" NMS 41 NMS "H7'2" "2H7'" H 0 0 N N N 18.637 8.740 50.114 -1.050 -1.607 1.376 "H7'2" NMS 42 NMS "H9'" "H9'" H 0 1 N N N 21.417 8.538 51.955 -1.295 -3.560 2.919 "H9'" NMS 43 NMS H101 1H10 H 0 0 N N N 20.298 7.762 54.570 -2.796 -4.170 4.635 H101 NMS 44 NMS H102 2H10 H 0 0 N N N 21.740 8.873 54.460 -2.637 -2.552 5.356 H102 NMS 45 NMS H103 3H10 H 0 0 N N N 20.008 9.441 54.383 -1.354 -3.758 5.590 H103 NMS 46 NMS HOP3 3HOP H 0 0 N N N -0.845 -0.393 -0.183 2.886 -1.617 -5.563 HOP3 NMS 47 # 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 NMS P OP2 SING N N 1 NMS P OP1 DOUB N N 2 NMS P "O5'" SING N N 3 NMS P OP3 SING N N 4 NMS OP2 HOP2 SING N N 5 NMS "O5'" "C5'" SING N N 6 NMS N1 C6 SING N N 7 NMS N1 C2 SING N N 8 NMS N1 "C1'" SING N N 9 NMS C6 C5 DOUB N N 10 NMS C6 H6 SING N N 11 NMS C2 O2 DOUB N N 12 NMS C2 N3 SING N N 13 NMS N3 C4 SING N N 14 NMS N3 HN3 SING N N 15 NMS C4 O4 DOUB N N 16 NMS C4 C5 SING N N 17 NMS C5 C5M SING N N 18 NMS C5M H71 SING N N 19 NMS C5M H72 SING N N 20 NMS C5M H73 SING N N 21 NMS "C2'" "C1'" SING N N 22 NMS "C2'" "C3'" SING N N 23 NMS "C2'" "O6'" SING N N 24 NMS "C2'" "H2'" SING N N 25 NMS "C5'" "C4'" SING N N 26 NMS "C5'" "H5'" SING N N 27 NMS "C5'" "H5''" SING N N 28 NMS "C4'" "O4'" SING N N 29 NMS "C4'" "C3'" SING N N 30 NMS "C4'" "H4'" SING N N 31 NMS "O4'" "C1'" SING N N 32 NMS "C1'" "H1'" SING N N 33 NMS "C3'" "O3'" SING N N 34 NMS "C3'" "H3'" SING N N 35 NMS "O3'" "HO3'" SING N N 36 NMS "O6'" "C7'" SING N N 37 NMS "C7'" "C8'" SING N N 38 NMS "C7'" "H7'1" SING N N 39 NMS "C7'" "H7'2" SING N N 40 NMS "C8'" "O8'" DOUB N N 41 NMS "C8'" "N9'" SING N N 42 NMS "N9'" C10 SING N N 43 NMS "N9'" "H9'" SING N N 44 NMS C10 H101 SING N N 45 NMS C10 H102 SING N N 46 NMS C10 H103 SING N N 47 NMS OP3 HOP3 SING N N 48 # 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 NMS SMILES ACDLabs 10.04 "O=C1NC(=O)N(C=C1C)C2OC(C(O)C2OCC(=O)NC)COP(=O)(O)O" NMS SMILES_CANONICAL CACTVS 3.341 "CNC(=O)CO[C@@H]1[C@H](O)[C@@H](CO[P](O)(O)=O)O[C@H]1N2C=C(C)C(=O)NC2=O" NMS SMILES CACTVS 3.341 "CNC(=O)CO[CH]1[CH](O)[CH](CO[P](O)(O)=O)O[CH]1N2C=C(C)C(=O)NC2=O" NMS SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "CC1=CN(C(=O)NC1=O)[C@H]2[C@@H]([C@@H]([C@H](O2)COP(=O)(O)O)O)OCC(=O)NC" NMS SMILES "OpenEye OEToolkits" 1.5.0 "CC1=CN(C(=O)NC1=O)C2C(C(C(O2)COP(=O)(O)O)O)OCC(=O)NC" NMS InChI InChI 1.03 "InChI=1S/C13H20N3O10P/c1-6-3-16(13(20)15-11(6)19)12-10(24-5-8(17)14-2)9(18)7(26-12)4-25-27(21,22)23/h3,7,9-10,12,18H,4-5H2,1-2H3,(H,14,17)(H,15,19,20)(H2,21,22,23)/t7-,9-,10-,12-/m1/s1" NMS InChIKey InChI 1.03 PQERMMDCFWNASH-UGKPPGOTSA-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 NMS "SYSTEMATIC NAME" ACDLabs 10.04 ;5-methyl-2'-O-[2-(methylamino)-2-oxoethyl]uridine 5'-(dihydrogen phosphate) ; NMS "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "[(2R,3R,4R,5R)-3-hydroxy-4-(2-methylamino-2-oxo-ethoxy)-5-(5-methyl-2,4-dioxo-pyrimidin-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 NMS "Create component" 2004-11-24 RCSB NMS "Modify descriptor" 2011-06-04 RCSB #