data_NMT # _chem_comp.id NMT _chem_comp.name "1-(O2-(METHYLCARBAMOYL)-O5-HYDROXYPHOSPHINYL-BETA-D-RIBOFURANOSYL)THYMINE" _chem_comp.type "DNA LINKING" _chem_comp.pdbx_type ATOMN _chem_comp.formula "C12 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 2004-11-22 _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 397.275 _chem_comp.one_letter_code T _chem_comp.three_letter_code NMT _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 1XUW _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 NMT P P P 0 1 N N N 16.777 16.674 7.656 2.787 0.324 -4.407 P NMT 1 NMT OP3 O3P O 0 1 N Y N 17.984 15.953 7.255 1.198 0.588 -4.548 OP3 NMT 2 NMT OP2 O2P O 0 1 N N N 16.842 18.013 8.292 2.921 -1.270 -4.647 OP2 NMT 3 NMT "O5'" O5* O 0 1 N N N 15.767 16.902 6.424 3.063 0.476 -2.819 "O5'" NMT 4 NMT N1 N1 N 0 1 N N N 12.293 18.488 5.568 0.452 2.524 0.177 N1 NMT 5 NMT C6 C6 C 0 1 N N N 13.107 18.762 6.629 0.309 2.663 -1.199 C6 NMT 6 NMT C2 C2 C 0 1 N N N 11.195 19.263 5.312 -0.300 3.336 1.055 C2 NMT 7 NMT O2 O2 O 0 1 N N N 10.432 19.056 4.366 -0.225 3.269 2.283 O2 NMT 8 NMT N3 N3 N 0 1 N N N 11.004 20.296 6.211 -1.159 4.248 0.431 N3 NMT 9 NMT C4 C4 C 0 1 N N N 11.797 20.620 7.311 -1.338 4.427 -0.932 C4 NMT 10 NMT O4 O4 O 0 1 N N N 11.476 21.575 7.987 -2.112 5.251 -1.413 O4 NMT 11 NMT C5 C5 C 0 1 N N N 12.939 19.749 7.500 -0.514 3.537 -1.792 C5 NMT 12 NMT C5M C5M C 0 1 N N N 13.833 20.047 8.675 -0.651 3.669 -3.275 C5M NMT 13 NMT "C2'" C2* C 0 1 N N R 13.218 17.774 3.392 0.748 0.163 0.786 "C2'" NMT 14 NMT "C5'" C5* C 0 1 N N N 15.566 15.836 5.507 2.282 -0.292 -1.921 "C5'" NMT 15 NMT "C4'" C4* C 0 1 N N R 14.503 16.172 4.557 2.725 0.023 -0.498 "C4'" NMT 16 NMT "O4'" O4* O 0 1 N N N 13.236 16.317 5.281 2.470 1.422 -0.246 "O4'" NMT 17 NMT "C1'" C1* C 0 1 N N R 12.500 17.339 4.577 1.373 1.543 0.675 "C1'" NMT 18 NMT "C3'" C3* C 0 1 N N R 14.630 17.513 3.861 1.940 -0.742 0.560 "C3'" NMT 19 NMT "O3'" O3* O 0 1 N N N 15.594 17.409 2.830 2.742 -0.809 1.739 "O3'" NMT 20 NMT "O6'" "O6'" O 0 1 N N N 13.015 16.912 2.326 0.137 -0.058 2.041 "O6'" NMT 21 NMT "C7'" "C7'" C 0 1 N N S 11.845 16.829 1.692 -0.929 -1.020 1.984 "C7'" NMT 22 NMT "N8'" "N8'" N 0 1 N N N 11.743 15.985 0.607 -1.544 -1.171 3.305 "N8'" NMT 23 NMT "C9'" "C9'" C 0 1 N N N 10.417 15.832 -0.001 -2.057 0.089 3.824 "C9'" NMT 24 NMT "O7'" "O7'" O 0 1 N N N 10.868 17.409 2.086 -0.453 -2.263 1.469 "O7'" NMT 25 NMT OP1 O1P O 0 1 N N N ? ? ? 3.659 1.172 -5.286 OP1 NMT 26 NMT HOP3 3HOP H 0 0 N N N 17.942 15.096 6.848 0.799 0.616 -5.443 HOP3 NMT 27 NMT HOP2 2HOP H 0 0 N N N 16.058 18.482 8.553 2.886 -1.617 -5.563 HOP2 NMT 28 NMT H6 H6 H 0 1 N N N 13.989 18.122 6.800 0.928 1.995 -1.790 H6 NMT 29 NMT HN3 HN3 H 0 1 N N N 10.188 20.884 6.044 -1.709 4.843 1.045 HN3 NMT 30 NMT H71 1H5M H 0 1 N N N 14.865 20.157 8.267 -1.057 2.748 -3.690 H71 NMT 31 NMT H72 2H5M H 0 1 N N N 13.692 20.876 9.407 0.324 3.866 -3.719 H72 NMT 32 NMT H73 3H5M H 0 1 N N N 13.896 19.107 9.271 -1.320 4.497 -3.510 H73 NMT 33 NMT "H2'" H2* H 0 1 N N N 12.942 18.801 3.057 -0.000 0.004 -0.000 "H2'" NMT 34 NMT "H5'" 1H5* H 0 1 N N N 15.366 14.871 6.029 1.229 -0.035 -2.051 "H5'" NMT 35 NMT "H5''" 2H5* H 0 0 N N N 16.511 15.551 4.989 2.428 -1.352 -2.133 "H5''" NMT 36 NMT "H4'" H4* H 0 1 N N N 14.563 15.347 3.809 3.804 -0.139 -0.410 "H4'" NMT 37 NMT "H1'" H1* H 0 1 N N N 11.518 16.953 4.217 1.754 1.910 1.633 "H1'" NMT 38 NMT "H3'" H3* H 0 1 N N N 14.994 18.361 4.487 1.675 -1.764 0.277 "H3'" NMT 39 NMT "HO3'" H3T H 0 0 N Y N 16.482 17.245 3.125 3.447 -0.153 1.628 "HO3'" NMT 40 NMT "H7'" "H7'" H 0 1 N N N 11.987 17.905 1.438 -1.686 -0.639 1.288 "H7'" NMT 41 NMT "H8'" "H8'" H 0 1 N N N 12.110 15.066 0.856 -2.300 -1.852 3.246 "H8'" NMT 42 NMT "H9'1" "1H9'" H 0 0 N N N 10.016 16.836 -0.274 -1.263 0.632 4.343 "H9'1" NMT 43 NMT "H9'2" "2H9'" H 0 0 N N N 10.335 15.149 -0.879 -2.874 -0.096 4.527 "H9'2" NMT 44 NMT "H9'3" "3H9'" H 0 0 N N N 9.685 15.521 0.780 -2.431 0.710 3.006 "H9'3" NMT 45 NMT H1 H1 H 0 1 N N N 10.034 17.350 1.634 -0.157 -2.788 2.232 H1 NMT 46 # 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 NMT P OP3 SING N N 1 NMT P OP2 SING N N 2 NMT P "O5'" SING N N 3 NMT P OP1 DOUB N N 4 NMT OP3 HOP3 SING N N 5 NMT OP2 HOP2 SING N N 6 NMT "O5'" "C5'" SING N N 7 NMT N1 C6 SING N N 8 NMT N1 C2 SING N N 9 NMT N1 "C1'" SING N N 10 NMT C6 C5 DOUB N N 11 NMT C6 H6 SING N N 12 NMT C2 O2 DOUB N N 13 NMT C2 N3 SING N N 14 NMT N3 C4 SING N N 15 NMT N3 HN3 SING N N 16 NMT C4 O4 DOUB N N 17 NMT C4 C5 SING N N 18 NMT C5 C5M SING N N 19 NMT C5M H71 SING N N 20 NMT C5M H72 SING N N 21 NMT C5M H73 SING N N 22 NMT "C2'" "C1'" SING N N 23 NMT "C2'" "C3'" SING N N 24 NMT "C2'" "O6'" SING N N 25 NMT "C2'" "H2'" SING N N 26 NMT "C5'" "C4'" SING N N 27 NMT "C5'" "H5'" SING N N 28 NMT "C5'" "H5''" SING N N 29 NMT "C4'" "O4'" SING N N 30 NMT "C4'" "C3'" SING N N 31 NMT "C4'" "H4'" SING N N 32 NMT "O4'" "C1'" SING N N 33 NMT "C1'" "H1'" SING N N 34 NMT "C3'" "O3'" SING N N 35 NMT "C3'" "H3'" SING N N 36 NMT "O3'" "HO3'" SING N N 37 NMT "O6'" "C7'" SING N N 38 NMT "C7'" "N8'" SING N N 39 NMT "C7'" "O7'" SING N N 40 NMT "C7'" "H7'" SING N N 41 NMT "N8'" "C9'" SING N N 42 NMT "N8'" "H8'" SING N N 43 NMT "C9'" "H9'1" SING N N 44 NMT "C9'" "H9'2" SING N N 45 NMT "C9'" "H9'3" SING N N 46 NMT "O7'" H1 SING N N 47 # 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 NMT SMILES ACDLabs 10.04 "O=C1NC(=O)N(C=C1C)C2OC(C(O)C2OC(O)NC)COP(=O)(O)O" NMT SMILES_CANONICAL CACTVS 3.341 "CN[C@@H](O)O[C@@H]1[C@H](O)[C@@H](CO[P](O)(O)=O)O[C@H]1N2C=C(C)C(=O)NC2=O" NMT SMILES CACTVS 3.341 "CN[CH](O)O[CH]1[CH](O)[CH](CO[P](O)(O)=O)O[CH]1N2C=C(C)C(=O)NC2=O" NMT 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)OC(NC)O" NMT SMILES "OpenEye OEToolkits" 1.5.0 "CC1=CN(C(=O)NC1=O)C2C(C(C(O2)COP(=O)(O)O)O)OC(NC)O" NMT InChI InChI 1.03 "InChI=1S/C12H20N3O10P/c1-5-3-15(11(18)14-9(5)17)10-8(25-12(19)13-2)7(16)6(24-10)4-23-26(20,21)22/h3,6-8,10,12-13,16,19H,4H2,1-2H3,(H,14,17,18)(H2,20,21,22)/t6-,7-,8-,10-,12+/m1/s1" NMT InChIKey InChI 1.03 NBDRJSHPMIOFTH-REKNECKOSA-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 NMT "SYSTEMATIC NAME" ACDLabs 10.04 ;2'-O-[(S)-hydroxy(methylamino)methyl]-5-methyluridine 5'-(dihydrogen phosphate) ; NMT "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "[(2R,3R,4R,5R)-3-hydroxy-4-(hydroxy-methylamino-methoxy)-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 NMT "Create component" 2004-11-22 RCSB NMT "Modify descriptor" 2011-06-04 RCSB #