data_2NT # _chem_comp.id 2NT _chem_comp.name ;2'-O-[2-[HYDROXY(METHYLENEAMINO)OXY]ETHYL THYMIDINE-5'-MONOPHOSPHATE ; _chem_comp.type "RNA LINKING" _chem_comp.pdbx_type ATOMN _chem_comp.formula "C13 H22 N3 O11 P" _chem_comp.mon_nstd_parent_comp_id DT _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2004-12-13 _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 427.301 _chem_comp.one_letter_code T _chem_comp.three_letter_code 2NT _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 1Y7F _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 2NT P P P 0 1 N N N 10.812 4.198 5.251 2.787 0.324 -4.407 P 2NT 1 2NT OP3 O3P O 0 1 N Y N 12.055 4.725 4.576 1.198 0.588 -4.548 OP3 2NT 2 2NT OP2 O2P O 0 1 N N N 10.970 3.446 6.484 2.921 -1.270 -4.647 OP2 2NT 3 2NT "O5'" O5* O 0 1 N N N 9.796 5.406 5.445 3.063 0.476 -2.819 "O5'" 2NT 4 2NT "C5'" C5* C 0 1 N N N 9.481 6.274 4.358 2.282 -0.292 -1.921 "C5'" 2NT 5 2NT "C4'" C4* C 0 1 N N R 8.456 7.290 4.789 2.725 0.023 -0.498 "C4'" 2NT 6 2NT "O4'" O4* O 0 1 N N N 7.180 6.619 4.967 2.470 1.422 -0.246 "O4'" 2NT 7 2NT "C1'" C1* C 0 1 N N R 6.482 7.220 6.046 1.373 1.543 0.675 "C1'" 2NT 8 2NT N1 N1 N 0 1 N N N 6.310 6.209 7.123 0.452 2.524 0.177 N1 2NT 9 2NT C6 C6 C 0 1 N N N 7.167 5.136 7.298 0.309 2.663 -1.199 C6 2NT 10 2NT C2 C2 C 0 1 N N N 5.250 6.413 7.964 -0.300 3.336 1.055 C2 2NT 11 2NT O2 O2 O 0 1 N N N 4.485 7.351 7.835 -0.225 3.269 2.283 O2 2NT 12 2NT N3 N3 N 0 1 N N N 5.123 5.493 8.968 -1.159 4.248 0.431 N3 2NT 13 2NT C4 C4 C 0 1 N N N 5.951 4.435 9.238 -1.338 4.427 -0.932 C4 2NT 14 2NT O4 O4 O 0 1 N N N 5.735 3.726 10.213 -2.111 5.251 -1.413 O4 2NT 15 2NT C5 C5 C 0 1 N N N 7.051 4.259 8.313 -0.514 3.537 -1.792 C5 2NT 16 2NT C5M C5M C 0 1 N N N 8.008 3.127 8.540 -0.651 3.669 -3.275 C5M 2NT 17 2NT "C2'" C2* C 0 1 N N R 7.308 8.419 6.525 0.748 0.163 0.786 "C2'" 2NT 18 2NT "O2'" O2* O 0 1 N N N 6.962 9.505 5.646 0.137 -0.058 2.041 "O2'" 2NT 19 2NT "CB'" "CB'" C 0 1 N N N 5.733 10.181 5.853 -0.332 -1.396 2.174 "CB'" 2NT 20 2NT "CC'" "CC'" C 0 1 N N N 5.667 11.256 4.785 -0.951 -1.569 3.547 "CC'" 2NT 21 2NT "OD'" "OD'" O 0 1 N N N 6.640 12.228 5.153 0.039 -1.320 4.537 "OD'" 2NT 22 2NT "NE'" "NE'" N 0 1 N N N 6.516 13.339 4.405 -0.589 -1.495 5.839 "NE'" 2NT 23 2NT "CF'" "CF'" C 0 1 N N N 7.552 14.088 4.493 0.419 -1.087 6.809 "CF'" 2NT 24 2NT "OG'" "OG'" O 0 1 N N N 7.880 14.404 5.840 1.486 -2.019 6.927 "OG'" 2NT 25 2NT "C3'" C3* C 0 1 N N R 8.704 7.964 6.124 1.940 -0.742 0.560 "C3'" 2NT 26 2NT "O3'" O3* O 0 1 N N N 9.662 9.009 6.062 2.742 -0.809 1.739 "O3'" 2NT 27 2NT OP1 O1P O 0 1 N N N ? ? ? 3.659 1.172 -5.286 OP1 2NT 28 2NT HOP3 3HOP H 0 0 N N N 11.952 5.217 3.770 0.799 0.616 -5.443 HOP3 2NT 29 2NT HOP2 2HOP H 0 0 N N N 10.188 3.114 6.909 2.886 -1.617 -5.563 HOP2 2NT 30 2NT "H5'" 1H5* H 0 1 N N N 9.155 5.709 3.454 1.229 -0.035 -2.051 "H5'" 2NT 31 2NT "H5''" 2H5* H 0 0 N N N 10.392 6.755 3.930 2.428 -1.352 -2.133 "H5''" 2NT 32 2NT "H4'" H4* H 0 1 N N N 8.494 8.064 3.987 3.804 -0.139 -0.410 "H4'" 2NT 33 2NT "H1'" H1* H 0 1 N N N 5.470 7.575 5.741 1.754 1.910 1.633 "H1'" 2NT 34 2NT H6 H6 H 0 1 N N N 7.992 4.970 6.585 0.928 1.995 -1.790 H6 2NT 35 2NT HN3 HN3 H 0 1 N N N 4.320 5.609 9.586 -1.709 4.843 1.045 HN3 2NT 36 2NT H71 1H5M H 0 1 N N N 9.032 3.566 8.597 -1.057 2.748 -3.690 H71 2NT 37 2NT H72 2H5M H 0 1 N N N 7.912 2.401 9.381 0.324 3.866 -3.719 H72 2NT 38 2NT H73 3H5M H 0 1 N N N 8.051 2.536 7.596 -1.320 4.497 -3.510 H73 2NT 39 2NT "H2'" H2* H 0 1 N N N 7.184 8.713 7.593 -0.000 0.004 -0.000 "H2'" 2NT 40 2NT "HB'1" "1HB'" H 0 0 N N N 5.609 10.574 6.889 -1.066 -1.580 1.383 "HB'1" 2NT 41 2NT "HB'2" "2HB'" H 0 0 N N N 4.847 9.504 5.860 0.520 -2.071 2.050 "HB'2" 2NT 42 2NT "HC'1" "1HC'" H 0 0 N N N 4.646 11.679 4.641 -1.324 -2.588 3.686 "HC'1" 2NT 43 2NT "HC'2" "2HC'" H 0 0 N N N 5.797 10.865 3.749 -1.768 -0.855 3.691 "HC'2" 2NT 44 2NT "HE'" "HE'" H 0 1 N N N 5.666 13.852 4.639 -1.325 -0.791 5.798 "HE'" 2NT 45 2NT "HF'1" "1HF'" H 0 0 N N N 7.433 15.012 3.881 0.835 -0.107 6.551 "HF'1" 2NT 46 2NT "HF'2" "2HF'" H 0 0 N N N 8.422 13.634 3.963 -0.048 -0.995 7.794 "HF'2" 2NT 47 2NT "HG'" "HG'" H 0 1 N N N 8.648 14.959 5.905 1.810 -2.189 6.026 "HG'" 2NT 48 2NT "H3'" H3* H 0 1 N N N 9.168 7.288 6.880 1.675 -1.764 0.277 "H3'" 2NT 49 2NT "HO3'" H3T H 0 0 N Y N 9.817 9.431 6.899 3.344 -1.558 1.619 "HO3'" 2NT 50 # 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 2NT P OP3 SING N N 1 2NT P OP2 SING N N 2 2NT P "O5'" SING N N 3 2NT P OP1 DOUB N N 4 2NT OP3 HOP3 SING N N 5 2NT OP2 HOP2 SING N N 6 2NT "O5'" "C5'" SING N N 7 2NT "C5'" "C4'" SING N N 8 2NT "C5'" "H5'" SING N N 9 2NT "C5'" "H5''" SING N N 10 2NT "C4'" "O4'" SING N N 11 2NT "C4'" "C3'" SING N N 12 2NT "C4'" "H4'" SING N N 13 2NT "O4'" "C1'" SING N N 14 2NT "C1'" N1 SING N N 15 2NT "C1'" "C2'" SING N N 16 2NT "C1'" "H1'" SING N N 17 2NT N1 C6 SING N N 18 2NT N1 C2 SING N N 19 2NT C6 C5 DOUB N N 20 2NT C6 H6 SING N N 21 2NT C2 O2 DOUB N N 22 2NT C2 N3 SING N N 23 2NT N3 C4 SING N N 24 2NT N3 HN3 SING N N 25 2NT C4 O4 DOUB N N 26 2NT C4 C5 SING N N 27 2NT C5 C5M SING N N 28 2NT C5M H71 SING N N 29 2NT C5M H72 SING N N 30 2NT C5M H73 SING N N 31 2NT "C2'" "O2'" SING N N 32 2NT "C2'" "C3'" SING N N 33 2NT "C2'" "H2'" SING N N 34 2NT "O2'" "CB'" SING N N 35 2NT "CB'" "CC'" SING N N 36 2NT "CB'" "HB'1" SING N N 37 2NT "CB'" "HB'2" SING N N 38 2NT "CC'" "OD'" SING N N 39 2NT "CC'" "HC'1" SING N N 40 2NT "CC'" "HC'2" SING N N 41 2NT "OD'" "NE'" SING N N 42 2NT "NE'" "CF'" SING N N 43 2NT "NE'" "HE'" SING N N 44 2NT "CF'" "OG'" SING N N 45 2NT "CF'" "HF'1" SING N N 46 2NT "CF'" "HF'2" SING N N 47 2NT "OG'" "HG'" SING N N 48 2NT "C3'" "O3'" SING N N 49 2NT "C3'" "H3'" SING N N 50 2NT "O3'" "HO3'" SING N N 51 # 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 2NT SMILES ACDLabs 10.04 "O=C1NC(=O)N(C=C1C)C2OC(C(O)C2OCCONCO)COP(=O)(O)O" 2NT SMILES_CANONICAL CACTVS 3.341 "CC1=CN([C@@H]2O[C@H](CO[P](O)(O)=O)[C@@H](O)[C@H]2OCCONCO)C(=O)NC1=O" 2NT SMILES CACTVS 3.341 "CC1=CN([CH]2O[CH](CO[P](O)(O)=O)[CH](O)[CH]2OCCONCO)C(=O)NC1=O" 2NT 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)OCCONCO" 2NT SMILES "OpenEye OEToolkits" 1.5.0 "CC1=CN(C(=O)NC1=O)C2C(C(C(O2)COP(=O)(O)O)O)OCCONCO" 2NT InChI InChI 1.03 "InChI=1S/C13H22N3O11P/c1-7-4-16(13(20)15-11(7)19)12-10(24-2-3-25-14-6-17)9(18)8(27-12)5-26-28(21,22)23/h4,8-10,12,14,17-18H,2-3,5-6H2,1H3,(H,15,19,20)(H2,21,22,23)/t8-,9-,10-,12-/m1/s1" 2NT InChIKey InChI 1.03 FVJMEWQZKWJLGQ-DNRKLUKYSA-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 2NT "SYSTEMATIC NAME" ACDLabs 10.04 ;2'-O-(2-{[(hydroxymethyl)amino]oxy}ethyl)-5-methyluridine 5'-(dihydrogen phosphate) ; 2NT "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "[(2R,3R,4R,5R)-3-hydroxy-4-[2-(hydroxymethylamino)oxyethoxy]-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 2NT "Create component" 2004-12-13 RCSB 2NT "Modify linking type" 2011-06-04 RCSB 2NT "Modify descriptor" 2011-06-04 RCSB #