data_NTT # _chem_comp.id NTT _chem_comp.name "[(1R,5R,7R,8S)-8-hydroxy-3-methyl-7-(5-methyl-2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-2,6-dioxa-3-azabicyclo[3.2.1]oct-5-yl]methyl dihydrogen phosphate" _chem_comp.type "DNA linking" _chem_comp.pdbx_type ATOMN _chem_comp.formula "C12 H18 N3 O9 P" _chem_comp.mon_nstd_parent_comp_id DT _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2014-08-05 _chem_comp.pdbx_modified_date 2015-08-14 _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 379.260 _chem_comp.one_letter_code ? _chem_comp.three_letter_code NTT _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 4U6K _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site PDBJ # 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 NTT P P1 P 0 1 N N N 30.987 9.812 60.579 4.046 1.498 0.278 P NTT 1 NTT OP1 O1 O 0 1 N N N 30.456 8.467 60.099 3.536 2.835 -0.099 OP1 NTT 2 NTT OP2 O2 O 0 1 N N N 32.399 10.348 60.374 4.753 1.581 1.722 OP2 NTT 3 NTT "O5'" O3 O 0 1 N N N 29.983 11.100 60.453 2.822 0.454 0.338 "O5'" NTT 4 NTT N1 N1 N 0 1 N N N 29.281 15.046 60.921 -2.316 0.025 0.359 N1 NTT 5 NTT C6 C1 C 0 1 N N N 30.494 14.321 60.883 -1.986 1.264 -0.118 C6 NTT 6 NTT C2 C2 C 0 1 N N N 29.295 16.464 61.011 -3.591 -0.273 0.670 C2 NTT 7 NTT O2 O4 O 0 1 N N N 28.247 17.126 61.036 -3.862 -1.380 1.093 O2 NTT 8 NTT N3 N2 N 0 1 N N N 30.553 17.097 61.064 -4.570 0.638 0.521 N3 NTT 9 NTT C4 C3 C 0 1 N N N 31.793 16.403 61.029 -4.286 1.871 0.054 C4 NTT 10 NTT O4 O5 O 0 1 N N N 32.829 17.081 61.080 -5.172 2.696 -0.082 O4 NTT 11 NTT C5 C4 C 0 1 N N N 31.726 14.922 60.929 -2.949 2.197 -0.278 C5 NTT 12 NTT C7 C5 C 0 1 N N N 32.986 14.148 60.877 -2.605 3.568 -0.801 C7 NTT 13 NTT "C2'" C6 C 0 1 N N R 27.602 14.283 59.350 -1.196 -1.881 -0.738 "C2'" NTT 14 NTT "C5'" C7 C 0 1 N N N 28.598 10.809 60.308 1.931 0.235 -0.758 "C5'" NTT 15 NTT "C4'" C8 C 0 1 N N R 27.824 12.133 60.087 0.890 -0.815 -0.366 "C4'" NTT 16 NTT "O4'" O6 O 0 1 N N N 28.107 12.947 61.259 0.004 -0.356 0.675 "O4'" NTT 17 NTT "C1'" C9 C 0 1 N N R 27.996 14.347 60.850 -1.273 -0.990 0.527 "C1'" NTT 18 NTT "C3'" C10 C 0 1 N N S 28.334 12.998 58.938 -0.058 -1.185 -1.541 "C3'" NTT 19 NTT "O3'" O7 O 0 1 N N N 27.946 12.524 57.658 0.569 -2.092 -2.450 "O3'" NTT 20 NTT "O2'" O8 O 0 1 N N N 26.207 14.127 59.146 -0.678 -3.157 -0.308 "O2'" NTT 21 NTT "C6'" C11 C 0 1 N N N 26.290 11.872 60.024 1.502 -2.179 0.143 "C6'" NTT 22 NTT "N6'" N3 N 0 1 N N N 25.584 13.213 60.006 0.419 -3.030 0.654 "N6'" NTT 23 NTT "C7'" C12 C 0 1 N N N 24.079 13.004 59.718 0.928 -4.351 1.048 "C7'" NTT 24 NTT HOP2 H2 H 0 0 N N N 32.914 9.710 59.893 5.501 2.192 1.759 HOP2 NTT 25 NTT H72 H3 H 0 1 N N N 30.448 13.244 60.815 -0.961 1.495 -0.365 H72 NTT 26 NTT H3 H4 H 0 1 N N N 30.575 18.095 61.130 -5.484 0.407 0.750 H3 NTT 27 NTT H71 H5 H 0 1 N N N 33.842 14.837 60.928 -2.680 3.570 -1.888 H71 NTT 28 NTT H1 H6 H 0 1 N N N 33.024 13.452 61.728 -3.298 4.299 -0.387 H1 NTT 29 NTT H73 H7 H 0 1 N N N 33.028 13.580 59.936 -1.587 3.824 -0.506 H73 NTT 30 NTT "H2'" H8 H 0 1 N N N 28.010 15.150 58.810 -2.137 -1.954 -1.282 "H2'" NTT 31 NTT "H5''" H9 H 0 0 N N N 28.228 10.313 61.218 1.429 1.169 -1.009 "H5''" NTT 32 NTT "H5'" H10 H 0 1 N N N 28.449 10.146 59.443 2.496 -0.117 -1.621 "H5'" NTT 33 NTT "H1'" H11 H 0 1 N N N 27.219 14.874 61.424 -1.489 -1.604 1.401 "H1'" NTT 34 NTT "H3'" H12 H 0 1 N N N 29.422 13.137 59.015 -0.420 -0.296 -2.056 "H3'" NTT 35 NTT "HO3'" H13 H 0 0 N Y N 28.427 11.731 57.454 -0.027 -2.450 -3.122 "HO3'" NTT 36 NTT H14 H14 H 0 1 N N N 25.973 11.296 60.906 2.006 -2.683 -0.681 H14 NTT 37 NTT H15 H15 H 0 1 N N N 26.045 11.309 59.111 2.216 -1.982 0.943 H15 NTT 38 NTT H16 H16 H 0 1 N N N 23.777 13.632 58.867 1.360 -4.848 0.179 H16 NTT 39 NTT H17 H17 H 0 1 N N N 23.895 11.947 59.476 1.693 -4.231 1.815 H17 NTT 40 NTT H18 H18 H 0 1 N N N 23.494 13.284 60.606 0.110 -4.954 1.442 H18 NTT 41 NTT OP3 OP3 O 0 1 N Y N 30.742 9.588 62.091 5.119 1.005 -0.817 OP3 NTT 42 NTT HOP3 HOP3 H 0 0 N N N 30.359 8.729 62.226 5.496 0.133 -0.634 HOP3 NTT 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 NTT "O3'" "C3'" SING N N 1 NTT "C3'" "C2'" SING N N 2 NTT "C3'" "C4'" SING N N 3 NTT "O2'" "C2'" SING N N 4 NTT "O2'" "N6'" SING N N 5 NTT "C2'" "C1'" SING N N 6 NTT "C7'" "N6'" SING N N 7 NTT "N6'" "C6'" SING N N 8 NTT "C6'" "C4'" SING N N 9 NTT "C4'" "C5'" SING N N 10 NTT "C4'" "O4'" SING N N 11 NTT OP1 P DOUB N N 12 NTT "C5'" "O5'" SING N N 13 NTT OP2 P SING N N 14 NTT "O5'" P SING N N 15 NTT "C1'" N1 SING N N 16 NTT "C1'" "O4'" SING N N 17 NTT C7 C5 SING N N 18 NTT C6 N1 SING N N 19 NTT C6 C5 DOUB N N 20 NTT N1 C2 SING N N 21 NTT C5 C4 SING N N 22 NTT C2 O2 DOUB N N 23 NTT C2 N3 SING N N 24 NTT C4 N3 SING N N 25 NTT C4 O4 DOUB N N 26 NTT OP2 HOP2 SING N N 27 NTT C6 H72 SING N N 28 NTT N3 H3 SING N N 29 NTT C7 H71 SING N N 30 NTT C7 H1 SING N N 31 NTT C7 H73 SING N N 32 NTT "C2'" "H2'" SING N N 33 NTT "C5'" "H5''" SING N N 34 NTT "C5'" "H5'" SING N N 35 NTT "C1'" "H1'" SING N N 36 NTT "C3'" "H3'" SING N N 37 NTT "O3'" "HO3'" SING N N 38 NTT "C6'" H14 SING N N 39 NTT "C6'" H15 SING N N 40 NTT "C7'" H16 SING N N 41 NTT "C7'" H17 SING N N 42 NTT "C7'" H18 SING N N 43 NTT P OP3 SING N N 44 NTT OP3 HOP3 SING N N 45 # 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 NTT SMILES ACDLabs 12.01 "O=C1C(=CN(C(=O)N1)C3OC2(C(O)C3ON(C)C2)COP(=O)(O)O)C" NTT InChI InChI 1.03 "InChI=1S/C12H18N3O9P/c1-6-3-15(11(18)13-9(6)17)10-7-8(16)12(23-10,4-14(2)24-7)5-22-25(19,20)21/h3,7-8,10,16H,4-5H2,1-2H3,(H,13,17,18)(H2,19,20,21)/t7-,8+,10-,12-/m1/s1" NTT InChIKey InChI 1.03 OFICQOIAWJEWLX-UJYYTQATSA-N NTT SMILES_CANONICAL CACTVS 3.385 "CN1C[C@]2(CO[P](O)(O)=O)O[C@H]([C@H](O1)[C@@H]2O)N3C=C(C)C(=O)NC3=O" NTT SMILES CACTVS 3.385 "CN1C[C]2(CO[P](O)(O)=O)O[CH]([CH](O1)[CH]2O)N3C=C(C)C(=O)NC3=O" NTT SMILES_CANONICAL "OpenEye OEToolkits" 1.9.2 "CC1=CN(C(=O)NC1=O)[C@H]2[C@H]3[C@@H]([C@@](O2)(CN(O3)C)COP(=O)(O)O)O" NTT SMILES "OpenEye OEToolkits" 1.9.2 "CC1=CN(C(=O)NC1=O)C2C3C(C(O2)(CN(O3)C)COP(=O)(O)O)O" # 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 NTT "SYSTEMATIC NAME" ACDLabs 12.01 "[(1R,5R,7R,8S)-8-hydroxy-3-methyl-7-(5-methyl-2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-2,6-dioxa-3-azabicyclo[3.2.1]oct-5-yl]methyl dihydrogen phosphate" NTT "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.9.2 "[(1R,5R,7R,8S)-3-methyl-7-[5-methyl-2,4-bis(oxidanylidene)pyrimidin-1-yl]-8-oxidanyl-2,6-dioxa-3-azabicyclo[3.2.1]octan-5-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 NTT "Create component" 2014-08-05 PDBJ NTT "Modify descriptor" 2014-09-05 RCSB NTT "Initial release" 2015-08-19 RCSB #