data_T2T # _chem_comp.id T2T _chem_comp.name ;[(2S,3S,5R)-3-[(2S)-3-({[(2R,3S,4R,5R)-3-HYDROXY-4-METHOXY-5-(5-METHYL-2,4-DIOXO-3,4-DIHYDROPYRIMIDIN-1(2H)-YL)TETRAHYDROFURAN-2-YL]METHYL}AMINO)-2-METHYL-3-OXOPROPYL]-5-(5-METHYL-2,4-DIOXO-3,4-DIHYDROPYRIMIDIN-1(2H)-YL)TETRAHYDROFURAN-2-YL]METHYL DIHYDROGEN PHOSPHATE ; _chem_comp.type "RNA LINKING" _chem_comp.pdbx_type ATOMN _chem_comp.formula "C25 H36 N5 O13 P" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2006-05-12 _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 645.553 _chem_comp.one_letter_code N _chem_comp.three_letter_code T2T _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 ? _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 T2T P P P 0 1 N N N 6.177 3.383 8.074 3.142 -1.904 -11.152 P T2T 1 T2T OP1 O1P O 0 1 N N N 7.448 3.347 7.300 3.020 -1.857 -12.647 OP1 T2T 2 T2T OP2 O2P O 0 1 N N N 6.216 3.476 9.566 2.277 -3.061 -10.424 OP2 T2T 3 T2T C4 C4 C 0 1 N N N 1.961 9.854 12.541 8.008 -4.601 -7.139 C4 T2T 4 T2T N3 N3 N 0 1 N N N 1.335 10.948 11.971 7.100 -5.593 -7.477 N3 T2T 5 T2T C2 C2 C 0 1 N N N 1.726 11.632 10.842 5.744 -5.644 -7.135 C2 T2T 6 T2T N1 N1 N 0 1 N N N 2.869 11.157 10.244 5.278 -4.557 -6.362 N1 T2T 7 T2T C6 C6 C 0 1 N N N 3.538 10.066 10.750 6.149 -3.537 -5.996 C6 T2T 8 T2T C5 C5 C 0 1 N N N 3.151 9.396 11.843 7.445 -3.490 -6.325 C5 T2T 9 T2T "O5'" O5* O 0 1 N N N 5.323 4.591 7.484 2.694 -0.551 -10.386 "O5'" T2T 10 T2T "C5'" C5* C 0 1 N N N 5.353 4.887 6.090 2.779 -0.516 -8.970 "C5'" T2T 11 T2T C4X C4X C 0 1 N N S 4.921 6.315 5.858 2.310 0.844 -8.484 C4X T2T 12 T2T O4X O4X O 0 1 N N N 3.503 6.454 6.146 0.937 1.039 -8.870 O4X T2T 13 T2T C1X C1X C 0 1 N N R 3.250 7.755 6.657 0.247 1.701 -7.799 C1X T2T 14 T2T N1B N1B N 0 1 N N N 2.470 7.638 7.916 -0.743 0.799 -7.276 N1B T2T 15 T2T C6B C6B C 0 1 N N N 2.741 6.660 8.854 -0.478 -0.564 -7.306 C6B T2T 16 T2T C2B C2B C 0 1 N N N 1.451 8.548 8.102 -1.957 1.278 -6.740 C2B T2T 17 T2T O2B O2B O 0 1 N N N 1.208 9.446 7.299 -2.259 2.471 -6.682 O2B T2T 18 T2T N3B N3B N 0 1 N N N 0.728 8.371 9.266 -2.826 0.288 -6.266 N3B T2T 19 T2T C4B C4B C 0 1 N N N 0.933 7.409 10.246 -2.613 -1.082 -6.273 C4B T2T 20 T2T O4B O4B O 0 1 N N N 0.195 7.364 11.247 -3.423 -1.897 -5.839 O4B T2T 21 T2T C5B C5B C 0 1 N N N 2.040 6.507 9.995 -1.311 -1.508 -6.851 C5B T2T 22 T2T CAB CAB C 0 1 N N N 2.353 5.457 11.014 -1.007 -2.971 -6.893 CAB T2T 23 T2T C2X C2X C 0 1 N N N 4.593 8.486 6.777 1.294 2.078 -6.764 C2X T2T 24 T2T C3X C3X C 0 1 N N S 5.579 7.319 6.790 2.345 1.002 -6.967 C3X T2T 25 T2T CH2 CH2 C 0 1 N N N 7.074 7.530 6.450 3.710 1.371 -6.413 CH2 T2T 26 T2T CP CP C 0 1 N N S 7.309 8.779 5.576 3.687 1.618 -4.894 CP T2T 27 T2T C2P C2P C 0 1 N N N 8.646 8.643 4.859 5.081 2.005 -4.397 C2P T2T 28 T2T CX CX C 0 1 N N N 7.344 10.019 6.462 3.216 0.388 -4.117 CX T2T 29 T2T OX OX O 0 1 N N N 7.928 11.030 6.080 2.223 0.395 -3.393 OX T2T 30 T2T N5X N5X N 0 1 N N N 6.826 9.958 7.777 4.016 -0.722 -4.349 N5X T2T 31 T2T C5X C5X C 0 1 N N N 6.864 11.155 8.652 3.752 -2.007 -3.746 C5X T2T 32 T2T "C4'" C4* C 0 1 N N R 5.622 11.967 8.411 2.839 -2.850 -4.627 "C4'" T2T 33 T2T "O4'" O4* O 0 1 N N N 4.458 11.107 8.514 3.520 -3.095 -5.877 "O4'" T2T 34 T2T "C1'" C1* C 0 1 N N R 3.368 11.847 9.037 3.910 -4.477 -5.937 "C1'" T2T 35 T2T O2 O2 O 0 1 N N N 1.102 12.588 10.409 5.031 -6.583 -7.496 O2 T2T 36 T2T O4 O4 O 0 1 N N N 1.500 9.339 13.574 9.189 -4.618 -7.475 O4 T2T 37 T2T C5A C5A C 0 1 N N N 3.886 8.202 12.362 8.363 -2.381 -5.920 C5A T2T 38 T2T "C2'" C2* C 0 1 N N R 3.852 13.285 9.265 3.700 -5.047 -4.545 "C2'" T2T 39 T2T "O2'" O2* O 0 1 N N N 3.514 14.061 8.131 3.409 -6.430 -4.563 "O2'" T2T 40 T2T CH3 CH3 C 0 1 N N N 1.981 14.047 8.010 3.092 -6.921 -3.264 CH3 T2T 41 T2T "C3'" C3* C 0 1 N N R 5.364 13.091 9.402 2.535 -4.222 -4.040 "C3'" T2T 42 T2T "O3'" O3* O 0 1 N N N 6.097 14.254 8.994 1.314 -4.685 -4.614 "O3'" T2T 43 T2T OP3 O3P O 0 1 N Y N ? ? ? 4.640 -2.154 -10.596 OP3 T2T 44 T2T HOP2 2HOP H 0 0 N N N 7.119 3.496 9.859 2.329 -3.979 -10.767 HOP2 T2T 45 T2T HN3 HN3 H 0 1 N N N 0.509 11.278 12.428 7.456 -6.365 -8.033 HN3 T2T 46 T2T H6 H6 H 0 1 N N N 4.427 9.731 10.236 5.698 -2.746 -5.404 H6 T2T 47 T2T "H5'" 1H5* H 0 1 N N N 4.666 4.210 5.561 2.148 -1.306 -8.556 "H5'" T2T 48 T2T "H5''" 2H5* H 0 0 N N N 6.376 4.750 5.711 3.816 -0.688 -8.672 "H5''" T2T 49 T2T H4X H4X H 0 1 N N N 5.199 6.520 4.814 2.899 1.627 -8.976 H4X T2T 50 T2T H1X H1X H 0 1 N N N 2.626 8.367 5.989 -0.282 2.575 -8.189 H1X T2T 51 T2T H6B H6B H 0 1 N N N 3.559 5.981 8.662 0.482 -0.833 -7.736 H6B T2T 52 T2T H3B H3B H 0 1 N N N -0.028 9.007 9.420 -3.708 0.610 -5.876 H3B T2T 53 T2T HAB1 1HAB H 0 0 N N N 2.108 4.466 10.606 -0.205 -3.160 -7.607 HAB1 T2T 54 T2T HAB2 2HAB H 0 0 N N N 1.758 5.638 11.921 -1.896 -3.524 -7.195 HAB2 T2T 55 T2T HAB3 3HAB H 0 0 N N N 3.424 5.496 11.264 -0.697 -3.311 -5.906 HAB3 T2T 56 T2T H2X1 1H2X H 0 0 N N N 4.666 9.139 7.659 0.909 2.119 -5.741 H2X1 T2T 57 T2T H2X2 2H2X H 0 0 N N N 4.770 9.170 5.934 1.717 3.061 -7.010 H2X2 T2T 58 T2T H3X H3X H 0 1 N N N 5.719 7.020 7.839 2.006 0.077 -6.484 H3X T2T 59 T2T HH21 1HH2 H 0 0 N N N 7.417 6.653 5.882 4.053 2.282 -6.922 HH21 T2T 60 T2T HH22 2HH2 H 0 0 N N N 7.632 7.652 7.390 4.430 0.581 -6.663 HH22 T2T 61 T2T H1P H1P H 0 1 N N N 6.583 8.867 4.896 3.000 2.448 -4.683 H1P T2T 62 T2T H2P1 1H2P H 0 0 N N N 9.142 7.716 5.181 5.800 1.196 -4.567 H2P1 T2T 63 T2T H2P2 2H2P H 0 0 N N N 9.283 9.505 5.106 5.445 2.900 -4.913 H2P2 T2T 64 T2T H2P3 3H2P H 0 0 N N N 8.478 8.610 3.772 5.076 2.219 -3.323 H2P3 T2T 65 T2T H5X H5X H 0 1 N N N 6.433 9.104 8.118 4.800 -0.650 -4.991 H5X T2T 66 T2T H5X1 1H5X H 0 0 N N N 7.756 11.758 8.424 4.712 -2.510 -3.598 H5X1 T2T 67 T2T H5X2 2H5X H 0 0 N N N 6.905 10.843 9.706 3.293 -1.829 -2.769 H5X2 T2T 68 T2T "H4'" H4* H 0 1 N N N 5.786 12.410 7.418 1.928 -2.285 -4.850 "H4'" T2T 69 T2T "H1'" H1* H 0 1 N N N 2.510 11.907 8.351 3.303 -4.983 -6.695 "H1'" T2T 70 T2T H5A1 1H5A H 0 0 N N N 3.788 7.372 11.647 7.921 -1.821 -5.097 H5A1 T2T 71 T2T H5A2 2H5A H 0 0 N N N 3.461 7.903 13.332 8.528 -1.713 -6.764 H5A2 T2T 72 T2T H5A3 3H5A H 0 0 N N N 4.950 8.452 12.489 9.320 -2.793 -5.603 H5A3 T2T 73 T2T "H2'" H2* H 0 1 N N N 3.416 13.804 10.131 4.581 -4.882 -3.914 "H2'" T2T 74 T2T HH31 1HH3 H 0 0 N N N 1.665 13.145 7.465 3.185 -8.009 -3.252 HH31 T2T 75 T2T HH32 2HH3 H 0 0 N N N 1.648 14.942 7.464 2.071 -6.629 -3.003 HH32 T2T 76 T2T HH33 3HH3 H 0 0 N N N 1.533 14.044 9.015 3.788 -6.489 -2.541 HH33 T2T 77 T2T "H3'" H3* H 0 1 N N N 5.674 12.890 10.438 2.421 -4.235 -2.953 "H3'" T2T 78 T2T "HO3'" H3T H 0 0 N Y N 5.502 14.989 8.904 0.861 -5.192 -3.923 "HO3'" T2T 79 T2T HOP3 3HOP H 0 0 N N N -0.811 0.023 0.494 5.175 -2.879 -10.983 HOP3 T2T 80 # 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 T2T P OP1 DOUB N N 1 T2T P OP2 SING N N 2 T2T P "O5'" SING N N 3 T2T P OP3 SING N N 4 T2T OP2 HOP2 SING N N 5 T2T C4 N3 SING N N 6 T2T C4 C5 SING N N 7 T2T C4 O4 DOUB N N 8 T2T N3 C2 SING N N 9 T2T N3 HN3 SING N N 10 T2T C2 N1 SING N N 11 T2T C2 O2 DOUB N N 12 T2T N1 C6 SING N N 13 T2T N1 "C1'" SING N N 14 T2T C6 C5 DOUB N N 15 T2T C6 H6 SING N N 16 T2T C5 C5A SING N N 17 T2T "O5'" "C5'" SING N N 18 T2T "C5'" C4X SING N N 19 T2T "C5'" "H5'" SING N N 20 T2T "C5'" "H5''" SING N N 21 T2T C4X O4X SING N N 22 T2T C4X C3X SING N N 23 T2T C4X H4X SING N N 24 T2T O4X C1X SING N N 25 T2T C1X N1B SING N N 26 T2T C1X C2X SING N N 27 T2T C1X H1X SING N N 28 T2T N1B C6B SING N N 29 T2T N1B C2B SING N N 30 T2T C6B C5B DOUB N N 31 T2T C6B H6B SING N N 32 T2T C2B O2B DOUB N N 33 T2T C2B N3B SING N N 34 T2T N3B C4B SING N N 35 T2T N3B H3B SING N N 36 T2T C4B O4B DOUB N N 37 T2T C4B C5B SING N N 38 T2T C5B CAB SING N N 39 T2T CAB HAB1 SING N N 40 T2T CAB HAB2 SING N N 41 T2T CAB HAB3 SING N N 42 T2T C2X C3X SING N N 43 T2T C2X H2X1 SING N N 44 T2T C2X H2X2 SING N N 45 T2T C3X CH2 SING N N 46 T2T C3X H3X SING N N 47 T2T CH2 CP SING N N 48 T2T CH2 HH21 SING N N 49 T2T CH2 HH22 SING N N 50 T2T CP C2P SING N N 51 T2T CP CX SING N N 52 T2T CP H1P SING N N 53 T2T C2P H2P1 SING N N 54 T2T C2P H2P2 SING N N 55 T2T C2P H2P3 SING N N 56 T2T CX OX DOUB N N 57 T2T CX N5X SING N N 58 T2T N5X C5X SING N N 59 T2T N5X H5X SING N N 60 T2T C5X "C4'" SING N N 61 T2T C5X H5X1 SING N N 62 T2T C5X H5X2 SING N N 63 T2T "C4'" "O4'" SING N N 64 T2T "C4'" "C3'" SING N N 65 T2T "C4'" "H4'" SING N N 66 T2T "O4'" "C1'" SING N N 67 T2T "C1'" "C2'" SING N N 68 T2T "C1'" "H1'" SING N N 69 T2T C5A H5A1 SING N N 70 T2T C5A H5A2 SING N N 71 T2T C5A H5A3 SING N N 72 T2T "C2'" "O2'" SING N N 73 T2T "C2'" "C3'" SING N N 74 T2T "C2'" "H2'" SING N N 75 T2T "O2'" CH3 SING N N 76 T2T CH3 HH31 SING N N 77 T2T CH3 HH32 SING N N 78 T2T CH3 HH33 SING N N 79 T2T "C3'" "O3'" SING N N 80 T2T "C3'" "H3'" SING N N 81 T2T "O3'" "HO3'" SING N N 82 T2T OP3 HOP3 SING N N 83 # 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 T2T SMILES ACDLabs 10.04 "O=C1C(=CN(C(=O)N1)C2OC(COP(=O)(O)O)C(C2)CC(C(=O)NCC4OC(N3C(=O)NC(=O)C(=C3)C)C(OC)C4O)C)C" T2T SMILES_CANONICAL CACTVS 3.341 "CO[C@@H]1[C@H](O)[C@@H](CNC(=O)[C@@H](C)C[C@H]2C[C@@H](O[C@@H]2CO[P](O)(O)=O)N3C=C(C)C(=O)NC3=O)O[C@H]1N4C=C(C)C(=O)NC4=O" T2T SMILES CACTVS 3.341 "CO[CH]1[CH](O)[CH](CNC(=O)[CH](C)C[CH]2C[CH](O[CH]2CO[P](O)(O)=O)N3C=C(C)C(=O)NC3=O)O[CH]1N4C=C(C)C(=O)NC4=O" T2T SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "CC1=CN(C(=O)NC1=O)[C@H]2C[C@@H]([C@H](O2)COP(=O)(O)O)C[C@H](C)C(=O)NC[C@@H]3[C@H]([C@H]([C@@H](O3)N4C=C(C(=O)NC4=O)C)OC)O" T2T SMILES "OpenEye OEToolkits" 1.5.0 "CC1=CN(C(=O)NC1=O)C2CC(C(O2)COP(=O)(O)O)CC(C)C(=O)NCC3C(C(C(O3)N4C=C(C(=O)NC4=O)C)OC)O" T2T InChI InChI 1.03 ;InChI=1S/C25H36N5O13P/c1-11(5-14-6-17(42-16(14)10-41-44(37,38)39)29-8-12(2)21(33)27-24(29)35)20(32)26-7-15-18(31)19(40-4)23(43-15)30-9-13(3)22(34)28-25(30)36/h8-9,11,14-19,23,31H,5-7,10H2,1-4H3,(H,26,32)(H,27,33,35)(H,28,34,36)(H2,37,38,39)/t11-,14-,15+,16+,17+,18+,19+,23+/m0/s1 ; T2T InChIKey InChI 1.03 ATFPAUAOEANBDJ-QCSMCPAWSA-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 T2T "SYSTEMATIC NAME" ACDLabs 10.04 ;[(2S,3S,5R)-3-[(2S)-3-({[(2R,3R,4R,5R)-3-hydroxy-4-methoxy-5-(5-methyl-2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)tetrahydrofuran-2-yl]methyl}amino)-2-methyl-3-oxopropyl]-5-(5-methyl-2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)tetrahydrofuran-2-yl]methyl dihydrogen phosphate (non-preferred name) ; T2T "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "[(2S,3S,5R)-3-[(2S)-3-[[(2R,3R,4R,5R)-3-hydroxy-4-methoxy-5-(5-methyl-2,4-dioxo-pyrimidin-1-yl)oxolan-2-yl]methylamino]-2-methyl-3-oxo-propyl]-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 T2T "Create component" 2006-05-12 RCSB T2T "Modify linking type" 2011-06-04 RCSB T2T "Modify descriptor" 2011-06-04 RCSB #